Difference: SpiderRefinement (1 vs. 2)

Revision 213 Jun 2008 - Main.BillRice

 
META TOPICPARENT name="CemIT"
Contents

Spider Refinement on the cluster

  • These scripts, modified slightly from the scripts provided with spider v. 15, are for use on the NYSBC cluster
  • Apart from filenames and paths, should not need much adjustment
  • To follow these directiosn, you should also follow the spider instructions on reconstruction and refinement

Reconstruction

  • Should work in your directory in /usr/data rather than /usr/home, as the re is much more space in /usr/data
  • All scripts in Reconstruction have extension spi
  • first, make 2 new directories a follows: 
mkdir Reconstruction
mkdir Reconstruction-batch
Changed:
<
<
>
>
  • unzip the file reconstruction_scripts.zip in the folder Reconstruction-batch
Added:
>
>
  • Put the reference 3d volume in the Reconstruction folder
  • Need to have set up params.ext, using the spider script ...
  • Need to have divided particles into defocus groups, and have a docfile for each df group
  • run the file win2stck to combine all particles in each defocus group into a stack
  • Edit and run 02_proj, to makew
 

subsub level topic

  • Set ALLOWTOPICVIEW =

-- BillRice - 13 Jun 2008

Revision 113 Jun 2008 - Main.BillRice

 
META TOPICPARENT name="CemIT"
Contents

Spider Refinement on the cluster

  • These scripts, modified slightly from the scripts provided with spider v. 15, are for use on the NYSBC cluster
  • Apart from filenames and paths, should not need much adjustment
  • To follow these directiosn, you should also follow the spider instructions on reconstruction and refinement

Reconstruction

  • Should work in your directory in /usr/data rather than /usr/home, as the re is much more space in /usr/data
  • All scripts in Reconstruction have extension spi
  • first, make 2 new directories a follows: 
mkdir Reconstruction
mkdir Reconstruction-batch

subsub level topic

  • Set ALLOWTOPICVIEW =

-- BillRice - 13 Jun 2008

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