Difference: CemCourseMaterials14 (1 vs. 25)

Revision 2510 Dec 2014 - Main.DannyHo

META TOPICPARENT	name="CemCourseGroup"

Contents

Player required for arf video files

nbr2player.msi: MS windows player for arf files

Lectures

Structure Validation and Fitting - Dec. 9

Lecture
- Structure_2008_Trabuco.pdf: Trabuco, et al. 2008 --> MDFF Paper
- J._Struct._Biol._2012_Ahmed.pdf: Ahmed, et al. JSB, 2012 --> Review of various flexible fitting methods
- fitting_S.pptx: Lecture slides: Fitting Methods
- validation.pdf: Validation lecture

Helical Processing

Lecture
- Helical3d_reconst_v3.pdf: Helical Reconstruction lecture slides

2D Crystallography II - Nov. 18

Lecture
- 2D_Crystallography_lecture_2-20141118_2115-1.arf: 2D_Crystallography_lecture_2-20141118_2115-1.arf

2D Crystallography I - Nov. 11

Lecture
- 2DX_EM_class_1-20141111_2103-1.arf: 2d crystal lecture 2

Single Particle III - Nov 4 - Joachim Frank (Columbia)

Lecture
- Single_Particle_III-20141104_2101-1.arf: single particle lecture 3

Single Particle II - Oct 28 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014-2.pptx: Single Particle Lecture 2 powerpoint

Single Particle I - Oct 21 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014_1.ppt: Single Particle Lecture 1 powerpoint

Tomography II - Oct 14 - David Stokes (NYU/NYSBC)

Lecture

Tomography I - Oct 7 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM3-tomography-2014.pptx: Tomography I lecture
- CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf: video of Tomography I

Fourier Series, Fourier Transform, Correlation, Convolution - Sept 30 - Bill Rice (NYSBC)

Lecture
- fft_lecture-sept30_2014.pptx: powerpoint of fft lecture
- CEM_2014_lecture_2_FFT-20140930_2008-1.arf: video of FFT lecture
- fft_lecture.mp3: audio of fft lecture in case audo in above file is poor (fixed week 3)

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt
Readings
- Hoffman(1997)_An_Introduction_to_Fourier_Theory.pdf: Hoffman Introduction to Fourier Theory
- fourier_intro_Shatkay.pdf: Shatkay Fourier Theory Intro
- http://www.med.harvard.edu/JPNM/physics/didactics/improc/intro/fourier1.html
Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

October 9 : etomo_demo_2014.pdf: Etomo demo
October 16: join_demo_2014.pdf: join tomogram demo

Single Particle Demos

October 23 - Nov 6
- nprot.2008.156.pdf: Nature Protocols paper
- nprot.2008.156-S1.pdf: Nature Protocols S1
- nprot.2008.156-S2.pdf: Nature Protocols S2
- nprot.2008.156-S3.pdf: Nature Protocols S3
- nprot.2008.156-S4.pdf: Nature Protocols S4
- notes-ref_based_2014.pdf: notes on ref based alignment
- ref_bias_2014.pdf: ref bias demo

- micrographs.zip: Micrographs for SP practical 3 (needed by mac people)
- eman2_demo.pdf: instructions for EMAN2 demo

Helical Demo

helical_demo_1.pdf: helical_demo_1.pdf

Molecular Fitting Demo

Dec. 11 2014
- chimera_fitting_data.zip: Files for Chimera Fitting practical workshop

Changed:

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- chimera_tutorial.pdf: Documentation for the Chimera Tutorial

Deleted:

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d148 1

Set ALLOWTOPICVIEW =

-- BillRice - 21 Sep 2014

META FILEATTACHMENT	attr="" autoattached="1" comment="Molecular Fittings - Ahmed et al, JSB 2012" date="1417749955" name="J._Struct._Biol._2012_Ahmed.pdf" path="J._Struct._Biol._2012_Ahmed.pdf" size="1440703" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="course logistics" date="1411487228" name="CryoEM-Course-logistics.doc" path="CryoEM-Course-logistics.doc" size="36864" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S4" date="1411301202" name="nprot.2008.156-S4.pdf" path="nprot.2008.156-S4.pdf" size="24949" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S1" date="1411301102" name="nprot.2008.156-S1.pdf" path="nprot.2008.156-S1.pdf" size="4990385" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="powerpoint of fft lecture" date="1412132447" name="fft_lecture-sept30_2014.pptx" path="fft_lecture-sept30_2014.pptx" size="16248705" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Validation lecture" date="1418171975" name="validation.pdf" path="validation.pdf" size="1711547" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="join tomogram demo" date="1411303057" name="join_demo_2014.pdf" path="join_demo_2014.pdf" size="4051662" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Chimera Tutorial - Document" date="1418245339" name="chimera_tutorial.pdf" path="chimera_tutorial.pdf" size="5725723" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417726358" name="helical_demo_1.pdf" path="helical_demo_1.pdf" size="2389231" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="video of Tomography I" date="1413315371" name="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" path="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" size="255161917" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Portocols paper" date="1411300831" name="nprot.2008.156.pdf" path="nprot.2008.156.pdf" size="3383115" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Single Particle Lecture 1" date="1414537834" name="NYSBC_2014_1.ppt" path="NYSBC_2014_1.ppt" size="23072768" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Helical Reconstruction lecture slides" date="1418172197" name="Helical3d_reconst_v3.pdf" path="Helical3d_reconst_v3.pdf" size="5095698" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="notes on ref based alignment" date="1414696759" name="notes-ref_based_2014.pdf" path="notes-ref_based_2014.pdf" size="62496" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Tomography I lecture" date="1412719549" name="NYSBC-EM3-tomography-2014.pptx" path="NYSBC-EM3-tomography-2014.pptx" size="16899636" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Micrographs for SP practical 3 (needed by mac people)" date="1415176808" name="micrographs.zip" path="micrographs.zip" size="255492671" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="instructions for EMAN2 demo" date="1415300832" name="eman2_demo.pdf" path="eman2_demo.pdf" size="1785498" user="Main.BillRice" version="2"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1411496912" name="NYSBC-EM1-intro-optics14.ppt" path="NYSBC-EM1-intro-optics14.ppt" size="41782784" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="audio of fft lecture" date="1412719576" name="fft_lecture.mp3" path="fft_lecture.mp3" size="106645264" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Etomo demo" date="1411302893" name="etomo_demo_2014.pdf" path="etomo_demo_2014.pdf" size="4470217" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Lecture slides: Fitting Methods" date="1418149815" name="fitting_S.pptx" path="fitting_S.pptx" size="11076279" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="MDFF - Trabuco et al, Structure 2008" date="1417749877" name="Structure_2008_Trabuco.pdf" path="Structure_2008_Trabuco.pdf" size="1735706" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="2d crystal lecture 2" date="1417558990" name="2DX_EM_class_1-20141111_2103-1.arf" path="2DX_EM_class_1-20141111_2103-1.arf" size="253608617" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="single particle lecture 3" date="1417559778" name="Single_Particle_III-20141104_2101-1.arf" path="Single_Particle_III-20141104_2101-1.arf" size="279190625" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="video of FFT lecture" date="1412139438" name="CEM_2014_lecture_2_FFT-20140930_2008-1.arf" path="CEM_2014_lecture_2_FFT-20140930_2008-1.arf" size="257526200" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="ref bias demo" date="1414696780" name="ref_bias_2014.pdf" path="ref_bias_2014.pdf" size="73733" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Player for arf files" date="1412138278" name="nbr2player.msi" path="nbr2player.msi" size="14838784" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Single Particle Lecture 2" date="1414538098" name="NYSBC_2014-2.pptx" path="NYSBC_2014-2.pptx" size="20402100" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Course questionnaire" date="1411487211" name="questionnaire.doc" path="questionnaire.doc" size="25600" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417558552" name="2D_Crystallography_lecture_2-20141118_2115-1.arf" path="2D_Crystallography_lecture_2-20141118_2115-1.arf" size="141023696" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S2" date="1411301145" name="nprot.2008.156-S2.pdf" path="nprot.2008.156-S2.pdf" size="207150" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Files for Chimera Fitting practical workshop" date="1415293937" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S3" date="1411301180" name="nprot.2008.156-S3.pdf" path="nprot.2008.156-S3.pdf" size="222608" user="Main.BillRice" version="1"

Revision 2409 Dec 2014 - Main.BillRice

META TOPICPARENT	name="CemCourseGroup"

Contents

Player required for arf video files

nbr2player.msi: MS windows player for arf files

Lectures

Structure Validation and Fitting - Dec. 9

Lecture
- Structure_2008_Trabuco.pdf: Trabuco, et al. 2008 --> MDFF Paper
- J._Struct._Biol._2012_Ahmed.pdf: Ahmed, et al. JSB, 2012 --> Review of various flexible fitting methods
- fitting_S.pptx: Lecture slides: Fitting Methods

Added:

>
>

- validation.pdf: Validation lecture

Added:

>
>

Helical Processing

Lecture

Added:

>
>

- Helical3d_reconst_v3.pdf: Helical Reconstruction lecture slides

Added:

>
>

2D Crystallography II - Nov. 18

Lecture
- 2D_Crystallography_lecture_2-20141118_2115-1.arf: 2D_Crystallography_lecture_2-20141118_2115-1.arf

2D Crystallography I - Nov. 11

Lecture
- 2DX_EM_class_1-20141111_2103-1.arf: 2d crystal lecture 2

Single Particle III - Nov 4 - Joachim Frank (Columbia)

Lecture
- Single_Particle_III-20141104_2101-1.arf: single particle lecture 3

Single Particle II - Oct 28 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014-2.pptx: Single Particle Lecture 2 powerpoint

Single Particle I - Oct 21 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014_1.ppt: Single Particle Lecture 1 powerpoint

Tomography II - Oct 14 - David Stokes (NYU/NYSBC)

Lecture

Tomography I - Oct 7 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM3-tomography-2014.pptx: Tomography I lecture
- CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf: video of Tomography I

Fourier Series, Fourier Transform, Correlation, Convolution - Sept 30 - Bill Rice (NYSBC)

Lecture
- fft_lecture-sept30_2014.pptx: powerpoint of fft lecture
- CEM_2014_lecture_2_FFT-20140930_2008-1.arf: video of FFT lecture
- fft_lecture.mp3: audio of fft lecture in case audo in above file is poor (fixed week 3)

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt
Readings
- Hoffman(1997)_An_Introduction_to_Fourier_Theory.pdf: Hoffman Introduction to Fourier Theory
- fourier_intro_Shatkay.pdf: Shatkay Fourier Theory Intro
- http://www.med.harvard.edu/JPNM/physics/didactics/improc/intro/fourier1.html
Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

October 9 : etomo_demo_2014.pdf: Etomo demo
October 16: join_demo_2014.pdf: join tomogram demo

Single Particle Demos

October 23 - Nov 6
- nprot.2008.156.pdf: Nature Protocols paper
- nprot.2008.156-S1.pdf: Nature Protocols S1
- nprot.2008.156-S2.pdf: Nature Protocols S2
- nprot.2008.156-S3.pdf: Nature Protocols S3
- nprot.2008.156-S4.pdf: Nature Protocols S4
- notes-ref_based_2014.pdf: notes on ref based alignment
- ref_bias_2014.pdf: ref bias demo

- micrographs.zip: Micrographs for SP practical 3 (needed by mac people)
- eman2_demo.pdf: instructions for EMAN2 demo

Helical Demo

helical_demo_1.pdf: helical_demo_1.pdf

Molecular Fitting Demo

Dec. 11 2014
- chimera_fitting_data.zip: Files for Chimera Fitting practical workshop

d148 1

Set ALLOWTOPICVIEW =

-- BillRice - 21 Sep 2014

Added:

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>

META FILEATTACHMENT	attr="" autoattached="1" comment="Molecular Fittings - Ahmed et al, JSB 2012" date="1417749955" name="J._Struct._Biol._2012_Ahmed.pdf" path="J._Struct._Biol._2012_Ahmed.pdf" size="1440703" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="course logistics" date="1411487228" name="CryoEM-Course-logistics.doc" path="CryoEM-Course-logistics.doc" size="36864" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S4" date="1411301202" name="nprot.2008.156-S4.pdf" path="nprot.2008.156-S4.pdf" size="24949" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S1" date="1411301102" name="nprot.2008.156-S1.pdf" path="nprot.2008.156-S1.pdf" size="4990385" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="powerpoint of fft lecture" date="1412132447" name="fft_lecture-sept30_2014.pptx" path="fft_lecture-sept30_2014.pptx" size="16248705" user="Main.BillRice" version="1"

Added:

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META FILEATTACHMENT	attr="" autoattached="1" comment="Validation lecture" date="1418171975" name="validation.pdf" path="validation.pdf" size="1711547" user="Main.BillRice" version="1"

META FILEATTACHMENT	attr="" autoattached="1" comment="join tomogram demo" date="1411303057" name="join_demo_2014.pdf" path="join_demo_2014.pdf" size="4051662" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Chimera Tutorial - Document" date="1418245339" name="chimera_tutorial.pdf" path="chimera_tutorial.pdf" size="5725723" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417726358" name="helical_demo_1.pdf" path="helical_demo_1.pdf" size="2389231" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="video of Tomography I" date="1413315371" name="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" path="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" size="255161917" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Portocols paper" date="1411300831" name="nprot.2008.156.pdf" path="nprot.2008.156.pdf" size="3383115" user="Main.BillRice" version="1"

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META FILEATTACHMENT	attr="" autoattached="1" comment="Single Particle Lecture 1" date="1414537834" name="NYSBC_2014_1.ppt" path="NYSBC_2014_1.ppt" size="23072768" user="Main.BillRice" version="1"

META FILEATTACHMENT	attr="" autoattached="1" comment="Helical Reconstruction lecture slides" date="1418172197" name="Helical3d_reconst_v3.pdf" path="Helical3d_reconst_v3.pdf" size="5095698" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="notes on ref based alignment" date="1414696759" name="notes-ref_based_2014.pdf" path="notes-ref_based_2014.pdf" size="62496" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Tomography I lecture" date="1412719549" name="NYSBC-EM3-tomography-2014.pptx" path="NYSBC-EM3-tomography-2014.pptx" size="16899636" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Micrographs for SP practical 3 (needed by mac people)" date="1415176808" name="micrographs.zip" path="micrographs.zip" size="255492671" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="instructions for EMAN2 demo" date="1415300832" name="eman2_demo.pdf" path="eman2_demo.pdf" size="1785498" user="Main.BillRice" version="2"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1411496912" name="NYSBC-EM1-intro-optics14.ppt" path="NYSBC-EM1-intro-optics14.ppt" size="41782784" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="audio of fft lecture" date="1412719576" name="fft_lecture.mp3" path="fft_lecture.mp3" size="106645264" user="Main.BillRice" version="1"

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META FILEATTACHMENT	attr="" autoattached="1" comment="Etomo demo" date="1411302893" name="etomo_demo_2014.pdf" path="etomo_demo_2014.pdf" size="4470217" user="Main.BillRice" version="1"

META FILEATTACHMENT	attr="" autoattached="1" comment="Lecture slides: Fitting Methods" date="1418149815" name="fitting_S.pptx" path="fitting_S.pptx" size="11076279" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="MDFF - Trabuco et al, Structure 2008" date="1417749877" name="Structure_2008_Trabuco.pdf" path="Structure_2008_Trabuco.pdf" size="1735706" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="2d crystal lecture 2" date="1417558990" name="2DX_EM_class_1-20141111_2103-1.arf" path="2DX_EM_class_1-20141111_2103-1.arf" size="253608617" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="single particle lecture 3" date="1417559778" name="Single_Particle_III-20141104_2101-1.arf" path="Single_Particle_III-20141104_2101-1.arf" size="279190625" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="video of FFT lecture" date="1412139438" name="CEM_2014_lecture_2_FFT-20140930_2008-1.arf" path="CEM_2014_lecture_2_FFT-20140930_2008-1.arf" size="257526200" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="ref bias demo" date="1414696780" name="ref_bias_2014.pdf" path="ref_bias_2014.pdf" size="73733" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Player for arf files" date="1412138278" name="nbr2player.msi" path="nbr2player.msi" size="14838784" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Single Particle Lecture 2" date="1414538098" name="NYSBC_2014-2.pptx" path="NYSBC_2014-2.pptx" size="20402100" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Course questionnaire" date="1411487211" name="questionnaire.doc" path="questionnaire.doc" size="25600" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417558552" name="2D_Crystallography_lecture_2-20141118_2115-1.arf" path="2D_Crystallography_lecture_2-20141118_2115-1.arf" size="141023696" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S2" date="1411301145" name="nprot.2008.156-S2.pdf" path="nprot.2008.156-S2.pdf" size="207150" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Files for Chimera Fitting practical workshop" date="1415293937" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" user="Main.DannyHo" version="1"

