Difference between revisions of "SCEDS for MR (using keyword input)"
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(Start SCEDS for MR tutorial) |
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− | ===Calmodulin=== | + | ===Calmodulin (Open)=== |
Data for this tutorial are found [http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials here] | Data for this tutorial are found [http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials here] | ||
− | Coordinates: | + | 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 | 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 | # Look at the logfile | ||
Line 12: | Line 35: | ||
#* 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]] |
Latest revision as of 11:35, 29 April 2014
Calmodulin (Open)
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