Difference: CemSingleParticleHelical (1 vs. 5)

Revision 525 Mar 2010 - Main.BillRice

 
META TOPICPARENT name="CemITApplications"
Contents

Notes on using the ingle particle helical suite of software

Source

Notes on running (using the supplied TMV particle images)

CTF

  • initial CTF determination: run ctffind3.perl
    • outputs ctffind_results.txt, which gives the CTF params for each micrograph
  • run readmrc.pl
    • creates a spider docfile with initial CTF params for each micrograph
    • output file is defocus.spd
  • ctftilt -- CTF determination with tilt axis
    • convert mrc images to spider, and shrink 2-fold: proc2d A00.mrc A00.spd spider-single
    • run ctftilt_wjr.spi -- window the files, convert back to mrc, create ctftilt.com scripts (one per micrograph)
      • spider spi/spd @ctftilt_wjr
    • run each of the ctftiltNN.com scripts -- this way, run all at same time to parallelize
    • run ctftilt_wjr2.spi -- convert the output from above files into a single spider docfile
      • spider spi/spd @ctftilt_wjr2 (needs to run readtilt.py, in current directory)
      • output file is defocus-tilt-pixs163.spd

Boxing

  • Open each micrograph in boxer
  • Box size 666
  • Put a box at the start and end of each filament
  • Save as ANN.box, where NN is file number
  • run script split_box_files.pl, which will make a new file for each pair of boxes (each filament)
  • for each micrograph:
    • temporarily move the micrograph and all associated .box files into a tmp subdirectory
    • in that directory, open the micrograph in boxer
    • Open the first box file, for the first filament
    • Set Box overlap to 606
    • Find the marked filament, and delete the pair of boxes
    • Click the "helix" button, and add a new pair of boxes which cover the filament
    • Should now get a set of overlapping boxes covering the entire filament
    • Save the box database by overwriting the .box file which you had opened
    • Clear the boxes
    • go on to next filament

Combine CTF and box information

  • With box files and ctf files in same directory, run doc-angle-ctftilt.amy
Added:
>
>
    • script is calc-ctftilt_0.amy, since the original assumes a file listing the out-of-plane tilt of each segment, and this file does not yet exist
    • this script requires spider version 13 or earlier.
 
    • outputs 051215_tmv-flood1x-cut-angle-ctftilt-doc20.spd

Overview of procedure

* overview:
spider_proc.png

  • Set ALLOWTOPICVIEW =

-- BillRice - 25 Mar 2010

META FILEATTACHMENT attachment="spider_proc.png" attr="" comment="overview" date="1269541988" name="spider_proc.png" path="spider_proc.png" size="222292" stream="spider_proc.png" user="Main.BillRice" version="0"

Revision 425 Mar 2010 - Main.BillRice

 
META TOPICPARENT name="CemITApplications"
Contents

Notes on using the ingle particle helical suite of software

Source

Notes on running (using the supplied TMV particle images)

CTF

  • initial CTF determination: run ctffind3.perl
    • outputs ctffind_results.txt, which gives the CTF params for each micrograph
  • run readmrc.pl
    • creates a spider docfile with initial CTF params for each micrograph
    • output file is defocus.spd
  • ctftilt -- CTF determination with tilt axis
    • convert mrc images to spider, and shrink 2-fold: proc2d A00.mrc A00.spd spider-single
    • run ctftilt_wjr.spi -- window the files, convert back to mrc, create ctftilt.com scripts (one per micrograph)
      • spider spi/spd @ctftilt_wjr
    • run each of the ctftiltNN.com scripts -- this way, run all at same time to parallelize
    • run ctftilt_wjr2.spi -- convert the output from above files into a single spider docfile
      • spider spi/spd @ctftilt_wjr2 (needs to run readtilt.py, in current directory)
      • output file is defocus-tilt-pixs163.spd