Deleted:

<
<

META FILEATTACHMENT	attachment="fitting_S.pptx" attr="" comment="Lecture slides: Fitting Methods" date="1418149815" name="fitting_S.pptx" path="fitting_S.pptx" size="11076279" stream="fitting_S.pptx" user="Main.DannyHo" version="1"

META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S3" date="1411301180" name="nprot.2008.156-S3.pdf" path="nprot.2008.156-S3.pdf" size="222608" user="Main.BillRice" version="1"

Revision 2309 Dec 2014 - Main.DannyHo

META TOPICPARENT	name="CemCourseGroup"

Contents

Player required for arf video files

nbr2player.msi: MS windows player for arf files

Lectures

Structure Validation and Fitting - Dec. 9

Lecture

Added:

>
>

- Structure_2008_Trabuco.pdf: Trabuco, et al. 2008 --> MDFF Paper
- J._Struct._Biol._2012_Ahmed.pdf: Ahmed, et al. JSB, 2012 --> Review of various flexible fitting methods
- fitting_S.pptx: Lecture slides: Fitting Methods

Deleted:

<
<

d164 1

Helical Processing

Lecture

2D Crystallography II - Nov. 18

Lecture
- 2D_Crystallography_lecture_2-20141118_2115-1.arf: 2D_Crystallography_lecture_2-20141118_2115-1.arf

2D Crystallography I - Nov. 11

Lecture
- 2DX_EM_class_1-20141111_2103-1.arf: 2d crystal lecture 2

Single Particle III - Nov 4 - Joachim Frank (Columbia)

Lecture
- Single_Particle_III-20141104_2101-1.arf: single particle lecture 3

Single Particle II - Oct 28 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014-2.pptx: Single Particle Lecture 2 powerpoint

Single Particle I - Oct 21 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014_1.ppt: Single Particle Lecture 1 powerpoint

Tomography II - Oct 14 - David Stokes (NYU/NYSBC)

Lecture

Tomography I - Oct 7 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM3-tomography-2014.pptx: Tomography I lecture
- CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf: video of Tomography I

Fourier Series, Fourier Transform, Correlation, Convolution - Sept 30 - Bill Rice (NYSBC)

Lecture
- fft_lecture-sept30_2014.pptx: powerpoint of fft lecture
- CEM_2014_lecture_2_FFT-20140930_2008-1.arf: video of FFT lecture
- fft_lecture.mp3: audio of fft lecture in case audo in above file is poor (fixed week 3)

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt
Readings
- Hoffman(1997)_An_Introduction_to_Fourier_Theory.pdf: Hoffman Introduction to Fourier Theory
- fourier_intro_Shatkay.pdf: Shatkay Fourier Theory Intro
- http://www.med.harvard.edu/JPNM/physics/didactics/improc/intro/fourier1.html
Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

October 9 : etomo_demo_2014.pdf: Etomo demo
October 16: join_demo_2014.pdf: join tomogram demo

Single Particle Demos

October 23 - Nov 6
- nprot.2008.156.pdf: Nature Protocols paper
- nprot.2008.156-S1.pdf: Nature Protocols S1
- nprot.2008.156-S2.pdf: Nature Protocols S2
- nprot.2008.156-S3.pdf: Nature Protocols S3
- nprot.2008.156-S4.pdf: Nature Protocols S4
- notes-ref_based_2014.pdf: notes on ref based alignment
- ref_bias_2014.pdf: ref bias demo

- micrographs.zip: Micrographs for SP practical 3 (needed by mac people)
- eman2_demo.pdf: instructions for EMAN2 demo

Helical Demo

helical_demo_1.pdf: helical_demo_1.pdf

Molecular Fitting Demo

Dec. 11 2014
- chimera_fitting_data.zip: Files for Chimera Fitting practical workshop

d148 1

Set ALLOWTOPICVIEW =

-- BillRice - 21 Sep 2014

Deleted:

<
<

* Structure_2008_Trabuco.pdf: MDFF - Trabuco et al, Structure 2008

Deleted:

<
<

* J._Struct._Biol._2012_Ahmed.pdf: Molecular Fittings - Ahmed et al, JSB 2012

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Changed:

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<

META FILEATTACHMENT	attachment="fitting_S.pptx" attr="" comment="" date="1418149395" name="fitting_S.pptx" path="fitting_S.pptx" size="11077547" stream="fitting_S.pptx" user="Main.DannyHo" version="1"

>
>

META FILEATTACHMENT	attachment="fitting_S.pptx" attr="" comment="Lecture slides: Fitting Methods" date="1418149815" name="fitting_S.pptx" path="fitting_S.pptx" size="11076279" stream="fitting_S.pptx" user="Main.DannyHo" version="1"

META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S3" date="1411301180" name="nprot.2008.156-S3.pdf" path="nprot.2008.156-S3.pdf" size="222608" user="Main.BillRice" version="1"

Revision 2209 Dec 2014 - Main.BillRice

META TOPICPARENT	name="CemCourseGroup"

Contents

Player required for arf video files

nbr2player.msi: MS windows player for arf files

Lectures

Structure Validation and Fitting - Dec. 9

Lecture

d164 1

Helical Processing

Lecture

2D Crystallography II - Nov. 18

Lecture
- 2D_Crystallography_lecture_2-20141118_2115-1.arf: 2D_Crystallography_lecture_2-20141118_2115-1.arf

2D Crystallography I - Nov. 11

Lecture
- 2DX_EM_class_1-20141111_2103-1.arf: 2d crystal lecture 2

Single Particle III - Nov 4 - Joachim Frank (Columbia)

Lecture
- Single_Particle_III-20141104_2101-1.arf: single particle lecture 3

Single Particle II - Oct 28 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014-2.pptx: Single Particle Lecture 2 powerpoint

Single Particle I - Oct 21 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014_1.ppt: Single Particle Lecture 1 powerpoint

Tomography II - Oct 14 - David Stokes (NYU/NYSBC)

Lecture

Tomography I - Oct 7 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM3-tomography-2014.pptx: Tomography I lecture
- CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf: video of Tomography I

Fourier Series, Fourier Transform, Correlation, Convolution - Sept 30 - Bill Rice (NYSBC)

Lecture
- fft_lecture-sept30_2014.pptx: powerpoint of fft lecture
- CEM_2014_lecture_2_FFT-20140930_2008-1.arf: video of FFT lecture
- fft_lecture.mp3: audio of fft lecture in case audo in above file is poor (fixed week 3)

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt
Readings
- Hoffman(1997)_An_Introduction_to_Fourier_Theory.pdf: Hoffman Introduction to Fourier Theory
- fourier_intro_Shatkay.pdf: Shatkay Fourier Theory Intro
- http://www.med.harvard.edu/JPNM/physics/didactics/improc/intro/fourier1.html
Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

October 9 : etomo_demo_2014.pdf: Etomo demo
October 16: join_demo_2014.pdf: join tomogram demo

Single Particle Demos

October 23 - Nov 6
- nprot.2008.156.pdf: Nature Protocols paper
- nprot.2008.156-S1.pdf: Nature Protocols S1
- nprot.2008.156-S2.pdf: Nature Protocols S2
- nprot.2008.156-S3.pdf: Nature Protocols S3
- nprot.2008.156-S4.pdf: Nature Protocols S4
- notes-ref_based_2014.pdf: notes on ref based alignment
- ref_bias_2014.pdf: ref bias demo

- micrographs.zip: Micrographs for SP practical 3 (needed by mac people)
- eman2_demo.pdf: instructions for EMAN2 demo

Helical Demo

helical_demo_1.pdf: helical_demo_1.pdf

Molecular Fitting Demo

Dec. 11 2014
- chimera_fitting_data.zip: Files for Chimera Fitting practical workshop

d148 1

Set ALLOWTOPICVIEW =

-- BillRice - 21 Sep 2014

Added:

>
>

* Structure_2008_Trabuco.pdf: MDFF - Trabuco et al, Structure 2008

* J._Struct._Biol._2012_Ahmed.pdf: Molecular Fittings - Ahmed et al, JSB 2012

META FILEATTACHMENT	attr="" autoattached="1" comment="Molecular Fittings - Ahmed et al, JSB 2012" date="1417749955" name="J._Struct._Biol._2012_Ahmed.pdf" path="J._Struct._Biol._2012_Ahmed.pdf" size="1440703" user="Main.DannyHo" version="1"
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META FILEATTACHMENT	attr="" autoattached="1" comment="instructions for EMAN2 demo" date="1415300832" name="eman2_demo.pdf" path="eman2_demo.pdf" size="1785498" user="Main.BillRice" version="2"
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META FILEATTACHMENT	attr="" autoattached="1" comment="MDFF - Trabuco et al, Structure 2008" date="1417749877" name="Structure_2008_Trabuco.pdf" path="Structure_2008_Trabuco.pdf" size="1735706" user="Main.DannyHo" version="1"
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META FILEATTACHMENT	attr="" autoattached="1" comment="Files for Chimera Fitting practical workshop" date="1415293937" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" user="Main.DannyHo" version="1"
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Revision 2108 Dec 2014 - Main.BillRice

META TOPICPARENT	name="CemCourseGroup"

Contents

Player required for arf video files

nbr2player.msi: MS windows player for arf files

Lectures

Structure Validation and Fitting - Dec. 9

Lecture

d164 1

Changed:

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Single Particle II - Oct 28 - Joachim Frank (Columbia)

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Helical Processing

Lecture

Added:

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2D Crystallography II - Nov. 18

Lecture
- 2D_Crystallography_lecture_2-20141118_2115-1.arf: 2D_Crystallography_lecture_2-20141118_2115-1.arf

Added:

>
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2D Crystallography I - Nov. 11

Lecture
- 2DX_EM_class_1-20141111_2103-1.arf: 2d crystal lecture 2

Single Particle III - Nov 4 - Joachim Frank (Columbia)

Lecture
- Single_Particle_III-20141104_2101-1.arf: single particle lecture 3

Single Particle II - Oct 28 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014-2.pptx: Single Particle Lecture 2 powerpoint

Single Particle I - Oct 21 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014_1.ppt: Single Particle Lecture 1 powerpoint

Tomography II - Oct 14 - David Stokes (NYU/NYSBC)

Lecture

Tomography I - Oct 7 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM3-tomography-2014.pptx: Tomography I lecture
- CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf: video of Tomography I

Fourier Series, Fourier Transform, Correlation, Convolution - Sept 30 - Bill Rice (NYSBC)

Lecture
- fft_lecture-sept30_2014.pptx: powerpoint of fft lecture
- CEM_2014_lecture_2_FFT-20140930_2008-1.arf: video of FFT lecture
- fft_lecture.mp3: audio of fft lecture in case audo in above file is poor (fixed week 3)

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt
Readings
- Hoffman(1997)_An_Introduction_to_Fourier_Theory.pdf: Hoffman Introduction to Fourier Theory
- fourier_intro_Shatkay.pdf: Shatkay Fourier Theory Intro
- http://www.med.harvard.edu/JPNM/physics/didactics/improc/intro/fourier1.html
Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

October 9 : etomo_demo_2014.pdf: Etomo demo
October 16: join_demo_2014.pdf: join tomogram demo

Single Particle Demos

October 23 - Nov 6
- nprot.2008.156.pdf: Nature Protocols paper
- nprot.2008.156-S1.pdf: Nature Protocols S1
- nprot.2008.156-S2.pdf: Nature Protocols S2
- nprot.2008.156-S3.pdf: Nature Protocols S3
- nprot.2008.156-S4.pdf: Nature Protocols S4
- notes-ref_based_2014.pdf: notes on ref based alignment
- ref_bias_2014.pdf: ref bias demo

- micrographs.zip: Micrographs for SP practical 3 (needed by mac people)
- eman2_demo.pdf: instructions for EMAN2 demo

Added:

>
>

Helical Demo

helical_demo_1.pdf: helical_demo_1.pdf

Molecular Fitting Demo

Dec. 11 2014
- chimera_fitting_data.zip: Files for Chimera Fitting practical workshop

d148 1

Set ALLOWTOPICVIEW =

-- BillRice - 21 Sep 2014

Changed:

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<

* 2D_Crystallography_lecture_2-20141118_2115-1.arf: 2D_Crystallography_lecture_2-20141118_2115-1.arf

>
>

Changed:

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* 2DX_EM_class_1-20141111_2103-1.arf: 2d crystal lecture 2

>
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Changed:

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* Single_Particle_III-20141104_2101-1.arf: single particle lecture 3

>
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Changed:

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* helical_demo_1.pdf: helical_demo_1.pdf

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Added:

>
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META FILEATTACHMENT	attr="" autoattached="1" comment="course logistics" date="1411487228" name="CryoEM-Course-logistics.doc" path="CryoEM-Course-logistics.doc" size="36864" user="Main.EdEng" version="1"
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META FILEATTACHMENT	attr="" autoattached="1" comment="notes on ref based alignment" date="1414696759" name="notes-ref_based_2014.pdf" path="notes-ref_based_2014.pdf" size="62496" user="Main.BillRice" version="1"
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META FILEATTACHMENT	attr="" autoattached="1" comment="Micrographs for SP practical 3 (needed by mac people)" date="1415176808" name="micrographs.zip" path="micrographs.zip" size="255492671" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="instructions for EMAN2 demo" date="1415300832" name="eman2_demo.pdf" path="eman2_demo.pdf" size="1785498" user="Main.BillRice" version="2"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1411496912" name="NYSBC-EM1-intro-optics14.ppt" path="NYSBC-EM1-intro-optics14.ppt" size="41782784" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="audio of fft lecture" date="1412719576" name="fft_lecture.mp3" path="fft_lecture.mp3" size="106645264" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Lecture slides: Fitting Methods" date="1418149815" name="fitting_S.pptx" path="fitting_S.pptx" size="11076279" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="MDFF - Trabuco et al, Structure 2008" date="1417749877" name="Structure_2008_Trabuco.pdf" path="Structure_2008_Trabuco.pdf" size="1735706" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="2d crystal lecture 2" date="1417558990" name="2DX_EM_class_1-20141111_2103-1.arf" path="2DX_EM_class_1-20141111_2103-1.arf" size="253608617" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="single particle lecture 3" date="1417559778" name="Single_Particle_III-20141104_2101-1.arf" path="Single_Particle_III-20141104_2101-1.arf" size="279190625" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="video of FFT lecture" date="1412139438" name="CEM_2014_lecture_2_FFT-20140930_2008-1.arf" path="CEM_2014_lecture_2_FFT-20140930_2008-1.arf" size="257526200" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="ref bias demo" date="1414696780" name="ref_bias_2014.pdf" path="ref_bias_2014.pdf" size="73733" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Player for arf files" date="1412138278" name="nbr2player.msi" path="nbr2player.msi" size="14838784" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Single Particle Lecture 2" date="1414538098" name="NYSBC_2014-2.pptx" path="NYSBC_2014-2.pptx" size="20402100" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Course questionnaire" date="1411487211" name="questionnaire.doc" path="questionnaire.doc" size="25600" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417558552" name="2D_Crystallography_lecture_2-20141118_2115-1.arf" path="2D_Crystallography_lecture_2-20141118_2115-1.arf" size="141023696" user="Main.BillRice" version="1"
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META FILEATTACHMENT	attr="" autoattached="1" comment="Files for Chimera Fitting practical workshop" date="1415293937" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" user="Main.DannyHo" version="1"

Deleted:

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META FILEATTACHMENT	attachment="J._Struct._Biol._2012_Ahmed.pdf" attr="" comment="Molecular Fittings - Ahmed et al, JSB 2012" date="1417749955" name="J._Struct._Biol._2012_Ahmed.pdf" path="J. Struct. Biol. 2012 Ahmed.pdf" size="1440703" stream="J. Struct. Biol. 2012 Ahmed.pdf" user="Main.DannyHo" version="1"

