Difference: CemHomework14 (1 vs. 2)

Revision 203 Nov 2014 - Main.BillRice

META TOPICPARENT	name="CemCourseGroup"

Contents

Homework Uploads
- Instructions for Practicals

Homework Uploads

To get the most out of this course, it is required to do all of the practical sessions
Students taking the course for credit are required to upload results of practicals
Please upload to your home page
You should be able to connect to a wireless network from your live boot course USB stick
If not, copy the required files to another USB stick then use this on another PC to upload

Instructions for Practicals

General

Browse to your home twiki page (link should be in sidebar)
Choose Attach
Browse to file
Give a meaningful comment
Choose to make a link to the file
Choose to show file in list (this is default behavior)

Tomography I: Tomograms

Archive the directory as follows:
- Boot to USB disk as usual, change dir to /media/nysbc/course, and source course1.bashrc

      cd /media/nysbc/course
      source course1.bashrc
      cd tutorialdata
      etomo

Choose File--> Open, and open the etomo datafile.
Go to Cleanup Window
Select all files and delete them
- This deletes unnecessary files and is ESSENTIAL for data management. All intermediate files deleted can be regenerated if necessary.
etomo before cleanup:
etomo after cleanup:
Quit etomo
Delete original .st files:

   rm BBa.st BBb.st

go up one directory and archive the results

   cd ..
   zip -r imod1.zip tutorialdata

upload imod1.zip to your home twiki page
My file: imod1.zip: tomography tutorial I results

Tomography II: joining serial tomograms

Archive the directory as follows:
- Boot to USB disk as usual, change dir to /media/nysbc/course, and source course1.bashrc
- Delete unnecessary files and archive directory as follows:

      cd /media/nysbc/course
      source course1.bashrc
      cd joinTutorialData
      mkdir ../junk
      mv *~ ../junk/.
      mv *trial.join ../junk/.
      mv *_modeled.join ../junk/.
      mv *.rec ../junk
      cd ..
      zip -r joinTutorialData.zip joinTutorialData

upload joinTutorialData.zip (about 33 MB in size) to your twiki home page
remove junk folder:

      rm -rf junk

My file: joinTutorialData.zip

Random Conical Tilt

      cd /media/nysbc/course
      source course1.bashrc
      cd Randomconical
      zip -r rct-r3d.zip r3d

upload rct-r3d.zip
My file: rct-r3d.zip: randomconical 3d recon

Changed:

<
<

Reference based Refinement

>
>

Reference based Reconstruction

Archive the reconstructed volumes and resolution:

      cd /media/nysbc/course
      source course1.bashrc
      cd Reference_based
      zip -r ref_recon.zip Reconstruction/volfq001.dat Reconstruction/vol001.dat Reconstruction/resolution.dat

Upload ref_recon.zip
My file: ref_recon.zip: reference_based reconstruction

Added:

>
>

Refinement

This is optional, no need to upload
to get it to work, you will probably need to make space on your disk:
- After running the first step (import data), do the following:
- Delete the original windowed files (
```
 rm  Reference_based/Particles/win/*.dat 
```
  )
- Delete the aligned particles (
```
 rm -r Reference_based/Alignment/ali/* 
```
  )
You will also need an updated plotref.spi script (goes in Reference_based/Refinement)
plotref_fixed.zip: fixed version of plotref.spi

Amplitude Correction

This is optional
To run it, you need to have done the refinement
Alternatively, down the following which contains the final aligned file and a fixed script:

If you did the Refinement,

Set ALLOWTOPICVIEW =

-- BillRice - 31 Oct 2014

Added:

>
>

META FILEATTACHMENT	attr="" autoattached="1" comment="tomography tutorial I results" date="1414728693" name="imod1.zip" path="imod1.zip" size="12458000" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="randomconical 3d recon" date="1414733173" name="rct-r3d.zip" path="rct-r3d.zip" size="6959781" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="etomo before cleanup" date="1414733495" name="before.png" path="before.png" size="87427" user="Main.BillRice" version="2"
META FILEATTACHMENT	attr="" autoattached="1" comment="etomo after cleanup" date="1414733529" name="after.png" path="after.png" size="63704" user="Main.BillRice" version="2"
META FILEATTACHMENT	attr="" autoattached="1" comment="reference_based reconstruction" date="1414734256" name="ref_recon.zip" path="ref_recon.zip" size="16382470" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="tomography tuitorial 2: join results" date="1414730729" name="joinTutorialData.zip" path="joinTutorialData.zip" size="34248249" user="Main.BillRice" version="1"

