Difference between revisions of "SCEDS for MR (using keyword input)"
From Phaserwiki
(Start SCEDS for MR tutorial) |
(→Calmodulin) |
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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 | ||
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 | ||
| + | |||
| + | 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 | ||
Revision as of 11:33, 29 April 2014
Calmodulin
Data for this tutorial are found here
Coordinates: 1CLL.pdb Reflections: 1ctr.mtz Sequence: 1CTR.seq
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
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