META FILEATTACHMENT	attachment="fitting_S.pptx" attr="" comment="" date="1418149395" name="fitting_S.pptx" path="fitting_S.pptx" size="11077547" stream="fitting_S.pptx" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S3" date="1411301180" name="nprot.2008.156-S3.pdf" path="nprot.2008.156-S3.pdf" size="222608" user="Main.BillRice" version="1"

Revision 2004 Dec 2014 - Main.DannyHo

META TOPICPARENT	name="CemCourseGroup"

Contents

Player required for arf video files

nbr2player.msi: MS windows player for arf files

Lectures

Structure Validation and Fitting - Dec. 9

Lecture

d164 1

Single Particle II - Oct 28 - Joachim Frank (Columbia)

Lecture

Single Particle II - Oct 28 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014-2.pptx: Single Particle Lecture 2 powerpoint

Single Particle I - Oct 21 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014_1.ppt: Single Particle Lecture 1 powerpoint

Tomography II - Oct 14 - David Stokes (NYU/NYSBC)

Lecture

Tomography I - Oct 7 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM3-tomography-2014.pptx: Tomography I lecture
- CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf: video of Tomography I

Fourier Series, Fourier Transform, Correlation, Convolution - Sept 30 - Bill Rice (NYSBC)

Lecture
- fft_lecture-sept30_2014.pptx: powerpoint of fft lecture
- CEM_2014_lecture_2_FFT-20140930_2008-1.arf: video of FFT lecture
- fft_lecture.mp3: audio of fft lecture in case audo in above file is poor (fixed week 3)

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt
Readings
- Hoffman(1997)_An_Introduction_to_Fourier_Theory.pdf: Hoffman Introduction to Fourier Theory
- fourier_intro_Shatkay.pdf: Shatkay Fourier Theory Intro
- http://www.med.harvard.edu/JPNM/physics/didactics/improc/intro/fourier1.html
Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

October 9 : etomo_demo_2014.pdf: Etomo demo
October 16: join_demo_2014.pdf: join tomogram demo

Single Particle Demos

October 23 - Nov 6
- nprot.2008.156.pdf: Nature Protocols paper
- nprot.2008.156-S1.pdf: Nature Protocols S1
- nprot.2008.156-S2.pdf: Nature Protocols S2
- nprot.2008.156-S3.pdf: Nature Protocols S3
- nprot.2008.156-S4.pdf: Nature Protocols S4
- notes-ref_based_2014.pdf: notes on ref based alignment
- ref_bias_2014.pdf: ref bias demo

- micrographs.zip: Micrographs for SP practical 3 (needed by mac people)
- eman2_demo.pdf: instructions for EMAN2 demo

Molecular Fitting Demo

Dec. 11 2014
- chimera_fitting_data.zip: Files for Chimera Fitting practical workshop

d148 1

Set ALLOWTOPICVIEW =

-- BillRice - 21 Sep 2014

* 2D_Crystallography_lecture_2-20141118_2115-1.arf: 2D_Crystallography_lecture_2-20141118_2115-1.arf

* 2DX_EM_class_1-20141111_2103-1.arf: 2d crystal lecture 2

* Single_Particle_III-20141104_2101-1.arf: single particle lecture 3

* helical_demo_1.pdf: helical_demo_1.pdf

META FILEATTACHMENT	attr="" autoattached="1" comment="course logistics" date="1411487228" name="CryoEM-Course-logistics.doc" path="CryoEM-Course-logistics.doc" size="36864" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S4" date="1411301202" name="nprot.2008.156-S4.pdf" path="nprot.2008.156-S4.pdf" size="24949" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S1" date="1411301102" name="nprot.2008.156-S1.pdf" path="nprot.2008.156-S1.pdf" size="4990385" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="powerpoint of fft lecture" date="1412132447" name="fft_lecture-sept30_2014.pptx" path="fft_lecture-sept30_2014.pptx" size="16248705" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="join tomogram demo" date="1411303057" name="join_demo_2014.pdf" path="join_demo_2014.pdf" size="4051662" user="Main.BillRice" version="1"

Added:

>
>

META FILEATTACHMENT	attr="" autoattached="1" comment="Chimera Tutorial - Document" date="1418245339" name="chimera_tutorial.pdf" path="chimera_tutorial.pdf" size="5725723" user="Main.DannyHo" version="1"

META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417726358" name="helical_demo_1.pdf" path="helical_demo_1.pdf" size="2389231" user="Main.BillRice" version="1"
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META FILEATTACHMENT	attr="" autoattached="1" comment="Helical Reconstruction lecture slides" date="1418172197" name="Helical3d_reconst_v3.pdf" path="Helical3d_reconst_v3.pdf" size="5095698" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="notes on ref based alignment" date="1414696759" name="notes-ref_based_2014.pdf" path="notes-ref_based_2014.pdf" size="62496" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Tomography I lecture" date="1412719549" name="NYSBC-EM3-tomography-2014.pptx" path="NYSBC-EM3-tomography-2014.pptx" size="16899636" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Micrographs for SP practical 3 (needed by mac people)" date="1415176808" name="micrographs.zip" path="micrographs.zip" size="255492671" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="instructions for EMAN2 demo" date="1415300832" name="eman2_demo.pdf" path="eman2_demo.pdf" size="1785498" user="Main.BillRice" version="2"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1411496912" name="NYSBC-EM1-intro-optics14.ppt" path="NYSBC-EM1-intro-optics14.ppt" size="41782784" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="audio of fft lecture" date="1412719576" name="fft_lecture.mp3" path="fft_lecture.mp3" size="106645264" user="Main.BillRice" version="1"

Added:

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META FILEATTACHMENT	attr="" autoattached="1" comment="Lecture slides: Fitting Methods" date="1418149815" name="fitting_S.pptx" path="fitting_S.pptx" size="11076279" user="Main.DannyHo" version="1"

META FILEATTACHMENT	attr="" autoattached="1" comment="MDFF - Trabuco et al, Structure 2008" date="1417749877" name="Structure_2008_Trabuco.pdf" path="Structure_2008_Trabuco.pdf" size="1735706" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="2d crystal lecture 2" date="1417558990" name="2DX_EM_class_1-20141111_2103-1.arf" path="2DX_EM_class_1-20141111_2103-1.arf" size="253608617" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="single particle lecture 3" date="1417559778" name="Single_Particle_III-20141104_2101-1.arf" path="Single_Particle_III-20141104_2101-1.arf" size="279190625" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="video of FFT lecture" date="1412139438" name="CEM_2014_lecture_2_FFT-20140930_2008-1.arf" path="CEM_2014_lecture_2_FFT-20140930_2008-1.arf" size="257526200" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="ref bias demo" date="1414696780" name="ref_bias_2014.pdf" path="ref_bias_2014.pdf" size="73733" user="Main.BillRice" version="1"
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META FILEATTACHMENT	attr="" autoattached="1" comment="Single Particle Lecture 2" date="1414538098" name="NYSBC_2014-2.pptx" path="NYSBC_2014-2.pptx" size="20402100" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Course questionnaire" date="1411487211" name="questionnaire.doc" path="questionnaire.doc" size="25600" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417558552" name="2D_Crystallography_lecture_2-20141118_2115-1.arf" path="2D_Crystallography_lecture_2-20141118_2115-1.arf" size="141023696" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S2" date="1411301145" name="nprot.2008.156-S2.pdf" path="nprot.2008.156-S2.pdf" size="207150" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Files for Chimera Fitting practical workshop" date="1415293937" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" user="Main.DannyHo" version="1"

Changed:

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META FILEATTACHMENT	attachment="helical_demo_1.pdf" attr="" comment="" date="1417726358" name="helical_demo_1.pdf" path="helical_demo_1.pdf" size="2389231" stream="helical_demo_1.pdf" user="Main.BillRice" version="1"

>
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META FILEATTACHMENT	attachment="J._Struct._Biol._2012_Ahmed.pdf" attr="" comment="Molecular Fittings - Ahmed et al, JSB 2012" date="1417749955" name="J._Struct._Biol._2012_Ahmed.pdf" path="J. Struct. Biol. 2012 Ahmed.pdf" size="1440703" stream="J. Struct. Biol. 2012 Ahmed.pdf" user="Main.DannyHo" version="1"

META FILEATTACHMENT	attachment="fitting_S.pptx" attr="" comment="" date="1418149395" name="fitting_S.pptx" path="fitting_S.pptx" size="11077547" stream="fitting_S.pptx" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S3" date="1411301180" name="nprot.2008.156-S3.pdf" path="nprot.2008.156-S3.pdf" size="222608" user="Main.BillRice" version="1"

Revision 1904 Dec 2014 - Main.BillRice

META TOPICPARENT	name="CemCourseGroup"

Contents

Player required for arf video files

nbr2player.msi: MS windows player for arf files

Lectures

Structure Validation and Fitting - Dec. 9

Lecture

d164 1

Single Particle II - Oct 28 - Joachim Frank (Columbia)

Lecture

Single Particle II - Oct 28 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014-2.pptx: Single Particle Lecture 2 powerpoint

Single Particle I - Oct 21 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014_1.ppt: Single Particle Lecture 1 powerpoint

Tomography II - Oct 14 - David Stokes (NYU/NYSBC)

Lecture

Tomography I - Oct 7 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM3-tomography-2014.pptx: Tomography I lecture
- CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf: video of Tomography I

Fourier Series, Fourier Transform, Correlation, Convolution - Sept 30 - Bill Rice (NYSBC)

Lecture
- fft_lecture-sept30_2014.pptx: powerpoint of fft lecture
- CEM_2014_lecture_2_FFT-20140930_2008-1.arf: video of FFT lecture
- fft_lecture.mp3: audio of fft lecture in case audo in above file is poor (fixed week 3)

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt
Readings
- Hoffman(1997)_An_Introduction_to_Fourier_Theory.pdf: Hoffman Introduction to Fourier Theory
- fourier_intro_Shatkay.pdf: Shatkay Fourier Theory Intro
- http://www.med.harvard.edu/JPNM/physics/didactics/improc/intro/fourier1.html
Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

October 9 : etomo_demo_2014.pdf: Etomo demo
October 16: join_demo_2014.pdf: join tomogram demo

Single Particle Demos

October 23 - Nov 6
- nprot.2008.156.pdf: Nature Protocols paper
- nprot.2008.156-S1.pdf: Nature Protocols S1
- nprot.2008.156-S2.pdf: Nature Protocols S2
- nprot.2008.156-S3.pdf: Nature Protocols S3
- nprot.2008.156-S4.pdf: Nature Protocols S4
- notes-ref_based_2014.pdf: notes on ref based alignment
- ref_bias_2014.pdf: ref bias demo

- micrographs.zip: Micrographs for SP practical 3 (needed by mac people)
- eman2_demo.pdf: instructions for EMAN2 demo

Molecular Fitting Demo

Dec. 11 2014
- chimera_fitting_data.zip: Files for Chimera Fitting practical workshop

d148 1

Set ALLOWTOPICVIEW =

-- BillRice - 21 Sep 2014

* 2D_Crystallography_lecture_2-20141118_2115-1.arf: 2D_Crystallography_lecture_2-20141118_2115-1.arf

* 2DX_EM_class_1-20141111_2103-1.arf: 2d crystal lecture 2

* Single_Particle_III-20141104_2101-1.arf: single particle lecture 3

Added:

>
>

* helical_demo_1.pdf: helical_demo_1.pdf

META FILEATTACHMENT	attr="" autoattached="1" comment="course logistics" date="1411487228" name="CryoEM-Course-logistics.doc" path="CryoEM-Course-logistics.doc" size="36864" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S4" date="1411301202" name="nprot.2008.156-S4.pdf" path="nprot.2008.156-S4.pdf" size="24949" user="Main.BillRice" version="1"
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META FILEATTACHMENT	attr="" autoattached="1" comment="notes on ref based alignment" date="1414696759" name="notes-ref_based_2014.pdf" path="notes-ref_based_2014.pdf" size="62496" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Tomography I lecture" date="1412719549" name="NYSBC-EM3-tomography-2014.pptx" path="NYSBC-EM3-tomography-2014.pptx" size="16899636" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Micrographs for SP practical 3 (needed by mac people)" date="1415176808" name="micrographs.zip" path="micrographs.zip" size="255492671" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="instructions for EMAN2 demo" date="1415300832" name="eman2_demo.pdf" path="eman2_demo.pdf" size="1785498" user="Main.BillRice" version="2"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1411496912" name="NYSBC-EM1-intro-optics14.ppt" path="NYSBC-EM1-intro-optics14.ppt" size="41782784" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="audio of fft lecture" date="1412719576" name="fft_lecture.mp3" path="fft_lecture.mp3" size="106645264" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="MDFF - Trabuco et al, Structure 2008" date="1417749877" name="Structure_2008_Trabuco.pdf" path="Structure_2008_Trabuco.pdf" size="1735706" user="Main.DannyHo" version="1"

Added:

>
>

META FILEATTACHMENT	attr="" autoattached="1" comment="2d crystal lecture 2" date="1417558990" name="2DX_EM_class_1-20141111_2103-1.arf" path="2DX_EM_class_1-20141111_2103-1.arf" size="253608617" user="Main.BillRice" version="1"

META FILEATTACHMENT	attr="" autoattached="1" comment="single particle lecture 3" date="1417559778" name="Single_Particle_III-20141104_2101-1.arf" path="Single_Particle_III-20141104_2101-1.arf" size="279190625" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="video of FFT lecture" date="1412139438" name="CEM_2014_lecture_2_FFT-20140930_2008-1.arf" path="CEM_2014_lecture_2_FFT-20140930_2008-1.arf" size="257526200" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="ref bias demo" date="1414696780" name="ref_bias_2014.pdf" path="ref_bias_2014.pdf" size="73733" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Player for arf files" date="1412138278" name="nbr2player.msi" path="nbr2player.msi" size="14838784" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Single Particle Lecture 2" date="1414538098" name="NYSBC_2014-2.pptx" path="NYSBC_2014-2.pptx" size="20402100" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Course questionnaire" date="1411487211" name="questionnaire.doc" path="questionnaire.doc" size="25600" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417558552" name="2D_Crystallography_lecture_2-20141118_2115-1.arf" path="2D_Crystallography_lecture_2-20141118_2115-1.arf" size="141023696" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S2" date="1411301145" name="nprot.2008.156-S2.pdf" path="nprot.2008.156-S2.pdf" size="207150" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Files for Chimera Fitting practical workshop" date="1415293937" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" user="Main.DannyHo" version="1"

Changed:

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META FILEATTACHMENT	attachment="Single_Particle_III-20141104_2101-1.arf" attr="" comment="single particle lecture 3" date="1417559776" name="Single_Particle_III-20141104_2101-1.arf" path="Single Particle III-20141104 2101-1.arf" size="279190625" stream="Single Particle III-20141104 2101-1.arf" user="Main.BillRice" version="1"

>
>

META FILEATTACHMENT	attachment="helical_demo_1.pdf" attr="" comment="" date="1417726358" name="helical_demo_1.pdf" path="helical_demo_1.pdf" size="2389231" stream="helical_demo_1.pdf" user="Main.BillRice" version="1"

META FILEATTACHMENT	attachment="fitting_S.pptx" attr="" comment="" date="1418149395" name="fitting_S.pptx" path="fitting_S.pptx" size="11077547" stream="fitting_S.pptx" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S3" date="1411301180" name="nprot.2008.156-S3.pdf" path="nprot.2008.156-S3.pdf" size="222608" user="Main.BillRice" version="1"

Revision 1802 Dec 2014 - Main.BillRice

META TOPICPARENT	name="CemCourseGroup"

Contents

Player required for arf video files

nbr2player.msi: MS windows player for arf files

Lectures

Structure Validation and Fitting - Dec. 9

Lecture

d164 1

Single Particle II - Oct 28 - Joachim Frank (Columbia)

Lecture

Single Particle II - Oct 28 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014-2.pptx: Single Particle Lecture 2 powerpoint

Single Particle I - Oct 21 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014_1.ppt: Single Particle Lecture 1 powerpoint

Tomography II - Oct 14 - David Stokes (NYU/NYSBC)

