Difference between revisions of "Task9 Hemochromatosis Protocol"

From Bioinformatikpedia
(ElNemo)
(Structure preparation)
 
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== Structure preparation ==
 
== Structure preparation ==
   
  +
Make both structures equal (especially for WEBnm@):
 
 
'perl repairPDB.pl 1a6z.ent C: -jprot -offset 22 > 1a6zC.pdb'
 
'perl repairPDB.pl 1a6z.ent C: -jprot -offset 22 > 1a6zC.pdb'
 
'perl repairPDB.pl 1de4.ent A: -jprot -offset 22 > 1de4A.pdb'
 
'perl repairPDB.pl 1de4.ent A: -jprot -offset 22 > 1de4A.pdb'

Latest revision as of 16:41, 25 July 2012

Structure preparation

Make both structures equal (especially for WEBnm@):

'perl repairPDB.pl 1a6z.ent C: -jprot -offset 22 > 1a6zC.pdb'
'perl repairPDB.pl 1de4.ent A: -jprot -offset 22 > 1de4A.pdb'


WEBnm@

Sample PyMol script for movie generation: <source lang="python">

  1. start

reinitialize load ../1a6zC.pdb, 1a6zC load ../webnma/modes_visualization/1a6zC.mode7.xyz, Mode load_traj ../webnma/modes_visualization/1a6zC.mode7.dcd, Mode

hide everything, all show cartoon, 1a6zC show spheres, Mode show mesh, Mode

color green, 1a6zC color red, Mode

mset 2 -10 -2 set ray_trace_frames, 1 set sphere_transparency, 0.7 </source>


ElNemo

Sample PyMol script for movie generation: <source lang="python">

  1. start

reinitialize load ../1a6zC.pdb, 1a6zC load ../elnemo/1a6zC/7.pdb, Mode

dss

hide everything, all show cartoon, all

color green, 1a6zC color red, Mode

mset 1 -11 -2 set ray_trace_frames, 1 </source>