SCEDS for MR (using keyword input)

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

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