Lecture

Tomography I - Oct 7 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM3-tomography-2014.pptx: Tomography I lecture
- CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf: video of Tomography I

Fourier Series, Fourier Transform, Correlation, Convolution - Sept 30 - Bill Rice (NYSBC)

Lecture
- fft_lecture-sept30_2014.pptx: powerpoint of fft lecture
- CEM_2014_lecture_2_FFT-20140930_2008-1.arf: video of FFT lecture
- fft_lecture.mp3: audio of fft lecture in case audo in above file is poor (fixed week 3)

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt
Readings
- Hoffman(1997)_An_Introduction_to_Fourier_Theory.pdf: Hoffman Introduction to Fourier Theory
- fourier_intro_Shatkay.pdf: Shatkay Fourier Theory Intro
- http://www.med.harvard.edu/JPNM/physics/didactics/improc/intro/fourier1.html
Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

October 9 : etomo_demo_2014.pdf: Etomo demo
October 16: join_demo_2014.pdf: join tomogram demo

Single Particle Demos

October 23 - Nov 6
- nprot.2008.156.pdf: Nature Protocols paper
- nprot.2008.156-S1.pdf: Nature Protocols S1
- nprot.2008.156-S2.pdf: Nature Protocols S2
- nprot.2008.156-S3.pdf: Nature Protocols S3
- nprot.2008.156-S4.pdf: Nature Protocols S4
- notes-ref_based_2014.pdf: notes on ref based alignment
- ref_bias_2014.pdf: ref bias demo

- micrographs.zip: Micrographs for SP practical 3 (needed by mac people)
- eman2_demo.pdf: instructions for EMAN2 demo

Molecular Fitting Demo

Dec. 11 2014
- chimera_fitting_data.zip: Files for Chimera Fitting practical workshop

d148 1

Set ALLOWTOPICVIEW =

-- BillRice - 21 Sep 2014

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* 2D_Crystallography_lecture_2-20141118_2115-1.arf: 2D_Crystallography_lecture_2-20141118_2115-1.arf

* 2DX_EM_class_1-20141111_2103-1.arf: 2d crystal lecture 2

* Single_Particle_III-20141104_2101-1.arf: single particle lecture 3

META FILEATTACHMENT	attr="" autoattached="1" comment="course logistics" date="1411487228" name="CryoEM-Course-logistics.doc" path="CryoEM-Course-logistics.doc" size="36864" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S4" date="1411301202" name="nprot.2008.156-S4.pdf" path="nprot.2008.156-S4.pdf" size="24949" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S1" date="1411301102" name="nprot.2008.156-S1.pdf" path="nprot.2008.156-S1.pdf" size="4990385" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="powerpoint of fft lecture" date="1412132447" name="fft_lecture-sept30_2014.pptx" path="fft_lecture-sept30_2014.pptx" size="16248705" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="join tomogram demo" date="1411303057" name="join_demo_2014.pdf" path="join_demo_2014.pdf" size="4051662" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417726358" name="helical_demo_1.pdf" path="helical_demo_1.pdf" size="2389231" user="Main.BillRice" version="1"
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META FILEATTACHMENT	attr="" autoattached="1" comment="Helical Reconstruction lecture slides" date="1418172197" name="Helical3d_reconst_v3.pdf" path="Helical3d_reconst_v3.pdf" size="5095698" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="notes on ref based alignment" date="1414696759" name="notes-ref_based_2014.pdf" path="notes-ref_based_2014.pdf" size="62496" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Tomography I lecture" date="1412719549" name="NYSBC-EM3-tomography-2014.pptx" path="NYSBC-EM3-tomography-2014.pptx" size="16899636" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Micrographs for SP practical 3 (needed by mac people)" date="1415176808" name="micrographs.zip" path="micrographs.zip" size="255492671" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="instructions for EMAN2 demo" date="1415300832" name="eman2_demo.pdf" path="eman2_demo.pdf" size="1785498" user="Main.BillRice" version="2"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1411496912" name="NYSBC-EM1-intro-optics14.ppt" path="NYSBC-EM1-intro-optics14.ppt" size="41782784" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="audio of fft lecture" date="1412719576" name="fft_lecture.mp3" path="fft_lecture.mp3" size="106645264" user="Main.BillRice" version="1"

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META FILEATTACHMENT	attr="" autoattached="1" comment="MDFF - Trabuco et al, Structure 2008" date="1417749877" name="Structure_2008_Trabuco.pdf" path="Structure_2008_Trabuco.pdf" size="1735706" user="Main.DannyHo" version="1"

META FILEATTACHMENT	attr="" autoattached="1" comment="single particle lecture 3" date="1417559778" name="Single_Particle_III-20141104_2101-1.arf" path="Single_Particle_III-20141104_2101-1.arf" size="279190625" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="video of FFT lecture" date="1412139438" name="CEM_2014_lecture_2_FFT-20140930_2008-1.arf" path="CEM_2014_lecture_2_FFT-20140930_2008-1.arf" size="257526200" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="ref bias demo" date="1414696780" name="ref_bias_2014.pdf" path="ref_bias_2014.pdf" size="73733" user="Main.BillRice" version="1"
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META FILEATTACHMENT	attr="" autoattached="1" comment="Single Particle Lecture 2" date="1414538098" name="NYSBC_2014-2.pptx" path="NYSBC_2014-2.pptx" size="20402100" user="Main.BillRice" version="1"

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META FILEATTACHMENT	attr="" autoattached="1" comment="Course questionnaire" date="1411487211" name="questionnaire.doc" path="questionnaire.doc" size="25600" user="Main.EdEng" version="1"

META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417558552" name="2D_Crystallography_lecture_2-20141118_2115-1.arf" path="2D_Crystallography_lecture_2-20141118_2115-1.arf" size="141023696" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S2" date="1411301145" name="nprot.2008.156-S2.pdf" path="nprot.2008.156-S2.pdf" size="207150" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Files for Chimera Fitting practical workshop" date="1415293937" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" user="Main.DannyHo" version="1"

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META FILEATTACHMENT	attachment="Single_Particle_III-20141104_2101-1.arf" attr="" comment="single particle lecture 3" date="1417559776" name="Single_Particle_III-20141104_2101-1.arf" path="Single Particle III-20141104 2101-1.arf" size="279190625" stream="Single Particle III-20141104 2101-1.arf" user="Main.BillRice" version="1"

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Revision 1706 Nov 2014 - Main.BillRice

META TOPICPARENT	name="CemCourseGroup"

Contents

Player required for arf video files

nbr2player.msi: MS windows player for arf files

Lectures

Structure Validation and Fitting - Dec. 9

Lecture

d164 1

Single Particle II - Oct 28 - Joachim Frank (Columbia)

Lecture

Single Particle II - Oct 28 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014-2.pptx: Single Particle Lecture 2 powerpoint

Single Particle I - Oct 21 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014_1.ppt: Single Particle Lecture 1 powerpoint

Tomography II - Oct 14 - David Stokes (NYU/NYSBC)

Lecture

Tomography I - Oct 7 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM3-tomography-2014.pptx: Tomography I lecture
- CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf: video of Tomography I

Fourier Series, Fourier Transform, Correlation, Convolution - Sept 30 - Bill Rice (NYSBC)

Lecture
- fft_lecture-sept30_2014.pptx: powerpoint of fft lecture
- CEM_2014_lecture_2_FFT-20140930_2008-1.arf: video of FFT lecture
- fft_lecture.mp3: audio of fft lecture in case audo in above file is poor (fixed week 3)

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt
Readings
- Hoffman(1997)_An_Introduction_to_Fourier_Theory.pdf: Hoffman Introduction to Fourier Theory
- fourier_intro_Shatkay.pdf: Shatkay Fourier Theory Intro
- http://www.med.harvard.edu/JPNM/physics/didactics/improc/intro/fourier1.html
Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

October 9 : etomo_demo_2014.pdf: Etomo demo
October 16: join_demo_2014.pdf: join tomogram demo

Single Particle Demos

October 23 - Nov 6
- nprot.2008.156.pdf: Nature Protocols paper
- nprot.2008.156-S1.pdf: Nature Protocols S1
- nprot.2008.156-S2.pdf: Nature Protocols S2
- nprot.2008.156-S3.pdf: Nature Protocols S3
- nprot.2008.156-S4.pdf: Nature Protocols S4
- notes-ref_based_2014.pdf: notes on ref based alignment
- ref_bias_2014.pdf: ref bias demo

- micrographs.zip: Micrographs for SP practical 3 (needed by mac people)

Added:

>
>

- eman2_demo.pdf: instructions for EMAN2 demo

Deleted:

<
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d78 1

Molecular Fitting Demo

Dec. 11 2014
- chimera_fitting_data.zip: Files for Chimera Fitting practical workshop

d148 1

Set ALLOWTOPICVIEW =

-- BillRice - 21 Sep 2014

Changed:

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* chimera_fitting_data.zip: Files for Chimera Fitting practical workshop

>
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Added:

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META FILEATTACHMENT	attr="" autoattached="1" comment="course logistics" date="1411487228" name="CryoEM-Course-logistics.doc" path="CryoEM-Course-logistics.doc" size="36864" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S4" date="1411301202" name="nprot.2008.156-S4.pdf" path="nprot.2008.156-S4.pdf" size="24949" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S1" date="1411301102" name="nprot.2008.156-S1.pdf" path="nprot.2008.156-S1.pdf" size="4990385" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="powerpoint of fft lecture" date="1412132447" name="fft_lecture-sept30_2014.pptx" path="fft_lecture-sept30_2014.pptx" size="16248705" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="join tomogram demo" date="1411303057" name="join_demo_2014.pdf" path="join_demo_2014.pdf" size="4051662" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417726358" name="helical_demo_1.pdf" path="helical_demo_1.pdf" size="2389231" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="video of Tomography I" date="1413315371" name="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" path="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" size="255161917" user="Main.BillRice" version="1"
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META FILEATTACHMENT	attr="" autoattached="1" comment="notes on ref based alignment" date="1414696759" name="notes-ref_based_2014.pdf" path="notes-ref_based_2014.pdf" size="62496" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Tomography I lecture" date="1412719549" name="NYSBC-EM3-tomography-2014.pptx" path="NYSBC-EM3-tomography-2014.pptx" size="16899636" user="Main.DavidStokes" version="1"

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META FILEATTACHMENT	attr="" autoattached="1" comment="Micrographs for SP practical 3 (needed by mac people)" date="1415176808" name="micrographs.zip" path="micrographs.zip" size="255492671" user="Main.BillRice" version="1"

META FILEATTACHMENT	attr="" autoattached="1" comment="instructions for EMAN2 demo" date="1415300832" name="eman2_demo.pdf" path="eman2_demo.pdf" size="1785498" user="Main.BillRice" version="2"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1411496912" name="NYSBC-EM1-intro-optics14.ppt" path="NYSBC-EM1-intro-optics14.ppt" size="41782784" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="audio of fft lecture" date="1412719576" name="fft_lecture.mp3" path="fft_lecture.mp3" size="106645264" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="single particle lecture 3" date="1417559778" name="Single_Particle_III-20141104_2101-1.arf" path="Single_Particle_III-20141104_2101-1.arf" size="279190625" user="Main.BillRice" version="1"
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META FILEATTACHMENT	attr="" autoattached="1" comment="ref bias demo" date="1414696780" name="ref_bias_2014.pdf" path="ref_bias_2014.pdf" size="73733" user="Main.BillRice" version="1"
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META FILEATTACHMENT	attr="" autoattached="1" comment="Single Particle Lecture 2" date="1414538098" name="NYSBC_2014-2.pptx" path="NYSBC_2014-2.pptx" size="20402100" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417558552" name="2D_Crystallography_lecture_2-20141118_2115-1.arf" path="2D_Crystallography_lecture_2-20141118_2115-1.arf" size="141023696" user="Main.BillRice" version="1"

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META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S2" date="1411301145" name="nprot.2008.156-S2.pdf" path="nprot.2008.156-S2.pdf" size="207150" user="Main.BillRice" version="1"

META FILEATTACHMENT	attr="" autoattached="1" comment="Files for Chimera Fitting practical workshop" date="1415293937" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" user="Main.DannyHo" version="1"

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META FILEATTACHMENT	attachment="chimera_fitting_data.zip" attr="" comment="Files for Chimera Fitting practical workshop" date="1415293936" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" stream="chimera_fitting_data.zip" user="Main.DannyHo" version="1"

META FILEATTACHMENT	attachment="fitting_S.pptx" attr="" comment="" date="1418149395" name="fitting_S.pptx" path="fitting_S.pptx" size="11077547" stream="fitting_S.pptx" user="Main.DannyHo" version="1"
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Revision 1606 Nov 2014 - Main.DannyHo

META TOPICPARENT	name="CemCourseGroup"

Contents

Player required for arf video files

nbr2player.msi: MS windows player for arf files

Lectures

Structure Validation and Fitting - Dec. 9

Lecture

d164 1

Single Particle II - Oct 28 - Joachim Frank (Columbia)

Lecture

Single Particle II - Oct 28 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014-2.pptx: Single Particle Lecture 2 powerpoint

Single Particle I - Oct 21 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014_1.ppt: Single Particle Lecture 1 powerpoint

Tomography II - Oct 14 - David Stokes (NYU/NYSBC)

Lecture

Tomography I - Oct 7 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM3-tomography-2014.pptx: Tomography I lecture
- CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf: video of Tomography I

Fourier Series, Fourier Transform, Correlation, Convolution - Sept 30 - Bill Rice (NYSBC)

Lecture
- fft_lecture-sept30_2014.pptx: powerpoint of fft lecture
- CEM_2014_lecture_2_FFT-20140930_2008-1.arf: video of FFT lecture
- fft_lecture.mp3: audio of fft lecture in case audo in above file is poor (fixed week 3)

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt
Readings
- Hoffman(1997)_An_Introduction_to_Fourier_Theory.pdf: Hoffman Introduction to Fourier Theory
- fourier_intro_Shatkay.pdf: Shatkay Fourier Theory Intro
- http://www.med.harvard.edu/JPNM/physics/didactics/improc/intro/fourier1.html
Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

October 9 : etomo_demo_2014.pdf: Etomo demo
October 16: join_demo_2014.pdf: join tomogram demo

Single Particle Demos

October 23 - Nov 6
- nprot.2008.156.pdf: Nature Protocols paper
- nprot.2008.156-S1.pdf: Nature Protocols S1
- nprot.2008.156-S2.pdf: Nature Protocols S2
- nprot.2008.156-S3.pdf: Nature Protocols S3
- nprot.2008.156-S4.pdf: Nature Protocols S4
- notes-ref_based_2014.pdf: notes on ref based alignment
- ref_bias_2014.pdf: ref bias demo

- micrographs.zip: Micrographs for SP practical 3 (needed by mac people)

d78 1

Molecular Fitting Demo

Dec. 11 2014
- chimera_fitting_data.zip: Files for Chimera Fitting practical workshop

d148 1

Set ALLOWTOPICVIEW =

-- BillRice - 21 Sep 2014

Added:

>
>

* chimera_fitting_data.zip: Files for Chimera Fitting practical workshop

META FILEATTACHMENT	attr="" autoattached="1" comment="course logistics" date="1411487228" name="CryoEM-Course-logistics.doc" path="CryoEM-Course-logistics.doc" size="36864" user="Main.EdEng" version="1"
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Added:

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>

META FILEATTACHMENT	attr="" autoattached="1" comment="Files for Chimera Fitting practical workshop" date="1415293937" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" user="Main.DannyHo" version="1"

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Revision 1506 Nov 2014 - Main.BillRice

META TOPICPARENT	name="CemCourseGroup"

Contents

Player required for arf video files

nbr2player.msi: MS windows player for arf files

Lectures

Added:

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>

Structure Validation and Fitting - Dec. 9

Lecture

d164 1

Single Particle II - Oct 28 - Joachim Frank (Columbia)

Lecture

Added:

>
>

Single Particle II - Oct 28 - Joachim Frank (Columbia)

Lecture

- NYSBC_2014-2.pptx: Single Particle Lecture 2 powerpoint

Single Particle I - Oct 21 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014_1.ppt: Single Particle Lecture 1 powerpoint

Tomography II - Oct 14 - David Stokes (NYU/NYSBC)