Added:

>
>

META FILEATTACHMENT	attr="" autoattached="1" comment="fixed version of plotref.zip" date="1415044670" name="plotref_fixed.zip" path="plotref_fixed.zip" size="1261" user="Main.BillRice" version="1"

Revision 131 Oct 2014 - Main.BillRice

META TOPICPARENT	name="CemCourseGroup"

Contents

Homework Uploads
- Instructions for Practicals

Homework Uploads

To get the most out of this course, it is required to do all of the practical sessions
Students taking the course for credit are required to upload results of practicals
Please upload to your home page
You should be able to connect to a wireless network from your live boot course USB stick
If not, copy the required files to another USB stick then use this on another PC to upload

Instructions for Practicals

General

Browse to your home twiki page (link should be in sidebar)
Choose Attach
Browse to file
Give a meaningful comment
Choose to make a link to the file
Choose to show file in list (this is default behavior)

Tomography I: Tomograms

Archive the directory as follows:
- Boot to USB disk as usual, change dir to /media/nysbc/course, and source course1.bashrc

      cd /media/nysbc/course
      source course1.bashrc
      cd tutorialdata
      etomo

Choose File--> Open, and open the etomo datafile.
Go to Cleanup Window
Select all files and delete them
- This deletes unnecessary files and is ESSENTIAL for data management. All intermediate files deleted can be regenerated if necessary.
etomo before cleanup:
etomo after cleanup:
Quit etomo
Delete original .st files:

   rm BBa.st BBb.st

go up one directory and archive the results

   cd ..
   zip -r imod1.zip tutorialdata

upload imod1.zip to your home twiki page
My file: imod1.zip: tomography tutorial I results

Tomography II: joining serial tomograms

Archive the directory as follows:
- Boot to USB disk as usual, change dir to /media/nysbc/course, and source course1.bashrc
- Delete unnecessary files and archive directory as follows:

      cd /media/nysbc/course
      source course1.bashrc
      cd joinTutorialData
      mkdir ../junk
      mv *~ ../junk/.
      mv *trial.join ../junk/.
      mv *_modeled.join ../junk/.
      mv *.rec ../junk
      cd ..
      zip -r joinTutorialData.zip joinTutorialData

upload joinTutorialData.zip (about 33 MB in size) to your twiki home page
remove junk folder:

      rm -rf junk

My file: joinTutorialData.zip

Random Conical Tilt

      cd /media/nysbc/course
      source course1.bashrc
      cd Randomconical
      zip -r rct-r3d.zip r3d

upload rct-r3d.zip
My file: rct-r3d.zip: randomconical 3d recon

Reference based Refinement

Archive the reconstructed volumes and resolution:

      cd /media/nysbc/course
      source course1.bashrc
      cd Reference_based
      zip -r ref_recon.zip Reconstruction/volfq001.dat Reconstruction/vol001.dat Reconstruction/resolution.dat

Upload ref_recon.zip
My file: ref_recon.zip: reference_based reconstruction

Set ALLOWTOPICVIEW =

-- BillRice - 31 Oct 2014

META FILEATTACHMENT	attr="" autoattached="1" comment="tomography tutorial I results" date="1414728693" name="imod1.zip" path="imod1.zip" size="12458000" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="randomconical 3d recon" date="1414733173" name="rct-r3d.zip" path="rct-r3d.zip" size="6959781" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="etomo before cleanup" date="1414733495" name="before.png" path="before.png" size="87427" user="Main.BillRice" version="2"
META FILEATTACHMENT	attr="" autoattached="1" comment="etomo after cleanup" date="1414733529" name="after.png" path="after.png" size="63704" user="Main.BillRice" version="2"
META FILEATTACHMENT	attr="" autoattached="1" comment="reference_based reconstruction" date="1414734256" name="ref_recon.zip" path="ref_recon.zip" size="16382470" user="Main.BillRice" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="tomography tuitorial 2: join results" date="1414730729" name="joinTutorialData.zip" path="joinTutorialData.zip" size="34248249" user="Main.BillRice" version="1"

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