Difference: CemCourseSyllabus11 (1 vs. 2)

Revision 211 Nov 2011 - Main.BillRice

 
META TOPICPARENT name="CemCourseGroup"
Contents

Practical Sessions

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Practical Exercises in Tomography and Single Particle Analysis - Nov 1-5

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Homework : preparation for practical session II

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  • Download and install IMOD on your mac/pc/linux system
  • Get the latest stable release
  • http://bio3d.colorado.edu/imod/download.html
  • Mac users -- install the version for your OS
  • Windows users:
    1. download the clickable installer for your particular version of windows
    2. download the Cygwin installer provided on the IMOD site (Do not use a Cygwin from another site)
    3. Install cygwin, following the instructions on the imod site
    4. Install imod using the clickable installer
    5. If you have trouble, you can bring your notebook to me (Bill) before the practical, but please try it for yourself first

  • EMIP and 2dx run on mac systems. I will provide USB disks with mac install versions
  • Windows users will be using a USB boot disk to run Emip and 2dx, as was done with spider. I will provide a new disk.

Practical Exercises in Tomography and Crystallography - Nov 28- Dec 2

  • Day 1: Tomography 1
    • Generation of tomograms with eTomo
  • Day 2: Tomography 2
    • Joining of serial sections with eTomo
  • Day 3 - Processing individual images of 2D crystals
    • 2dx software package
  • Day 4 - Processing individual images of Helical Crystals
    • EMIP software package
  • Day 5 - Merging of data from Helical Crystals and 3D reconstruction * EMIP software package

Practical Exercises in Single Particle Analysis - Nov 1-5

 
  • Day 1 (Nov. 1): single particle analysis 1
    • Generation of initial model by Random Conical Tilt * use SPIDER

  • Day 2 (Nov. 2): single particle analysis 2
    • Generation of initial model by Common Lines
    • use both SPIDER and EMAN

  • Day 3 (Nov. 3): single particle analysis 3
    • Model generation and refinement using Projection Matching
    • SPIDER
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  • Day 4 (Nov. 4): Tomography 1
    • Generation of tomograms with eTomo
    • Joining of serial sections with eTomo
 

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-- BillRice - 13 Oct 2011

Revision 113 Oct 2011 - Main.BillRice

 
META TOPICPARENT name="CemCourseGroup"
Contents

Practical Sessions

Practical Exercises in Tomography and Single Particle Analysis - Nov 1-5

  • Day 1 (Nov. 1): single particle analysis 1
    • Generation of initial model by Random Conical Tilt * use SPIDER

  • Day 2 (Nov. 2): single particle analysis 2
    • Generation of initial model by Common Lines
    • use both SPIDER and EMAN

  • Day 3 (Nov. 3): single particle analysis 3
    • Model generation and refinement using Projection Matching
    • SPIDER

  • Day 4 (Nov. 4): Tomography 1
    • Generation of tomograms with eTomo
    • Joining of serial sections with eTomo

Sublevel topic

subsub level topic

  • Set ALLOWTOPICVIEW =

-- BillRice - 13 Oct 2011

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