Lecture

Tomography I - Oct 7 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM3-tomography-2014.pptx: Tomography I lecture
- CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf: video of Tomography I

Fourier Series, Fourier Transform, Correlation, Convolution - Sept 30 - Bill Rice (NYSBC)

Lecture
- fft_lecture-sept30_2014.pptx: powerpoint of fft lecture
- CEM_2014_lecture_2_FFT-20140930_2008-1.arf: video of FFT lecture
- fft_lecture.mp3: audio of fft lecture in case audo in above file is poor (fixed week 3)

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt
Readings
- Hoffman(1997)_An_Introduction_to_Fourier_Theory.pdf: Hoffman Introduction to Fourier Theory
- fourier_intro_Shatkay.pdf: Shatkay Fourier Theory Intro
- http://www.med.harvard.edu/JPNM/physics/didactics/improc/intro/fourier1.html
Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

October 9 : etomo_demo_2014.pdf: Etomo demo
October 16: join_demo_2014.pdf: join tomogram demo

Single Particle Demos

October 23 - Nov 6
- nprot.2008.156.pdf: Nature Protocols paper
- nprot.2008.156-S1.pdf: Nature Protocols S1
- nprot.2008.156-S2.pdf: Nature Protocols S2
- nprot.2008.156-S3.pdf: Nature Protocols S3
- nprot.2008.156-S4.pdf: Nature Protocols S4
- notes-ref_based_2014.pdf: notes on ref based alignment
- ref_bias_2014.pdf: ref bias demo

- micrographs.zip: Micrographs for SP practical 3 (needed by mac people)

Added:

>
>

d78 1

Molecular Fitting Demo

Dec. 11 2014

- chimera_fitting_data.zip: Files for Chimera Fitting practical workshop

d148 1

Set ALLOWTOPICVIEW =

-- BillRice - 21 Sep 2014

META FILEATTACHMENT	attr="" autoattached="1" comment="course logistics" date="1411487228" name="CryoEM-Course-logistics.doc" path="CryoEM-Course-logistics.doc" size="36864" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S4" date="1411301202" name="nprot.2008.156-S4.pdf" path="nprot.2008.156-S4.pdf" size="24949" user="Main.BillRice" version="1"
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META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417726358" name="helical_demo_1.pdf" path="helical_demo_1.pdf" size="2389231" user="Main.BillRice" version="1"
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Revision 1405 Nov 2014 - Main.BillRice

META TOPICPARENT	name="CemCourseGroup"

Contents

Player required for arf video files

nbr2player.msi: MS windows player for arf files

Lectures

Single Particle II - Oct 28 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014-2.pptx: Single Particle Lecture 2 powerpoint

Single Particle I - Oct 21 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014_1.ppt: Single Particle Lecture 1 powerpoint

Tomography II - Oct 14 - David Stokes (NYU/NYSBC)

Lecture

Tomography I - Oct 7 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM3-tomography-2014.pptx: Tomography I lecture
- CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf: video of Tomography I

Fourier Series, Fourier Transform, Correlation, Convolution - Sept 30 - Bill Rice (NYSBC)

Lecture
- fft_lecture-sept30_2014.pptx: powerpoint of fft lecture
- CEM_2014_lecture_2_FFT-20140930_2008-1.arf: video of FFT lecture
- fft_lecture.mp3: audio of fft lecture in case audo in above file is poor (fixed week 3)

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt
Readings
- Hoffman(1997)_An_Introduction_to_Fourier_Theory.pdf: Hoffman Introduction to Fourier Theory
- fourier_intro_Shatkay.pdf: Shatkay Fourier Theory Intro
- http://www.med.harvard.edu/JPNM/physics/didactics/improc/intro/fourier1.html
Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

October 9 : etomo_demo_2014.pdf: Etomo demo
October 16: join_demo_2014.pdf: join tomogram demo

Single Particle Demos

October 23 - Nov 6
- nprot.2008.156.pdf: Nature Protocols paper
- nprot.2008.156-S1.pdf: Nature Protocols S1
- nprot.2008.156-S2.pdf: Nature Protocols S2
- nprot.2008.156-S3.pdf: Nature Protocols S3
- nprot.2008.156-S4.pdf: Nature Protocols S4

Added:

>
>

- notes-ref_based_2014.pdf: notes on ref based alignment
- ref_bias_2014.pdf: ref bias demo

Added:

>
>

- micrographs.zip: Micrographs for SP practical 3 (needed by mac people)

Added:

>
>

- chimera_fitting_data.zip: Files for Chimera Fitting practical workshop

d148 1

Set ALLOWTOPICVIEW =

-- BillRice - 21 Sep 2014

Deleted:

<
<

* notes-ref_based_2014.pdf: notes on ref based alignment

Deleted:

<
<

* ref_bias_2014.pdf: ref bias demo

* micrographs.zip: Micrographs for SP practical 3 (needed by mac people) d101 1

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META FILEATTACHMENT	attr="" autoattached="1" comment="instructions for EMAN2 demo" date="1415300832" name="eman2_demo.pdf" path="eman2_demo.pdf" size="1785498" user="Main.BillRice" version="2"
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Deleted:

<
<

META FILEATTACHMENT	attachment="micrographs.zip" attr="" comment="Micrographs for SP practical 3 (needed by mac people)" date="1415176804" name="micrographs.zip" path="micrographs.zip" size="255492671" stream="micrographs.zip" user="Main.BillRice" version="1"

META FILEATTACHMENT	attachment="chimera_fitting_data.zip" attr="" comment="Files for Chimera Fitting practical workshop" date="1415293936" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" stream="chimera_fitting_data.zip" user="Main.DannyHo" version="1"
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META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S3" date="1411301180" name="nprot.2008.156-S3.pdf" path="nprot.2008.156-S3.pdf" size="222608" user="Main.BillRice" version="1"

Revision 1305 Nov 2014 - Main.BillRice

META TOPICPARENT	name="CemCourseGroup"

Contents

Player required for arf video files

nbr2player.msi: MS windows player for arf files

Lectures

Single Particle II - Oct 28 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014-2.pptx: Single Particle Lecture 2 powerpoint

Single Particle I - Oct 21 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014_1.ppt: Single Particle Lecture 1 powerpoint

Tomography II - Oct 14 - David Stokes (NYU/NYSBC)

Lecture

Tomography I - Oct 7 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM3-tomography-2014.pptx: Tomography I lecture
- CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf: video of Tomography I

Fourier Series, Fourier Transform, Correlation, Convolution - Sept 30 - Bill Rice (NYSBC)

Lecture
- fft_lecture-sept30_2014.pptx: powerpoint of fft lecture
- CEM_2014_lecture_2_FFT-20140930_2008-1.arf: video of FFT lecture
- fft_lecture.mp3: audio of fft lecture in case audo in above file is poor (fixed week 3)

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt
Readings
- Hoffman(1997)_An_Introduction_to_Fourier_Theory.pdf: Hoffman Introduction to Fourier Theory
- fourier_intro_Shatkay.pdf: Shatkay Fourier Theory Intro
- http://www.med.harvard.edu/JPNM/physics/didactics/improc/intro/fourier1.html
Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

October 9 : etomo_demo_2014.pdf: Etomo demo
October 16: join_demo_2014.pdf: join tomogram demo

Single Particle Demos

October 23 - Nov 6
- nprot.2008.156.pdf: Nature Protocols paper
- nprot.2008.156-S1.pdf: Nature Protocols S1
- nprot.2008.156-S2.pdf: Nature Protocols S2
- nprot.2008.156-S3.pdf: Nature Protocols S3
- nprot.2008.156-S4.pdf: Nature Protocols S4

d148 1

Set ALLOWTOPICVIEW =

-- BillRice - 21 Sep 2014

* notes-ref_based_2014.pdf: notes on ref based alignment

* ref_bias_2014.pdf: ref bias demo

Added:

>
>

* micrographs.zip: Micrographs for SP practical 3 (needed by mac people) d101 1

META FILEATTACHMENT	attr="" autoattached="1" comment="course logistics" date="1411487228" name="CryoEM-Course-logistics.doc" path="CryoEM-Course-logistics.doc" size="36864" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S4" date="1411301202" name="nprot.2008.156-S4.pdf" path="nprot.2008.156-S4.pdf" size="24949" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S1" date="1411301102" name="nprot.2008.156-S1.pdf" path="nprot.2008.156-S1.pdf" size="4990385" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="powerpoint of fft lecture" date="1412132447" name="fft_lecture-sept30_2014.pptx" path="fft_lecture-sept30_2014.pptx" size="16248705" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="join tomogram demo" date="1411303057" name="join_demo_2014.pdf" path="join_demo_2014.pdf" size="4051662" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417726358" name="helical_demo_1.pdf" path="helical_demo_1.pdf" size="2389231" user="Main.BillRice" version="1"
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META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Portocols paper" date="1411300831" name="nprot.2008.156.pdf" path="nprot.2008.156.pdf" size="3383115" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Helical Reconstruction lecture slides" date="1418172197" name="Helical3d_reconst_v3.pdf" path="Helical3d_reconst_v3.pdf" size="5095698" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="notes on ref based alignment" date="1414696759" name="notes-ref_based_2014.pdf" path="notes-ref_based_2014.pdf" size="62496" user="Main.BillRice" version="1"
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META FILEATTACHMENT	attr="" autoattached="1" comment="instructions for EMAN2 demo" date="1415300832" name="eman2_demo.pdf" path="eman2_demo.pdf" size="1785498" user="Main.BillRice" version="2"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1411496912" name="NYSBC-EM1-intro-optics14.ppt" path="NYSBC-EM1-intro-optics14.ppt" size="41782784" user="Main.DavidStokes" version="1"

Added:

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META FILEATTACHMENT	attr="" autoattached="1" comment="audio of fft lecture" date="1412719576" name="fft_lecture.mp3" path="fft_lecture.mp3" size="106645264" user="Main.BillRice" version="1"

META FILEATTACHMENT	attr="" autoattached="1" comment="single particle lecture 3" date="1417559778" name="Single_Particle_III-20141104_2101-1.arf" path="Single_Particle_III-20141104_2101-1.arf" size="279190625" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="video of FFT lecture" date="1412139438" name="CEM_2014_lecture_2_FFT-20140930_2008-1.arf" path="CEM_2014_lecture_2_FFT-20140930_2008-1.arf" size="257526200" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="ref bias demo" date="1414696780" name="ref_bias_2014.pdf" path="ref_bias_2014.pdf" size="73733" user="Main.BillRice" version="1"
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META FILEATTACHMENT	attr="" autoattached="1" comment="Single Particle Lecture 2" date="1414538098" name="NYSBC_2014-2.pptx" path="NYSBC_2014-2.pptx" size="20402100" user="Main.BillRice" version="1"

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META FILEATTACHMENT	attachment="ref_bias_2014.pdf" attr="" comment="ref bias demo" date="1414696779" name="ref_bias_2014.pdf" path="ref_bias_2014.pdf" size="73733" stream="ref_bias_2014.pdf" user="Main.BillRice" version="1"

>
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META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417558552" name="2D_Crystallography_lecture_2-20141118_2115-1.arf" path="2D_Crystallography_lecture_2-20141118_2115-1.arf" size="141023696" user="Main.BillRice" version="1"

META FILEATTACHMENT	attachment="micrographs.zip" attr="" comment="Micrographs for SP practical 3 (needed by mac people)" date="1415176804" name="micrographs.zip" path="micrographs.zip" size="255492671" stream="micrographs.zip" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="chimera_fitting_data.zip" attr="" comment="Files for Chimera Fitting practical workshop" date="1415293936" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" stream="chimera_fitting_data.zip" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attachment="fitting_S.pptx" attr="" comment="" date="1418149395" name="fitting_S.pptx" path="fitting_S.pptx" size="11077547" stream="fitting_S.pptx" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S3" date="1411301180" name="nprot.2008.156-S3.pdf" path="nprot.2008.156-S3.pdf" size="222608" user="Main.BillRice" version="1"

Revision 1230 Oct 2014 - Main.BillRice

META TOPICPARENT	name="CemCourseGroup"

Contents

Player required for arf video files

nbr2player.msi: MS windows player for arf files

Lectures

Single Particle II - Oct 28 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014-2.pptx: Single Particle Lecture 2 powerpoint

Single Particle I - Oct 21 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014_1.ppt: Single Particle Lecture 1 powerpoint

Tomography II - Oct 14 - David Stokes (NYU/NYSBC)

Lecture

Tomography I - Oct 7 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM3-tomography-2014.pptx: Tomography I lecture
- CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf: video of Tomography I

Fourier Series, Fourier Transform, Correlation, Convolution - Sept 30 - Bill Rice (NYSBC)

Lecture
- fft_lecture-sept30_2014.pptx: powerpoint of fft lecture
- CEM_2014_lecture_2_FFT-20140930_2008-1.arf: video of FFT lecture
- fft_lecture.mp3: audio of fft lecture in case audo in above file is poor (fixed week 3)

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt
Readings
- Hoffman(1997)_An_Introduction_to_Fourier_Theory.pdf: Hoffman Introduction to Fourier Theory
- fourier_intro_Shatkay.pdf: Shatkay Fourier Theory Intro
- http://www.med.harvard.edu/JPNM/physics/didactics/improc/intro/fourier1.html
Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

October 9 : etomo_demo_2014.pdf: Etomo demo
October 16: join_demo_2014.pdf: join tomogram demo

Single Particle Demos

October 23 - Nov 6
- nprot.2008.156.pdf: Nature Protocols paper
- nprot.2008.156-S1.pdf: Nature Protocols S1
- nprot.2008.156-S2.pdf: Nature Protocols S2
- nprot.2008.156-S3.pdf: Nature Protocols S3
- nprot.2008.156-S4.pdf: Nature Protocols S4

d148 1

Set ALLOWTOPICVIEW =

-- BillRice - 21 Sep 2014

Added:

>
>

* notes-ref_based_2014.pdf: notes on ref based alignment

Added:

>
>

* ref_bias_2014.pdf: ref bias demo

META FILEATTACHMENT	attr="" autoattached="1" comment="course logistics" date="1411487228" name="CryoEM-Course-logistics.doc" path="CryoEM-Course-logistics.doc" size="36864" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S4" date="1411301202" name="nprot.2008.156-S4.pdf" path="nprot.2008.156-S4.pdf" size="24949" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S1" date="1411301102" name="nprot.2008.156-S1.pdf" path="nprot.2008.156-S1.pdf" size="4990385" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="powerpoint of fft lecture" date="1412132447" name="fft_lecture-sept30_2014.pptx" path="fft_lecture-sept30_2014.pptx" size="16248705" user="Main.BillRice" version="1"
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META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417726358" name="helical_demo_1.pdf" path="helical_demo_1.pdf" size="2389231" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="video of Tomography I" date="1413315371" name="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" path="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" size="255161917" user="Main.BillRice" version="1"

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META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Portocols paper" date="1411300831" name="nprot.2008.156.pdf" path="nprot.2008.156.pdf" size="3383115" user="Main.BillRice" version="1"

META FILEATTACHMENT	attr="" autoattached="1" comment="Helical Reconstruction lecture slides" date="1418172197" name="Helical3d_reconst_v3.pdf" path="Helical3d_reconst_v3.pdf" size="5095698" user="Main.BillRice" version="1"
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META FILEATTACHMENT	attachment="micrographs.zip" attr="" comment="Micrographs for SP practical 3 (needed by mac people)" date="1415176804" name="micrographs.zip" path="micrographs.zip" size="255492671" stream="micrographs.zip" user="Main.BillRice" version="1"
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Revision 1128 Oct 2014 - Main.BillRice

META TOPICPARENT	name="CemCourseGroup"

Contents

Player required for arf video files

nbr2player.msi: MS windows player for arf files

Lectures

Changed:

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<

Tomography II - Oct 14 - David Stokes x(NYU/NYSBC)

>
>

Single Particle II - Oct 28 - Joachim Frank (Columbia)

Lecture

Added:

>
>

- NYSBC_2014-2.pptx: Single Particle Lecture 2 powerpoint

Added:

>
>

Single Particle I - Oct 21 - Joachim Frank (Columbia)

Lecture
- NYSBC_2014_1.ppt: Single Particle Lecture 1 powerpoint

Added:

>
>

Tomography II - Oct 14 - David Stokes (NYU/NYSBC)

