Difference between revisions of "SCEDS for MR (using keyword input)"
From Phaserwiki
(→Calmodulin) |
(→Calmodulin) |
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Reflections: 1ctr.mtz | Reflections: 1ctr.mtz | ||
Sequence: 1CTR.seq | Sequence: 1CTR.seq | ||
+ | Script: sceds_tutorial.csh | ||
This tutorial demonstrates SCEDS domain division followed by MR using the domains generated | This tutorial demonstrates SCEDS domain division followed by MR using the domains generated | ||
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eof | eof | ||
+ | #! /bin/csh | ||
phaser << eof >> sceds_tutorial.log | phaser << eof >> sceds_tutorial.log | ||
MODE MR_AUTO | MODE MR_AUTO | ||
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#* Find the number of residues not included in any of the top domains. | #* Find the number of residues not included in any of the top domains. | ||
# Look at the pdb files containing the domains with Coot | # Look at the pdb files containing the domains with Coot | ||
+ | # Overlay the coordinates output from the MR solution (sceds_tutorial.1.pdb) with the pdb file 1CTR.pdb | ||
[[Category:Tutorial]] | [[Category:Tutorial]] |
Revision as of 11:35, 29 April 2014
Calmodulin
Data for this tutorial are found here
Coordinates: 1CLL.pdb Reflections: 1ctr.mtz Sequence: 1CTR.seq Script: sceds_tutorial.csh
This tutorial demonstrates SCEDS domain division followed by MR using the domains generated
#! /bin/csh phaser << eof >> sceds_tutorial.log MODE SCEDS ENSEmble test PDBFile 1CLL.pdb RMS 2.0 ROOT sceds_tutorial eof
#! /bin/csh phaser << eof >> sceds_tutorial.log MODE MR_AUTO HKLIn 1ctr.mtz LABIn F = F SIGF = SIGF ENSEmble dom1 PDBFile sceds_tutorial.domain.1.pdb ID 1 ENSEmble dom2 PDBFile sceds_tutorial.domain.2.pdb ID 1 COMPOSITION PROTEIN SEQ 1CTR.seq NUM 1 SEAR ENSEMBLE dom1 NUM 1 SEAR ENSEMBLE dom2 NUM 1 ROOT sceds_tutorial eof
- Look at the logfile
- What are the residues included in each of the SCEDS domains produced?
- Find the normal modes used for the perturbation that generated the SCEDS domains.
- Find the number of residues not included in any of the top domains.
- Look at the pdb files containing the domains with Coot
- Overlay the coordinates output from the MR solution (sceds_tutorial.1.pdb) with the pdb file 1CTR.pdb