Show bumps - Revision history

Bell: 4 revisions

2014-03-28T03:36:07Z

4 revisions

Speleo3: Related Settings

2012-07-01T07:21:47Z

Related Settings

New page

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

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

[[Image:sb.png|300px]]

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 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)

[[Category:Script_Library]]
[[Category:Pymol-script-repo]]

Speleo3: moved to github

2012-05-21T09:00:41Z

moved to github

Speleo3: 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..."

2011-06-06T15:15:50Z

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..."

New page

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 pymol-users mailing list].

= The Script =

<source lang="python">
from pymol import cmd

def show_bumps(selection='(all)', name='bump_check', quiet=1):
'''
DESCRIPTION

Visualize VDW clashes

ARGUMENTS

selection = string: atom selection {default: all}

name = string: name of CGO object to create {default: bump_check}
'''
cmd.delete(name)
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)
</source>

← Older revision	Revision as of 03:36, 28 March 2014
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@@ Line 1: / Line 1: @@
 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 pymol-users mailing list].
-= The Script =
+== Usage ==
-    name = string: name of CGO object to create {default: bump_check}
+ show_bumps [ selection [, name ]]
-cmd.extend('show_bumps', show_bumps)
+[[Category:Script_Library]]
-</source>
+[[Category:Pymol-script-repo]]