Lecture

Tomography I - Oct 7 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM3-tomography-2014.pptx: Tomography I lecture
- CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf: video of Tomography I

Fourier Series, Fourier Transform, Correlation, Convolution - Sept 30 - Bill Rice (NYSBC)

Lecture
- fft_lecture-sept30_2014.pptx: powerpoint of fft lecture
- CEM_2014_lecture_2_FFT-20140930_2008-1.arf: video of FFT lecture
- fft_lecture.mp3: audio of fft lecture in case audo in above file is poor (fixed week 3)

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt
Readings
- Hoffman(1997)_An_Introduction_to_Fourier_Theory.pdf: Hoffman Introduction to Fourier Theory
- fourier_intro_Shatkay.pdf: Shatkay Fourier Theory Intro
- http://www.med.harvard.edu/JPNM/physics/didactics/improc/intro/fourier1.html
Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

October 9 : etomo_demo_2014.pdf: Etomo demo
October 16: join_demo_2014.pdf: join tomogram demo

Single Particle Demos

October 23 - Nov 6
- nprot.2008.156.pdf: Nature Protocols paper
- nprot.2008.156-S1.pdf: Nature Protocols S1
- nprot.2008.156-S2.pdf: Nature Protocols S2
- nprot.2008.156-S3.pdf: Nature Protocols S3
- nprot.2008.156-S4.pdf: Nature Protocols S4

d148 1

Set ALLOWTOPICVIEW =

-- BillRice - 21 Sep 2014

Added:

>
>

META FILEATTACHMENT	attr="" autoattached="1" comment="course logistics" date="1411487228" name="CryoEM-Course-logistics.doc" path="CryoEM-Course-logistics.doc" size="36864" user="Main.EdEng" version="1"
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META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417726358" name="helical_demo_1.pdf" path="helical_demo_1.pdf" size="2389231" user="Main.BillRice" version="1"

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META FILEATTACHMENT	attr="" autoattached="1" comment="video of Tomography I" date="1413315371" name="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" path="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" size="255161917" user="Main.BillRice" version="1"

META FILEATTACHMENT	attr="" autoattached="1" comment="Helical Reconstruction lecture slides" date="1418172197" name="Helical3d_reconst_v3.pdf" path="Helical3d_reconst_v3.pdf" size="5095698" user="Main.BillRice" version="1"
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Added:

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META FILEATTACHMENT	attr="" autoattached="1" comment="video of FFT lecture" date="1412139438" name="CEM_2014_lecture_2_FFT-20140930_2008-1.arf" path="CEM_2014_lecture_2_FFT-20140930_2008-1.arf" size="257526200" user="Main.BillRice" version="1"

META FILEATTACHMENT	attr="" autoattached="1" comment="ref bias demo" date="1414696780" name="ref_bias_2014.pdf" path="ref_bias_2014.pdf" size="73733" user="Main.BillRice" version="1"
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META FILEATTACHMENT	attachment="micrographs.zip" attr="" comment="Micrographs for SP practical 3 (needed by mac people)" date="1415176804" name="micrographs.zip" path="micrographs.zip" size="255492671" stream="micrographs.zip" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="chimera_fitting_data.zip" attr="" comment="Files for Chimera Fitting practical workshop" date="1415293936" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" stream="chimera_fitting_data.zip" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attachment="fitting_S.pptx" attr="" comment="" date="1418149395" name="fitting_S.pptx" path="fitting_S.pptx" size="11077547" stream="fitting_S.pptx" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S3" date="1411301180" name="nprot.2008.156-S3.pdf" path="nprot.2008.156-S3.pdf" size="222608" user="Main.BillRice" version="1"

Revision 1014 Oct 2014 - Main.BillRice

META TOPICPARENT	name="CemCourseGroup"

Contents

Player required for arf video files

nbr2player.msi: MS windows player for arf files

Lectures

Added:

>
>

Tomography II - Oct 14 - David Stokes x(NYU/NYSBC)

Lecture

Tomography I - Oct 7 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM3-tomography-2014.pptx: Tomography I lecture
- CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf: video of Tomography I

Fourier Series, Fourier Transform, Correlation, Convolution - Sept 30 - Bill Rice (NYSBC)

Lecture
- fft_lecture-sept30_2014.pptx: powerpoint of fft lecture
- CEM_2014_lecture_2_FFT-20140930_2008-1.arf: video of FFT lecture
- fft_lecture.mp3: audio of fft lecture in case audo in above file is poor (fixed week 3)

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt
Readings
- Hoffman(1997)_An_Introduction_to_Fourier_Theory.pdf: Hoffman Introduction to Fourier Theory
- fourier_intro_Shatkay.pdf: Shatkay Fourier Theory Intro
- http://www.med.harvard.edu/JPNM/physics/didactics/improc/intro/fourier1.html
Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

October 9 : etomo_demo_2014.pdf: Etomo demo
October 16: join_demo_2014.pdf: join tomogram demo

Single Particle Demos

October 23 - Nov 6
- nprot.2008.156.pdf: Nature Protocols paper
- nprot.2008.156-S1.pdf: Nature Protocols S1
- nprot.2008.156-S2.pdf: Nature Protocols S2
- nprot.2008.156-S3.pdf: Nature Protocols S3
- nprot.2008.156-S4.pdf: Nature Protocols S4

d148 1

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-- BillRice - 21 Sep 2014

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* NYSBC-EM3-tomography-2014.pptx: Tomography I lecture d70 1

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* CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf: video of Tomography I

Added:

>
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META FILEATTACHMENT	attr="" autoattached="1" comment="course logistics" date="1411487228" name="CryoEM-Course-logistics.doc" path="CryoEM-Course-logistics.doc" size="36864" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S4" date="1411301202" name="nprot.2008.156-S4.pdf" path="nprot.2008.156-S4.pdf" size="24949" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S1" date="1411301102" name="nprot.2008.156-S1.pdf" path="nprot.2008.156-S1.pdf" size="4990385" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="powerpoint of fft lecture" date="1412132447" name="fft_lecture-sept30_2014.pptx" path="fft_lecture-sept30_2014.pptx" size="16248705" user="Main.BillRice" version="1"

Added:

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META FILEATTACHMENT	attr="" autoattached="1" comment="join tomogram demo" date="1411303057" name="join_demo_2014.pdf" path="join_demo_2014.pdf" size="4051662" user="Main.BillRice" version="1"

META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417726358" name="helical_demo_1.pdf" path="helical_demo_1.pdf" size="2389231" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Helical Reconstruction lecture slides" date="1418172197" name="Helical3d_reconst_v3.pdf" path="Helical3d_reconst_v3.pdf" size="5095698" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="notes on ref based alignment" date="1414696759" name="notes-ref_based_2014.pdf" path="notes-ref_based_2014.pdf" size="62496" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Tomography I lecture" date="1412719549" name="NYSBC-EM3-tomography-2014.pptx" path="NYSBC-EM3-tomography-2014.pptx" size="16899636" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="instructions for EMAN2 demo" date="1415300832" name="eman2_demo.pdf" path="eman2_demo.pdf" size="1785498" user="Main.BillRice" version="2"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1411496912" name="NYSBC-EM1-intro-optics14.ppt" path="NYSBC-EM1-intro-optics14.ppt" size="41782784" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="single particle lecture 3" date="1417559778" name="Single_Particle_III-20141104_2101-1.arf" path="Single_Particle_III-20141104_2101-1.arf" size="279190625" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="ref bias demo" date="1414696780" name="ref_bias_2014.pdf" path="ref_bias_2014.pdf" size="73733" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Player for arf files" date="1412138278" name="nbr2player.msi" path="nbr2player.msi" size="14838784" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Single Particle Lecture 2" date="1414538098" name="NYSBC_2014-2.pptx" path="NYSBC_2014-2.pptx" size="20402100" user="Main.BillRice" version="1"

Deleted:

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META FILEATTACHMENT	attachment="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" attr="" comment="video of Tomography I" date="1413315369" name="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" path="CEM course 2014 lecture 3 Tomography-20141007 2001-1.arf" size="255161917" stream="CEM course 2014 lecture 3 Tomography-20141007 2001-1.arf" user="Main.BillRice" version="1"

META FILEATTACHMENT	attachment="micrographs.zip" attr="" comment="Micrographs for SP practical 3 (needed by mac people)" date="1415176804" name="micrographs.zip" path="micrographs.zip" size="255492671" stream="micrographs.zip" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="chimera_fitting_data.zip" attr="" comment="Files for Chimera Fitting practical workshop" date="1415293936" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" stream="chimera_fitting_data.zip" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attachment="fitting_S.pptx" attr="" comment="" date="1418149395" name="fitting_S.pptx" path="fitting_S.pptx" size="11077547" stream="fitting_S.pptx" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S3" date="1411301180" name="nprot.2008.156-S3.pdf" path="nprot.2008.156-S3.pdf" size="222608" user="Main.BillRice" version="1"

Revision 914 Oct 2014 - Main.BillRice

META TOPICPARENT	name="CemCourseGroup"

Contents

Player required for arf video files

nbr2player.msi: MS windows player for arf files

Lectures

Fourier Series, Fourier Transform, Correlation, Convolution - Sept 30 - Bill Rice (NYSBC)

Lecture
- fft_lecture-sept30_2014.pptx: powerpoint of fft lecture
- CEM_2014_lecture_2_FFT-20140930_2008-1.arf: video of FFT lecture
- fft_lecture.mp3: audio of fft lecture in case audo in above file is poor (fixed week 3)

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt
Readings
- Hoffman(1997)_An_Introduction_to_Fourier_Theory.pdf: Hoffman Introduction to Fourier Theory
- fourier_intro_Shatkay.pdf: Shatkay Fourier Theory Intro
- http://www.med.harvard.edu/JPNM/physics/didactics/improc/intro/fourier1.html
Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

October 9 : etomo_demo_2014.pdf: Etomo demo
October 16: join_demo_2014.pdf: join tomogram demo

Single Particle Demos

October 23 - Nov 6
- nprot.2008.156.pdf: Nature Protocols paper
- nprot.2008.156-S1.pdf: Nature Protocols S1
- nprot.2008.156-S2.pdf: Nature Protocols S2
- nprot.2008.156-S3.pdf: Nature Protocols S3
- nprot.2008.156-S4.pdf: Nature Protocols S4

d148 1

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-- BillRice - 21 Sep 2014

* NYSBC-EM3-tomography-2014.pptx: Tomography I lecture d70 1

Added:

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* CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf: video of Tomography I

META FILEATTACHMENT	attr="" autoattached="1" comment="course logistics" date="1411487228" name="CryoEM-Course-logistics.doc" path="CryoEM-Course-logistics.doc" size="36864" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S4" date="1411301202" name="nprot.2008.156-S4.pdf" path="nprot.2008.156-S4.pdf" size="24949" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S1" date="1411301102" name="nprot.2008.156-S1.pdf" path="nprot.2008.156-S1.pdf" size="4990385" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="powerpoint of fft lecture" date="1412132447" name="fft_lecture-sept30_2014.pptx" path="fft_lecture-sept30_2014.pptx" size="16248705" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417726358" name="helical_demo_1.pdf" path="helical_demo_1.pdf" size="2389231" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Helical Reconstruction lecture slides" date="1418172197" name="Helical3d_reconst_v3.pdf" path="Helical3d_reconst_v3.pdf" size="5095698" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="notes on ref based alignment" date="1414696759" name="notes-ref_based_2014.pdf" path="notes-ref_based_2014.pdf" size="62496" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Tomography I lecture" date="1412719549" name="NYSBC-EM3-tomography-2014.pptx" path="NYSBC-EM3-tomography-2014.pptx" size="16899636" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="instructions for EMAN2 demo" date="1415300832" name="eman2_demo.pdf" path="eman2_demo.pdf" size="1785498" user="Main.BillRice" version="2"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1411496912" name="NYSBC-EM1-intro-optics14.ppt" path="NYSBC-EM1-intro-optics14.ppt" size="41782784" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="single particle lecture 3" date="1417559778" name="Single_Particle_III-20141104_2101-1.arf" path="Single_Particle_III-20141104_2101-1.arf" size="279190625" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="ref bias demo" date="1414696780" name="ref_bias_2014.pdf" path="ref_bias_2014.pdf" size="73733" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Player for arf files" date="1412138278" name="nbr2player.msi" path="nbr2player.msi" size="14838784" user="Main.BillRice" version="1"

Added:

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META FILEATTACHMENT	attr="" autoattached="1" comment="Single Particle Lecture 2" date="1414538098" name="NYSBC_2014-2.pptx" path="NYSBC_2014-2.pptx" size="20402100" user="Main.BillRice" version="1"

META FILEATTACHMENT	attachment="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" attr="" comment="video of Tomography I" date="1413315369" name="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" path="CEM course 2014 lecture 3 Tomography-20141007 2001-1.arf" size="255161917" stream="CEM course 2014 lecture 3 Tomography-20141007 2001-1.arf" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="micrographs.zip" attr="" comment="Micrographs for SP practical 3 (needed by mac people)" date="1415176804" name="micrographs.zip" path="micrographs.zip" size="255492671" stream="micrographs.zip" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="chimera_fitting_data.zip" attr="" comment="Files for Chimera Fitting practical workshop" date="1415293936" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" stream="chimera_fitting_data.zip" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attachment="fitting_S.pptx" attr="" comment="" date="1418149395" name="fitting_S.pptx" path="fitting_S.pptx" size="11077547" stream="fitting_S.pptx" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S3" date="1411301180" name="nprot.2008.156-S3.pdf" path="nprot.2008.156-S3.pdf" size="222608" user="Main.BillRice" version="1"

Revision 807 Oct 2014 - Main.BillRice

META TOPICPARENT	name="CemCourseGroup"

Contents

Player required for arf video files

nbr2player.msi: MS windows player for arf files

Lectures

Deleted:

<
<

Tomography I - Oct 7 - David Stokes (NYU)

Lecture
- NYSBC-EM3-tomography-2014.pptx: Tomography I lecture

d50 12

Fourier Series, Fourier Transform, Correlation, Convolution - Sept 30 - Bill Rice (NYSBC)

Lecture
- fft_lecture-sept30_2014.pptx: powerpoint of fft lecture
- CEM_2014_lecture_2_FFT-20140930_2008-1.arf: video of FFT lecture

Added:

>
>

- fft_lecture.mp3: audio of fft lecture in case audo in above file is poor (fixed week 3)

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt
Readings
- Hoffman(1997)_An_Introduction_to_Fourier_Theory.pdf: Hoffman Introduction to Fourier Theory
- fourier_intro_Shatkay.pdf: Shatkay Fourier Theory Intro
- http://www.med.harvard.edu/JPNM/physics/didactics/improc/intro/fourier1.html
Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

Changed:

<
<

etomo_demo_2014.pdf: Etomo demo
join_demo_2014.pdf: join tomogram demo

>
>

October 9 : etomo_demo_2014.pdf: Etomo demo
October 16: join_demo_2014.pdf: join tomogram demo

Single Particle Demos

Changed:

<
<

nprot.2008.156.pdf: Nature Protocols paper
nprot.2008.156-S1.pdf: Nature Protocols S1
nprot.2008.156-S2.pdf: Nature Protocols S2
nprot.2008.156-S3.pdf: Nature Protocols S3
nprot.2008.156-S4.pdf: Nature Protocols S4

>
>

October 23 - Nov 6
- nprot.2008.156.pdf: Nature Protocols paper
- nprot.2008.156-S1.pdf: Nature Protocols S1
- nprot.2008.156-S2.pdf: Nature Protocols S2
- nprot.2008.156-S3.pdf: Nature Protocols S3

Added:

>
>

- nprot.2008.156-S4.pdf: Nature Protocols S4

d148 1

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-- BillRice - 21 Sep 2014

* NYSBC-EM3-tomography-2014.pptx: Tomography I lecture d70 1

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* fft_lecture.mp3: audio of fft lecture

