Hi Doran, this is a python script, so you must load it with "run".
http://www.pymolwiki.org/index.php/Running_Scripts Use the "get" command to query default values of settings: PyMOL>get sculpt_vdw_vis_max get: sculpt_vdw_vis_max = 0.30000 So the complete procedure should look like this: run show_bumps_wikiscript.py load yourmolecule.pdb set sculpt_vdw_vis_min, 0 set sculpt_vdw_vis_mid, 0.2 set sculpt_vdw_vis_max, 0.4 show_bumps all Cheers, Thomas doran...@post.tau.ac.il wrote, On 05/21/12 09:49: > Hi Thomas, > Thank you for your reply. > > I tried running the show_bumps.py script I copied from PymolWiki using > @,however pymol gives me the following error : > NameError: name 'show_bumps' is not defined > How can I define it? > Also, do you know what are the values that sculpt_vdw_vis_max, mid and > min are set to by default? > > Thank you, > Doran > Quoting Thomas Holder <spel...@users.sourceforge.net>: > >> Hi Doran, >> >> there is a script on the PyMOLWiki that shows VDW clashes: >> >> http://pymolwiki.org/index.php/Show_bumps >> >> There are several sculpt_vdw_vis_* settings which control the >> visualization: >> >> sculpt_vdw_vis_max >> sculpt_vdw_vis_mid >> sculpt_vdw_vis_min >> >> Cheers, >> Thomas >> >> doran...@post.tau.ac.il wrote, On 05/20/12 18:26: >>> Hi, >>> I want to make pymol show me clashes between residues vdw spheres >>> only if the clashes are above a certain clash cut off, say if the >>> clashing residues overlap by x square angstrom than its o.k, but if >>> they overlap by more then x it's should show as a clash. >>> Does anyone know of a way to do it in pymol? >>> >>> Thank you, >>> Doran -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
