Difference between revisions of "Show bumps"

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

Revision as of 09:00, 21 May 2012

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

show_bumps [ selection [, name ]]

@@ Line 1: / Line 1: @@
+{{Infobox script-repo
+|type      = module
+|filename  = show_bumps.py
+|author    = [[User:Speleo3|Thomas Holder]]
+|license   = BSD-2-Clause
+}}
 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 ==
-<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}
+ show_bumps [ selection [, name ]]
-    '''
-    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)
+[[Category:Script_Library]]
-</source>
+[[Category:Pymol-script-repo]]