>
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META FILEATTACHMENT	attr="" autoattached="1" comment="course logistics" date="1411487228" name="CryoEM-Course-logistics.doc" path="CryoEM-Course-logistics.doc" size="36864" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S4" date="1411301202" name="nprot.2008.156-S4.pdf" path="nprot.2008.156-S4.pdf" size="24949" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S1" date="1411301102" name="nprot.2008.156-S1.pdf" path="nprot.2008.156-S1.pdf" size="4990385" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="powerpoint of fft lecture" date="1412132447" name="fft_lecture-sept30_2014.pptx" path="fft_lecture-sept30_2014.pptx" size="16248705" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417726358" name="helical_demo_1.pdf" path="helical_demo_1.pdf" size="2389231" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Helical Reconstruction lecture slides" date="1418172197" name="Helical3d_reconst_v3.pdf" path="Helical3d_reconst_v3.pdf" size="5095698" user="Main.BillRice" version="1"

Changed:

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META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1412719576" name="fft_lecture.mp3" path="fft_lecture.mp3" size="106645264" user="UnknownUser" version=""

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META FILEATTACHMENT	attr="" autoattached="1" comment="notes on ref based alignment" date="1414696759" name="notes-ref_based_2014.pdf" path="notes-ref_based_2014.pdf" size="62496" user="Main.BillRice" version="1"

META FILEATTACHMENT	attr="" autoattached="1" comment="Tomography I lecture" date="1412719549" name="NYSBC-EM3-tomography-2014.pptx" path="NYSBC-EM3-tomography-2014.pptx" size="16899636" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="instructions for EMAN2 demo" date="1415300832" name="eman2_demo.pdf" path="eman2_demo.pdf" size="1785498" user="Main.BillRice" version="2"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1411496912" name="NYSBC-EM1-intro-optics14.ppt" path="NYSBC-EM1-intro-optics14.ppt" size="41782784" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="single particle lecture 3" date="1417559778" name="Single_Particle_III-20141104_2101-1.arf" path="Single_Particle_III-20141104_2101-1.arf" size="279190625" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="ref bias demo" date="1414696780" name="ref_bias_2014.pdf" path="ref_bias_2014.pdf" size="73733" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Player for arf files" date="1412138278" name="nbr2player.msi" path="nbr2player.msi" size="14838784" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" attr="" comment="video of Tomography I" date="1413315369" name="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" path="CEM course 2014 lecture 3 Tomography-20141007 2001-1.arf" size="255161917" stream="CEM course 2014 lecture 3 Tomography-20141007 2001-1.arf" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="micrographs.zip" attr="" comment="Micrographs for SP practical 3 (needed by mac people)" date="1415176804" name="micrographs.zip" path="micrographs.zip" size="255492671" stream="micrographs.zip" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="chimera_fitting_data.zip" attr="" comment="Files for Chimera Fitting practical workshop" date="1415293936" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" stream="chimera_fitting_data.zip" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attachment="fitting_S.pptx" attr="" comment="" date="1418149395" name="fitting_S.pptx" path="fitting_S.pptx" size="11077547" stream="fitting_S.pptx" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S3" date="1411301180" name="nprot.2008.156-S3.pdf" path="nprot.2008.156-S3.pdf" size="222608" user="Main.BillRice" version="1"

Revision 707 Oct 2014 - Main.DavidStokes

META TOPICPARENT	name="CemCourseGroup"

Contents

Player required for arf video files

nbr2player.msi: MS windows player for arf files

Lectures

Added:

>
>

Tomography I - Oct 7 - David Stokes (NYU)

Lecture
- NYSBC-EM3-tomography-2014.pptx: Tomography I lecture

d50 12

Fourier Series, Fourier Transform, Correlation, Convolution - Sept 30 - Bill Rice (NYSBC)

Lecture
- fft_lecture-sept30_2014.pptx: powerpoint of fft lecture
- CEM_2014_lecture_2_FFT-20140930_2008-1.arf: video of FFT lecture

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt
Readings
- Hoffman(1997)_An_Introduction_to_Fourier_Theory.pdf: Hoffman Introduction to Fourier Theory
- fourier_intro_Shatkay.pdf: Shatkay Fourier Theory Intro
- http://www.med.harvard.edu/JPNM/physics/didactics/improc/intro/fourier1.html
Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

etomo_demo_2014.pdf: Etomo demo
join_demo_2014.pdf: join tomogram demo

Single Particle Demos

nprot.2008.156.pdf: Nature Protocols paper
nprot.2008.156-S1.pdf: Nature Protocols S1
nprot.2008.156-S2.pdf: Nature Protocols S2
nprot.2008.156-S3.pdf: Nature Protocols S3
nprot.2008.156-S4.pdf: Nature Protocols S4

d148 1

Set ALLOWTOPICVIEW =

-- BillRice - 21 Sep 2014

Deleted:

<
<

Deleted:

<
<

d61 1

Added:

>
>

* NYSBC-EM3-tomography-2014.pptx: Tomography I lecture

d70 1 * fft_lecture.mp3: audio of fft lecture

META FILEATTACHMENT	attr="" autoattached="1" comment="course logistics" date="1411487228" name="CryoEM-Course-logistics.doc" path="CryoEM-Course-logistics.doc" size="36864" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S4" date="1411301202" name="nprot.2008.156-S4.pdf" path="nprot.2008.156-S4.pdf" size="24949" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S1" date="1411301102" name="nprot.2008.156-S1.pdf" path="nprot.2008.156-S1.pdf" size="4990385" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="powerpoint of fft lecture" date="1412132447" name="fft_lecture-sept30_2014.pptx" path="fft_lecture-sept30_2014.pptx" size="16248705" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417726358" name="helical_demo_1.pdf" path="helical_demo_1.pdf" size="2389231" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Helical Reconstruction lecture slides" date="1418172197" name="Helical3d_reconst_v3.pdf" path="Helical3d_reconst_v3.pdf" size="5095698" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1412719576" name="fft_lecture.mp3" path="fft_lecture.mp3" size="106645264" user="UnknownUser" version=""
META FILEATTACHMENT	attr="" autoattached="1" comment="Tomography I lecture" date="1412719549" name="NYSBC-EM3-tomography-2014.pptx" path="NYSBC-EM3-tomography-2014.pptx" size="16899636" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="instructions for EMAN2 demo" date="1415300832" name="eman2_demo.pdf" path="eman2_demo.pdf" size="1785498" user="Main.BillRice" version="2"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1411496912" name="NYSBC-EM1-intro-optics14.ppt" path="NYSBC-EM1-intro-optics14.ppt" size="41782784" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="single particle lecture 3" date="1417559778" name="Single_Particle_III-20141104_2101-1.arf" path="Single_Particle_III-20141104_2101-1.arf" size="279190625" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="ref bias demo" date="1414696780" name="ref_bias_2014.pdf" path="ref_bias_2014.pdf" size="73733" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Player for arf files" date="1412138278" name="nbr2player.msi" path="nbr2player.msi" size="14838784" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" attr="" comment="video of Tomography I" date="1413315369" name="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" path="CEM course 2014 lecture 3 Tomography-20141007 2001-1.arf" size="255161917" stream="CEM course 2014 lecture 3 Tomography-20141007 2001-1.arf" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="micrographs.zip" attr="" comment="Micrographs for SP practical 3 (needed by mac people)" date="1415176804" name="micrographs.zip" path="micrographs.zip" size="255492671" stream="micrographs.zip" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="chimera_fitting_data.zip" attr="" comment="Files for Chimera Fitting practical workshop" date="1415293936" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" stream="chimera_fitting_data.zip" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attachment="fitting_S.pptx" attr="" comment="" date="1418149395" name="fitting_S.pptx" path="fitting_S.pptx" size="11077547" stream="fitting_S.pptx" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S3" date="1411301180" name="nprot.2008.156-S3.pdf" path="nprot.2008.156-S3.pdf" size="222608" user="Main.BillRice" version="1"

Revision 601 Oct 2014 - Main.BillRice

META TOPICPARENT	name="CemCourseGroup"

Contents

Added:

>
>

Player required for arf video files

nbr2player.msi: MS windows player for arf files

Lectures

Added:

>
>

Fourier Series, Fourier Transform, Correlation, Convolution - Sept 30 - Bill Rice (NYSBC)

Lecture
- fft_lecture-sept30_2014.pptx: powerpoint of fft lecture
- CEM_2014_lecture_2_FFT-20140930_2008-1.arf: video of FFT lecture

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt
Readings
- Hoffman(1997)_An_Introduction_to_Fourier_Theory.pdf: Hoffman Introduction to Fourier Theory
- fourier_intro_Shatkay.pdf: Shatkay Fourier Theory Intro
- http://www.med.harvard.edu/JPNM/physics/didactics/improc/intro/fourier1.html
Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

etomo_demo_2014.pdf: Etomo demo
join_demo_2014.pdf: join tomogram demo

Single Particle Demos

nprot.2008.156.pdf: Nature Protocols paper
nprot.2008.156-S1.pdf: Nature Protocols S1
nprot.2008.156-S2.pdf: Nature Protocols S2
nprot.2008.156-S3.pdf: Nature Protocols S3
nprot.2008.156-S4.pdf: Nature Protocols S4

Added:

>
>

d148 1

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* fft_lecture-sept30_2014.pptx: powerpoint of fft lecture

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META FILEATTACHMENT	attachment="fft_lecture-sept30_2014.pptx" attr="" comment="powerpoint of fft lecture" date="1412132447" name="fft_lecture-sept30_2014.pptx" path="fft_lecture-sept30_2014.pptx" size="16248705" stream="fft_lecture-sept30_2014.pptx" user="Main.BillRice" version="1"

META FILEATTACHMENT	attr="" autoattached="1" comment="course logistics" date="1411487228" name="CryoEM-Course-logistics.doc" path="CryoEM-Course-logistics.doc" size="36864" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S4" date="1411301202" name="nprot.2008.156-S4.pdf" path="nprot.2008.156-S4.pdf" size="24949" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S1" date="1411301102" name="nprot.2008.156-S1.pdf" path="nprot.2008.156-S1.pdf" size="4990385" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="powerpoint of fft lecture" date="1412132447" name="fft_lecture-sept30_2014.pptx" path="fft_lecture-sept30_2014.pptx" size="16248705" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417726358" name="helical_demo_1.pdf" path="helical_demo_1.pdf" size="2389231" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Helical Reconstruction lecture slides" date="1418172197" name="Helical3d_reconst_v3.pdf" path="Helical3d_reconst_v3.pdf" size="5095698" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1412719576" name="fft_lecture.mp3" path="fft_lecture.mp3" size="106645264" user="UnknownUser" version=""
META FILEATTACHMENT	attr="" autoattached="1" comment="Tomography I lecture" date="1412719549" name="NYSBC-EM3-tomography-2014.pptx" path="NYSBC-EM3-tomography-2014.pptx" size="16899636" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="instructions for EMAN2 demo" date="1415300832" name="eman2_demo.pdf" path="eman2_demo.pdf" size="1785498" user="Main.BillRice" version="2"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1411496912" name="NYSBC-EM1-intro-optics14.ppt" path="NYSBC-EM1-intro-optics14.ppt" size="41782784" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="single particle lecture 3" date="1417559778" name="Single_Particle_III-20141104_2101-1.arf" path="Single_Particle_III-20141104_2101-1.arf" size="279190625" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="ref bias demo" date="1414696780" name="ref_bias_2014.pdf" path="ref_bias_2014.pdf" size="73733" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Player for arf files" date="1412138278" name="nbr2player.msi" path="nbr2player.msi" size="14838784" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" attr="" comment="video of Tomography I" date="1413315369" name="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" path="CEM course 2014 lecture 3 Tomography-20141007 2001-1.arf" size="255161917" stream="CEM course 2014 lecture 3 Tomography-20141007 2001-1.arf" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="micrographs.zip" attr="" comment="Micrographs for SP practical 3 (needed by mac people)" date="1415176804" name="micrographs.zip" path="micrographs.zip" size="255492671" stream="micrographs.zip" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="chimera_fitting_data.zip" attr="" comment="Files for Chimera Fitting practical workshop" date="1415293936" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" stream="chimera_fitting_data.zip" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attachment="fitting_S.pptx" attr="" comment="" date="1418149395" name="fitting_S.pptx" path="fitting_S.pptx" size="11077547" stream="fitting_S.pptx" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S3" date="1411301180" name="nprot.2008.156-S3.pdf" path="nprot.2008.156-S3.pdf" size="222608" user="Main.BillRice" version="1"

Revision 530 Sep 2014 - Main.BillRice

META TOPICPARENT	name="CemCourseGroup"

Contents

Lectures

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Lecture
- NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt
Readings
- Hoffman(1997)_An_Introduction_to_Fourier_Theory.pdf: Hoffman Introduction to Fourier Theory
- fourier_intro_Shatkay.pdf: Shatkay Fourier Theory Intro
- http://www.med.harvard.edu/JPNM/physics/didactics/improc/intro/fourier1.html
Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

etomo_demo_2014.pdf: Etomo demo
join_demo_2014.pdf: join tomogram demo

Single Particle Demos

nprot.2008.156.pdf: Nature Protocols paper
nprot.2008.156-S1.pdf: Nature Protocols S1
nprot.2008.156-S2.pdf: Nature Protocols S2
nprot.2008.156-S3.pdf: Nature Protocols S3
nprot.2008.156-S4.pdf: Nature Protocols S4

d148 1

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-- BillRice - 21 Sep 2014

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* fft_lecture-sept30_2014.pptx: powerpoint of fft lecture

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>

Added:

>
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META FILEATTACHMENT	attachment="fft_lecture-sept30_2014.pptx" attr="" comment="powerpoint of fft lecture" date="1412132447" name="fft_lecture-sept30_2014.pptx" path="fft_lecture-sept30_2014.pptx" size="16248705" stream="fft_lecture-sept30_2014.pptx" user="Main.BillRice" version="1"

META FILEATTACHMENT	attr="" autoattached="1" comment="course logistics" date="1411487228" name="CryoEM-Course-logistics.doc" path="CryoEM-Course-logistics.doc" size="36864" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S4" date="1411301202" name="nprot.2008.156-S4.pdf" path="nprot.2008.156-S4.pdf" size="24949" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S1" date="1411301102" name="nprot.2008.156-S1.pdf" path="nprot.2008.156-S1.pdf" size="4990385" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="powerpoint of fft lecture" date="1412132447" name="fft_lecture-sept30_2014.pptx" path="fft_lecture-sept30_2014.pptx" size="16248705" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417726358" name="helical_demo_1.pdf" path="helical_demo_1.pdf" size="2389231" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Helical Reconstruction lecture slides" date="1418172197" name="Helical3d_reconst_v3.pdf" path="Helical3d_reconst_v3.pdf" size="5095698" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1412719576" name="fft_lecture.mp3" path="fft_lecture.mp3" size="106645264" user="UnknownUser" version=""
META FILEATTACHMENT	attr="" autoattached="1" comment="Tomography I lecture" date="1412719549" name="NYSBC-EM3-tomography-2014.pptx" path="NYSBC-EM3-tomography-2014.pptx" size="16899636" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="instructions for EMAN2 demo" date="1415300832" name="eman2_demo.pdf" path="eman2_demo.pdf" size="1785498" user="Main.BillRice" version="2"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1411496912" name="NYSBC-EM1-intro-optics14.ppt" path="NYSBC-EM1-intro-optics14.ppt" size="41782784" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="single particle lecture 3" date="1417559778" name="Single_Particle_III-20141104_2101-1.arf" path="Single_Particle_III-20141104_2101-1.arf" size="279190625" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="ref bias demo" date="1414696780" name="ref_bias_2014.pdf" path="ref_bias_2014.pdf" size="73733" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Player for arf files" date="1412138278" name="nbr2player.msi" path="nbr2player.msi" size="14838784" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" attr="" comment="video of Tomography I" date="1413315369" name="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" path="CEM course 2014 lecture 3 Tomography-20141007 2001-1.arf" size="255161917" stream="CEM course 2014 lecture 3 Tomography-20141007 2001-1.arf" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="micrographs.zip" attr="" comment="Micrographs for SP practical 3 (needed by mac people)" date="1415176804" name="micrographs.zip" path="micrographs.zip" size="255492671" stream="micrographs.zip" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="chimera_fitting_data.zip" attr="" comment="Files for Chimera Fitting practical workshop" date="1415293936" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" stream="chimera_fitting_data.zip" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attachment="fitting_S.pptx" attr="" comment="" date="1418149395" name="fitting_S.pptx" path="fitting_S.pptx" size="11077547" stream="fitting_S.pptx" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S3" date="1411301180" name="nprot.2008.156-S3.pdf" path="nprot.2008.156-S3.pdf" size="222608" user="Main.BillRice" version="1"

