SCEDS for MR (using keyword input)

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

1. 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.
2. Look at the pdb files containing the domains with Coot
3. Overlay the coordinates output from the MR solution (sceds_tutorial.1.pdb) with the pdb file 1CTR.pdb