Show bumps: Difference between revisions

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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.
{{Infobox script-repo
|type      = module
|filename  = show_bumps.py
|author    = [[User:Speleo3|Thomas Holder]]
|license  = BSD-2-Clause
}}


Posted on [http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg09190.html pymol-users mailing list].
The red discs in the image below show vdW overlaps or steric clashing. This script will create those bumps for your chosen molecule.


= The Script =
[[Image:sb.png|300px]]


<source lang="python">
This is a script to visualize VDW clashes, just like the [[mutagenesis]] wizard does.
from pymol import cmd


def show_bumps(selection='(all)', name='bump_check', quiet=1):
Posted on [http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg09190.html pymol-users mailing list].
    '''
DESCRIPTION


    Visualize VDW clashes
== Usage ==


ARGUMENTS
show_bumps [ selection [, name ]]


    selection = string: atom selection {default: all}
== Related Settings ==


    name = string: name of CGO object to create {default: bump_check}
* sculpt_vdw_vis_max (default: 0.3)
    '''
* sculpt_vdw_vis_mid (default: 0.1)
    cmd.delete(name)
* sculpt_vdw_vis_min (default: -0.1)
    cmd.create(name, selection, zoom=0)
    cmd.sculpt_activate(name)
    cmd.show_as('cgo', name)
    cmd.set('sculpt_vdw_vis_mode', 1, name)
    cmd.set('sculpt_field_mask', 0x020) # cSculptVDW
    strain = cmd.sculpt_iterate(name, cycles=1)
    if not int(quiet):
        print 'VDW Strain:', strain
    return strain


cmd.extend('show_bumps', show_bumps)
[[Category:Script_Library]]
</source>
[[Category:Pymol-script-repo]]

Latest revision as of 02:21, 1 July 2012

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 "https://pymolwiki.org/index.php?title=Show_bumps&oldid=10776"