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(Created page with "This is a script to visualize VDW clashes, just like the mutagenesis wizard does. Posted on [http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg09190.html pymo...")
 
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This is a script to visualize VDW clashes, just like the [[mutagenesis]] wizard does.
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{{Infobox script-repo
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|type      = module
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|filename  = show_bumps.py
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|author    = [[User:Speleo3|Thomas Holder]]
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|license  = BSD-2-Clause
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}}
  
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Posted on [http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg09190.html pymol-users mailing list].
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The red discs in the image below show vdW overlaps or steric clashing. This script will create those bumps for your chosen molecule.
  
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= The Script =
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[[Image:sb.png|300px]]
  
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<source lang="python">
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This is a script to visualize VDW clashes, just like the [[mutagenesis]] wizard does.
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from pymol import cmd
 
  
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def show_bumps(selection='(all)', name='bump_check', quiet=1):
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Posted on [http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg09190.html pymol-users mailing list].
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    '''
 
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DESCRIPTION
 
  
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    Visualize VDW clashes
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== Usage ==
  
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ARGUMENTS
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show_bumps [ selection [, name ]]
  
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    selection = string: atom selection {default: all}
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== Related Settings ==
  
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    name = string: name of CGO object to create {default: bump_check}
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* sculpt_vdw_vis_max (default: 0.3)
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    '''
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* sculpt_vdw_vis_mid (default: 0.1)
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    cmd.delete(name)
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* sculpt_vdw_vis_min (default: -0.1)
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    cmd.create(name, selection, zoom=0)
 
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    cmd.sculpt_activate(name)
 
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    cmd.show_as('cgo', name)
 
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    cmd.set('sculpt_vdw_vis_mode', 1, name)
 
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    cmd.set('sculpt_field_mask', 0x020) # cSculptVDW
 
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    strain = cmd.sculpt_iterate(name, cycles=1)
 
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    if not int(quiet):
 
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        print 'VDW Strain:', strain
 
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    return strain
 
  
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cmd.extend('show_bumps', show_bumps)
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[[Category:Script_Library]]
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</source>
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[[Category:Pymol-script-repo]]

Latest revision as of 03:36, 28 March 2014

Type Python Module
Download show_bumps.py
Author(s) Thomas Holder
License BSD-2-Clause
This code has been put under version control in the project Pymol-script-repo

The red discs in the image below show vdW overlaps or steric clashing. This script will create those bumps for your chosen molecule.

Sb.png

This is a script to visualize VDW clashes, just like the mutagenesis wizard does.

Posted on pymol-users mailing list.

Usage

show_bumps [ selection [, name ]]

Related Settings

  • sculpt_vdw_vis_max (default: 0.3)
  • sculpt_vdw_vis_mid (default: 0.1)
  • sculpt_vdw_vis_min (default: -0.1)
Retrieved from "http://wiki.pymol.org/index.php?title=Show_bumps&oldid=8861"