Thomas, another nice solution. John, I suggest passing an object name, however, or your new load command will preset every object not just the one you loaded.
Cheers, -- Jason On Wed, Jul 11, 2012 at 4:22 PM, John Amraph <[email protected]> wrote: > Thank you, Thomas. > > Putting code below to python script and adding run script.py to pymolrc have > helped! > from pymol import cmd, preset > load_orig = cmd.load > def load_new(*args, **kwargs): > load_orig(*args, **kwargs) > preset.ligand_cartoon('all') > cmd.load = load_new > > > > On Wed, Jul 11, 2012 at 4:59 PM, Thomas Holder > <[email protected]> wrote: >> >> Or overload the cmd.load function: >> >> python >> from pymol import cmd, preset >> load_orig = cmd.load >> def load_new(*args, **kwargs): >> load_orig(*args, **kwargs) >> preset.ligand_cartoon('all') >> cmd.load = load_new >> python end >> >> Cheers, >> Thomas >> >> Jason Vertrees wrote, On 07/11/12 22:06: >> >>> John, >>> >>> Put this in your ~/.pymolrc: >>> >>> import pymol >>> >>> def my_load(file,obj): >>> cmd.load(file,obj) >>> preset.ligand_cartoon(obj) >>> >>> cmd.extend("my_load", my_load) >>> >>> Then you can load files as, >>> >>> my_load /path/to/file, object_name >>> >>> >>> Cheers, >>> >>> -- Jason >>> >>> On Wed, Jul 11, 2012 at 12:48 PM, John Amraph <[email protected]> >>> wrote: >>>> >>>> Dear collegues, >>>> >>>> I need your help in following question. I want to visualize pdb in the >>>> preset.ligand_cartoon("all",_self=cmd) mode when Pymol is opening the >>>> pdb >>>> file. >>>> I tried several options: >>>> >>>> include preset.ligand_cartoon("all",_self=cmd) in pymolrc >>>> making a pymol script(from pymol import cmd\ >>>> preset.ligand_cartoon("all",_self=cmd)) and adding run script.py in >>>> pymolrc >>>> >>>> But that doesn't work. >>>> >>>> Thank you! >>>> John Amraph >>>> >>>> PS: OS - Win7, pymol v0.9 >> >> >> -- >> 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 ([email protected]) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/[email protected] -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) [email protected] (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ 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 ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