Boxing

  • Open each micrograph in boxer
  • Box size 666
  • Put a box at the start and end of each filament
  • Save as ANN.box, where NN is file number
  • run script split_box_files.pl, which will make a new file for each pair of boxes (each filament)
  • for each micrograph:
    • temporarily move the micrograph and all associated .box files into a tmp subdirectory
    • in that directory, open the micrograph in boxer
    • Open the first box file, for the first filament
    • Set Box overlap to 606
    • Find the marked filament, and delete the pair of boxes
    • Click the "helix" button, and add a new pair of boxes which cover the filament
    • Should now get a set of overlapping boxes covering the entire filament
    • Save the box database by overwriting the .box file which you had opened
    • Clear the boxes
    • go on to next filament

Combine CTF and box information

  • With box files and ctf files in same directory, run doc-angle-ctftilt.amy
    • outputs 051215_tmv-flood1x-cut-angle-ctftilt-doc20.spd
Deleted:
<
<
  • Set ALLOWTOPICVIEW =
 
Changed:
<
<		-- BillRice - 25 Mar 2010
>
>

Overview of procedure

  * overview:
spider_proc.png
Added:
>
>
  • Set ALLOWTOPICVIEW =

-- BillRice - 25 Mar 2010

 
META FILEATTACHMENT attachment="spider_proc.png" attr="" comment="overview" date="1269541988" name="spider_proc.png" path="spider_proc.png" size="222292" stream="spider_proc.png" user="Main.BillRice" version="0"

Revision 325 Mar 2010 - Main.BillRice

 
META TOPICPARENT name="CemITApplications"
Contents

Notes on using the ingle particle helical suite of software

Source

Notes on running (using the supplied TMV particle images)

CTF

  • initial CTF determination: run ctffind3.perl
    • outputs ctffind_results.txt, which gives the CTF params for each micrograph
  • run readmrc.pl
    • creates a spider docfile with initial CTF params for each micrograph
    • output file is defocus.spd
  • ctftilt -- CTF determination with tilt axis
    • convert mrc images to spider, and shrink 2-fold: proc2d A00.mrc A00.spd spider-single
    • run ctftilt_wjr.spi -- window the files, convert back to mrc, create ctftilt.com scripts (one per micrograph)
      • spider spi/spd @ctftilt_wjr
    • run each of the ctftiltNN.com scripts -- this way, run all at same time to parallelize
    • run ctftilt_wjr2.spi -- convert the output from above files into a single spider docfile
      • spider spi/spd @ctftilt_wjr2 (needs to run readtilt.py, in current directory)
      • output file is defocus-tilt-pixs163.spd

Boxing

  • Open each micrograph in boxer
  • Box size 666
  • Put a box at the start and end of each filament
  • Save as ANN.box, where NN is file number
  • run script split_box_files.pl, which will make a new file for each pair of boxes (each filament)
  • for each micrograph:
    • temporarily move the micrograph and all associated .box files into a tmp subdirectory
    • in that directory, open the micrograph in boxer
    • Open the first box file, for the first filament
    • Set Box overlap to 606
    • Find the marked filament, and delete the pair of boxes
    • Click the "helix" button, and add a new pair of boxes which cover the filament
    • Should now get a set of overlapping boxes covering the entire filament
    • Save the box database by overwriting the .box file which you had opened
    • Clear the boxes
    • go on to next filament

Combine CTF and box information

  • With box files and ctf files in same directory, run doc-angle-ctftilt.amy
    • outputs 051215_tmv-flood1x-cut-angle-ctftilt-doc20.spd

  • Set ALLOWTOPICVIEW =

-- BillRice - 25 Mar 2010

Added:
>
>		 * overview:
spider_proc.png

META FILEATTACHMENT attachment="spider_proc.png" attr="" comment="overview" date="1269541988" name="spider_proc.png" path="spider_proc.png" size="222292" stream="spider_proc.png" user="Main.BillRice" version="0"
 

Revision 225 Mar 2010 - Main.BillRice

 
META TOPICPARENT name="CemITApplications"
Contents

Notes on using the ingle particle helical suite of software

Source

Notes on running (using the supplied TMV particle images)