Revision 424 Sep 2014 - Main.DavidStokes

META TOPICPARENT	name="CemCourseGroup"

Contents

Lectures
- Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Lectures

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Added:

>
>

Lecture
- NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt
Readings
- Hoffman(1997)_An_Introduction_to_Fourier_Theory.pdf: Hoffman Introduction to Fourier Theory
- fourier_intro_Shatkay.pdf: Shatkay Fourier Theory Intro
- http://www.med.harvard.edu/JPNM/physics/didactics/improc/intro/fourier1.html

Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

etomo_demo_2014.pdf: Etomo demo
join_demo_2014.pdf: join tomogram demo

Single Particle Demos

nprot.2008.156.pdf: Nature Protocols paper
nprot.2008.156-S1.pdf: Nature Protocols S1
nprot.2008.156-S2.pdf: Nature Protocols S2
nprot.2008.156-S3.pdf: Nature Protocols S3
nprot.2008.156-S4.pdf: Nature Protocols S4

d148 1

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-- BillRice - 21 Sep 2014

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* NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt

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Deleted:

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META FILEATTACHMENT	attachment="NYSBC-EM1-intro-optics14.ppt" attr="" comment="" date="1411496911" name="NYSBC-EM1-intro-optics14.ppt" path="NYSBC-EM1-intro-optics14.ppt" size="41782784" stream="NYSBC-EM1-intro-optics14.ppt" user="Main.DavidStokes" version="1"

META FILEATTACHMENT	attr="" autoattached="1" comment="course logistics" date="1411487228" name="CryoEM-Course-logistics.doc" path="CryoEM-Course-logistics.doc" size="36864" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S4" date="1411301202" name="nprot.2008.156-S4.pdf" path="nprot.2008.156-S4.pdf" size="24949" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S1" date="1411301102" name="nprot.2008.156-S1.pdf" path="nprot.2008.156-S1.pdf" size="4990385" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="powerpoint of fft lecture" date="1412132447" name="fft_lecture-sept30_2014.pptx" path="fft_lecture-sept30_2014.pptx" size="16248705" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417726358" name="helical_demo_1.pdf" path="helical_demo_1.pdf" size="2389231" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Helical Reconstruction lecture slides" date="1418172197" name="Helical3d_reconst_v3.pdf" path="Helical3d_reconst_v3.pdf" size="5095698" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1412719576" name="fft_lecture.mp3" path="fft_lecture.mp3" size="106645264" user="UnknownUser" version=""
META FILEATTACHMENT	attr="" autoattached="1" comment="Tomography I lecture" date="1412719549" name="NYSBC-EM3-tomography-2014.pptx" path="NYSBC-EM3-tomography-2014.pptx" size="16899636" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="instructions for EMAN2 demo" date="1415300832" name="eman2_demo.pdf" path="eman2_demo.pdf" size="1785498" user="Main.BillRice" version="2"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1411496912" name="NYSBC-EM1-intro-optics14.ppt" path="NYSBC-EM1-intro-optics14.ppt" size="41782784" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="single particle lecture 3" date="1417559778" name="Single_Particle_III-20141104_2101-1.arf" path="Single_Particle_III-20141104_2101-1.arf" size="279190625" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="ref bias demo" date="1414696780" name="ref_bias_2014.pdf" path="ref_bias_2014.pdf" size="73733" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Player for arf files" date="1412138278" name="nbr2player.msi" path="nbr2player.msi" size="14838784" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" attr="" comment="video of Tomography I" date="1413315369" name="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" path="CEM course 2014 lecture 3 Tomography-20141007 2001-1.arf" size="255161917" stream="CEM course 2014 lecture 3 Tomography-20141007 2001-1.arf" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="micrographs.zip" attr="" comment="Micrographs for SP practical 3 (needed by mac people)" date="1415176804" name="micrographs.zip" path="micrographs.zip" size="255492671" stream="micrographs.zip" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="chimera_fitting_data.zip" attr="" comment="Files for Chimera Fitting practical workshop" date="1415293936" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" stream="chimera_fitting_data.zip" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attachment="fitting_S.pptx" attr="" comment="" date="1418149395" name="fitting_S.pptx" path="fitting_S.pptx" size="11077547" stream="fitting_S.pptx" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S3" date="1411301180" name="nprot.2008.156-S3.pdf" path="nprot.2008.156-S3.pdf" size="222608" user="Main.BillRice" version="1"

Revision 323 Sep 2014 - Main.DavidStokes

META TOPICPARENT	name="CemCourseGroup"

Contents

Lectures

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

etomo_demo_2014.pdf: Etomo demo
join_demo_2014.pdf: join tomogram demo

Single Particle Demos

nprot.2008.156.pdf: Nature Protocols paper
nprot.2008.156-S1.pdf: Nature Protocols S1
nprot.2008.156-S2.pdf: Nature Protocols S2
nprot.2008.156-S3.pdf: Nature Protocols S3
nprot.2008.156-S4.pdf: Nature Protocols S4

d148 1

Set ALLOWTOPICVIEW =

-- BillRice - 21 Sep 2014

Added:

>
>

* NYSBC-EM1-intro-optics14.ppt: NYSBC-EM1-intro-optics14.ppt

Added:

>
>

Added:

>
>

META FILEATTACHMENT	attachment="NYSBC-EM1-intro-optics14.ppt" attr="" comment="" date="1411496911" name="NYSBC-EM1-intro-optics14.ppt" path="NYSBC-EM1-intro-optics14.ppt" size="41782784" stream="NYSBC-EM1-intro-optics14.ppt" user="Main.DavidStokes" version="1"

META FILEATTACHMENT	attr="" autoattached="1" comment="course logistics" date="1411487228" name="CryoEM-Course-logistics.doc" path="CryoEM-Course-logistics.doc" size="36864" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S4" date="1411301202" name="nprot.2008.156-S4.pdf" path="nprot.2008.156-S4.pdf" size="24949" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S1" date="1411301102" name="nprot.2008.156-S1.pdf" path="nprot.2008.156-S1.pdf" size="4990385" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="powerpoint of fft lecture" date="1412132447" name="fft_lecture-sept30_2014.pptx" path="fft_lecture-sept30_2014.pptx" size="16248705" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417726358" name="helical_demo_1.pdf" path="helical_demo_1.pdf" size="2389231" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Helical Reconstruction lecture slides" date="1418172197" name="Helical3d_reconst_v3.pdf" path="Helical3d_reconst_v3.pdf" size="5095698" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1412719576" name="fft_lecture.mp3" path="fft_lecture.mp3" size="106645264" user="UnknownUser" version=""
META FILEATTACHMENT	attr="" autoattached="1" comment="Tomography I lecture" date="1412719549" name="NYSBC-EM3-tomography-2014.pptx" path="NYSBC-EM3-tomography-2014.pptx" size="16899636" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="instructions for EMAN2 demo" date="1415300832" name="eman2_demo.pdf" path="eman2_demo.pdf" size="1785498" user="Main.BillRice" version="2"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1411496912" name="NYSBC-EM1-intro-optics14.ppt" path="NYSBC-EM1-intro-optics14.ppt" size="41782784" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="single particle lecture 3" date="1417559778" name="Single_Particle_III-20141104_2101-1.arf" path="Single_Particle_III-20141104_2101-1.arf" size="279190625" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="ref bias demo" date="1414696780" name="ref_bias_2014.pdf" path="ref_bias_2014.pdf" size="73733" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Player for arf files" date="1412138278" name="nbr2player.msi" path="nbr2player.msi" size="14838784" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" attr="" comment="video of Tomography I" date="1413315369" name="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" path="CEM course 2014 lecture 3 Tomography-20141007 2001-1.arf" size="255161917" stream="CEM course 2014 lecture 3 Tomography-20141007 2001-1.arf" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="micrographs.zip" attr="" comment="Micrographs for SP practical 3 (needed by mac people)" date="1415176804" name="micrographs.zip" path="micrographs.zip" size="255492671" stream="micrographs.zip" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="chimera_fitting_data.zip" attr="" comment="Files for Chimera Fitting practical workshop" date="1415293936" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" stream="chimera_fitting_data.zip" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attachment="fitting_S.pptx" attr="" comment="" date="1418149395" name="fitting_S.pptx" path="fitting_S.pptx" size="11077547" stream="fitting_S.pptx" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S3" date="1411301180" name="nprot.2008.156-S3.pdf" path="nprot.2008.156-S3.pdf" size="222608" user="Main.BillRice" version="1"

Revision 223 Sep 2014 - Main.EdEng

META TOPICPARENT	name="CemCourseGroup"

Contents

Added:

>
>

Lectures

Intro to EM Optics, image formation and Diffraction - Sept 23 - David Stokes (NYU/NYSBC)

Course Logistics
- questionnaire.doc: Course questionnaire
- CryoEM-Course-logistics.doc: course logistics

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

etomo_demo_2014.pdf: Etomo demo
join_demo_2014.pdf: join tomogram demo

Single Particle Demos

nprot.2008.156.pdf: Nature Protocols paper
nprot.2008.156-S1.pdf: Nature Protocols S1
nprot.2008.156-S2.pdf: Nature Protocols S2
nprot.2008.156-S3.pdf: Nature Protocols S3
nprot.2008.156-S4.pdf: Nature Protocols S4

d148 1

Set ALLOWTOPICVIEW =

-- BillRice - 21 Sep 2014

Added:

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Added:

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Added:

>
>

META FILEATTACHMENT	attr="" autoattached="1" comment="course logistics" date="1411487228" name="CryoEM-Course-logistics.doc" path="CryoEM-Course-logistics.doc" size="36864" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S4" date="1411301202" name="nprot.2008.156-S4.pdf" path="nprot.2008.156-S4.pdf" size="24949" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S1" date="1411301102" name="nprot.2008.156-S1.pdf" path="nprot.2008.156-S1.pdf" size="4990385" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="powerpoint of fft lecture" date="1412132447" name="fft_lecture-sept30_2014.pptx" path="fft_lecture-sept30_2014.pptx" size="16248705" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417726358" name="helical_demo_1.pdf" path="helical_demo_1.pdf" size="2389231" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Helical Reconstruction lecture slides" date="1418172197" name="Helical3d_reconst_v3.pdf" path="Helical3d_reconst_v3.pdf" size="5095698" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1412719576" name="fft_lecture.mp3" path="fft_lecture.mp3" size="106645264" user="UnknownUser" version=""
META FILEATTACHMENT	attr="" autoattached="1" comment="Tomography I lecture" date="1412719549" name="NYSBC-EM3-tomography-2014.pptx" path="NYSBC-EM3-tomography-2014.pptx" size="16899636" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="instructions for EMAN2 demo" date="1415300832" name="eman2_demo.pdf" path="eman2_demo.pdf" size="1785498" user="Main.BillRice" version="2"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1411496912" name="NYSBC-EM1-intro-optics14.ppt" path="NYSBC-EM1-intro-optics14.ppt" size="41782784" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="single particle lecture 3" date="1417559778" name="Single_Particle_III-20141104_2101-1.arf" path="Single_Particle_III-20141104_2101-1.arf" size="279190625" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="ref bias demo" date="1414696780" name="ref_bias_2014.pdf" path="ref_bias_2014.pdf" size="73733" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Player for arf files" date="1412138278" name="nbr2player.msi" path="nbr2player.msi" size="14838784" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" attr="" comment="video of Tomography I" date="1413315369" name="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" path="CEM course 2014 lecture 3 Tomography-20141007 2001-1.arf" size="255161917" stream="CEM course 2014 lecture 3 Tomography-20141007 2001-1.arf" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="micrographs.zip" attr="" comment="Micrographs for SP practical 3 (needed by mac people)" date="1415176804" name="micrographs.zip" path="micrographs.zip" size="255492671" stream="micrographs.zip" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="chimera_fitting_data.zip" attr="" comment="Files for Chimera Fitting practical workshop" date="1415293936" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" stream="chimera_fitting_data.zip" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attachment="fitting_S.pptx" attr="" comment="" date="1418149395" name="fitting_S.pptx" path="fitting_S.pptx" size="11077547" stream="fitting_S.pptx" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S3" date="1411301180" name="nprot.2008.156-S3.pdf" path="nprot.2008.156-S3.pdf" size="222608" user="Main.BillRice" version="1"

Revision 121 Sep 2014 - Main.BillRice

META TOPICPARENT	name="CemCourseGroup"

Contents

Practicals
- Tomography Demos
- Single Particle Demos

Practicals

All data and software are on the supplied USB sticks
Instructions are here; please print out and bring to class Thursday

Tomography Demos

etomo_demo_2014.pdf: Etomo demo
join_demo_2014.pdf: join tomogram demo

Single Particle Demos

nprot.2008.156.pdf: Nature Protocols paper
nprot.2008.156-S1.pdf: Nature Protocols S1
nprot.2008.156-S2.pdf: Nature Protocols S2
nprot.2008.156-S3.pdf: Nature Protocols S3
nprot.2008.156-S4.pdf: Nature Protocols S4

d148 1

Set ALLOWTOPICVIEW =

-- BillRice - 21 Sep 2014

META FILEATTACHMENT	attr="" autoattached="1" comment="course logistics" date="1411487228" name="CryoEM-Course-logistics.doc" path="CryoEM-Course-logistics.doc" size="36864" user="Main.EdEng" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S4" date="1411301202" name="nprot.2008.156-S4.pdf" path="nprot.2008.156-S4.pdf" size="24949" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S1" date="1411301102" name="nprot.2008.156-S1.pdf" path="nprot.2008.156-S1.pdf" size="4990385" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="powerpoint of fft lecture" date="1412132447" name="fft_lecture-sept30_2014.pptx" path="fft_lecture-sept30_2014.pptx" size="16248705" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1417726358" name="helical_demo_1.pdf" path="helical_demo_1.pdf" size="2389231" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Helical Reconstruction lecture slides" date="1418172197" name="Helical3d_reconst_v3.pdf" path="Helical3d_reconst_v3.pdf" size="5095698" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1412719576" name="fft_lecture.mp3" path="fft_lecture.mp3" size="106645264" user="UnknownUser" version=""
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META FILEATTACHMENT	attr="" autoattached="1" comment="instructions for EMAN2 demo" date="1415300832" name="eman2_demo.pdf" path="eman2_demo.pdf" size="1785498" user="Main.BillRice" version="2"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1411496912" name="NYSBC-EM1-intro-optics14.ppt" path="NYSBC-EM1-intro-optics14.ppt" size="41782784" user="Main.DavidStokes" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="single particle lecture 3" date="1417559778" name="Single_Particle_III-20141104_2101-1.arf" path="Single_Particle_III-20141104_2101-1.arf" size="279190625" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="ref bias demo" date="1414696780" name="ref_bias_2014.pdf" path="ref_bias_2014.pdf" size="73733" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Player for arf files" date="1412138278" name="nbr2player.msi" path="nbr2player.msi" size="14838784" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" attr="" comment="video of Tomography I" date="1413315369" name="CEM_course_2014_lecture_3_Tomography-20141007_2001-1.arf" path="CEM course 2014 lecture 3 Tomography-20141007 2001-1.arf" size="255161917" stream="CEM course 2014 lecture 3 Tomography-20141007 2001-1.arf" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="micrographs.zip" attr="" comment="Micrographs for SP practical 3 (needed by mac people)" date="1415176804" name="micrographs.zip" path="micrographs.zip" size="255492671" stream="micrographs.zip" user="Main.BillRice" version="1"
META FILEATTACHMENT	attachment="chimera_fitting_data.zip" attr="" comment="Files for Chimera Fitting practical workshop" date="1415293936" name="chimera_fitting_data.zip" path="chimera_fitting_data.zip" size="117140705" stream="chimera_fitting_data.zip" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attachment="fitting_S.pptx" attr="" comment="" date="1418149395" name="fitting_S.pptx" path="fitting_S.pptx" size="11077547" stream="fitting_S.pptx" user="Main.DannyHo" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Nature Protocols S3" date="1411301180" name="nprot.2008.156-S3.pdf" path="nprot.2008.156-S3.pdf" size="222608" user="Main.BillRice" version="1"

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