For the sake of completeness, let's make sure some answers post to the list:
# with "pymol" in your path, you can issue from the command-shell (all one line...) pymol mol1.pdb mol2.pdb mol3.pdb -d 'as ribbon;spectrum count;set seq_view' # or if you have a command script, you can do something like: pymol mol1.pdb mol2.pdb mol3.pdb my_script.pml # which loads the files first then runs the script, # or you can provide arguments directly to a Python program with something like pymol my_program.py -- mol1.pdb mol2.pdb mol3.pdb # where my_program.py processes the files one by one through use of sys.argv Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -----Original Message----- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of David Shin Sent: Thursday, September 04, 2008 2:26 AM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] combine opening pymol --> never mind I regret I didn't follow the normal mode of operations... Search the web, pymol wiki, .pymolrc On Thu, 4 Sep 2008, David Shin wrote: > Hi - > > Basically I have a bunch of .pdb's with the same name, but with > different coordinates, that all reside in different directories. > > I want to put a script in my personal bin directory such that I can > run pymol and open that set of .pdb's, but then also run a pymol > script to set up the session. > > ie. combine something like this: > > #!/bin/sh > pymol mol1.pdb mol2.pdb mol3.pdb > > > with something like this: > cmd.hide("everything","all") > cmd.show("ribbon" ,"all") > cmd.spectrum("count",selection="all",byres=1) > cmd.set('''seq_view''','''1''',quiet=0) > > > Thanks, > Dave > > ---------------------------------------------------------------------- > --- This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge Build the coolest Linux based applications with Moblin SDK & > win great prizes Grand prize is a trip for two to an Open Source event > anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