CTF

  • initial CTF determination: run ctffind3.perl
    • outputs ctffind_results.txt, which gives the CTF params for each micrograph
  • run readmrc.pl
    • creates a spider docfile with initial CTF params for each micrograph
    • output file is defocus.spd
  • ctftilt -- CTF determination with tilt axis
    • convert mrc images to spider, and shrink 2-fold: proc2d A00.mrc A00.spd spider-single
    • run ctftilt_wjr.spi -- window the files, convert back to mrc, create ctftilt.com scripts (one per micrograph)
      • spider spi/spd @ctftilt_wjr
    • run each of the ctftiltNN.com scripts -- this way, run all at same time to parallelize
    • run ctftilt_wjr2.spi -- convert the output from above files into a single spider docfile
      • spider spi/spd @ctftilt_wjr2 (needs to run readtilt.py, in current directory)
      • output file is defocus-tilt-pixs163.spd

Boxing

  • Open each micrograph in boxer
  • Box size 666
  • Put a box at the start and end of each filament
  • Save as ANN.box, where NN is file number
  • run script split_box_files.pl, which will make a new file for each pair of boxes (each filament)
  • for each micrograph:
    • temporarily move the micrograph and all associated .box files into a tmp subdirectory
    • in that directory, open the micrograph in boxer
    • Open the first box file, for the first filament
    • Set Box overlap to 606
    • Find the marked filament, and delete the pair of boxes
    • Click the "helix" button, and add a new pair of boxes which cover the filament
    • Should now get a set of overlapping boxes covering the entire filament
    • Save the box database by overwriting the .box file which you had opened
    • Clear the boxes
    • go on to next filament
Added:
>
>

Combine CTF and box information

  • With box files and ctf files in same directory, run doc-angle-ctftilt.amy
    • outputs 051215_tmv-flood1x-cut-angle-ctftilt-doc20.spd
 
  • Set ALLOWTOPICVIEW =

-- BillRice - 25 Mar 2010

Revision 125 Mar 2010 - Main.BillRice

 
META TOPICPARENT name="CemITApplications"
Contents

Notes on using the ingle particle helical suite of software

Source

Notes on running (using the supplied TMV particle images)

CTF

  • initial CTF determination: run ctffind3.perl
    • outputs ctffind_results.txt, which gives the CTF params for each micrograph
  • run readmrc.pl
    • creates a spider docfile with initial CTF params for each micrograph
    • output file is defocus.spd
  • ctftilt -- CTF determination with tilt axis
    • convert mrc images to spider, and shrink 2-fold: proc2d A00.mrc A00.spd spider-single
    • run ctftilt_wjr.spi -- window the files, convert back to mrc, create ctftilt.com scripts (one per micrograph)
      • spider spi/spd @ctftilt_wjr
    • run each of the ctftiltNN.com scripts -- this way, run all at same time to parallelize
    • run ctftilt_wjr2.spi -- convert the output from above files into a single spider docfile
      • spider spi/spd @ctftilt_wjr2 (needs to run readtilt.py, in current directory)
      • output file is defocus-tilt-pixs163.spd

Boxing

  • Open each micrograph in boxer
  • Box size 666
  • Put a box at the start and end of each filament
  • Save as ANN.box, where NN is file number
  • run script split_box_files.pl, which will make a new file for each pair of boxes (each filament)
  • for each micrograph:
    • temporarily move the micrograph and all associated .box files into a tmp subdirectory
    • in that directory, open the micrograph in boxer
    • Open the first box file, for the first filament
    • Set Box overlap to 606
    • Find the marked filament, and delete the pair of boxes
    • Click the "helix" button, and add a new pair of boxes which cover the filament
    • Should now get a set of overlapping boxes covering the entire filament
    • Save the box database by overwriting the .box file which you had opened
    • Clear the boxes
    • go on to next filament

  • Set ALLOWTOPICVIEW =

-- BillRice - 25 Mar 2010

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