From: John R. <lam...@gm...> - 2011-02-17 11:22:31
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Thank you, this indeed solves the problem! Now everything seems to work smoothely. I also set an alias to mypymol="pyplot -r script.py -- " so now everything is very simple. Thanks to all for the help. John On 02/17/2011 07:30 PM, David Hall wrote: > No idea if this will fix your problem, but what I've found is portable > across binaries from Delano Scientific/Schroedinger and > OS/self-compiled versions of pymol is to instead run: > > pymol -r examply.py -- mymolecule.xyz > > (or if I'm making pngs, usually pymol -qrck examply.py -- mymolecule.xyz ) > > The -- makes it so mymolecule.xyz is passed as an argument to the > python script instead of as an argument to pymol > > Then examply.py is just > > from pymol import cmd > import argv > import mymodule > > cmd.load(sys.argv[1]) > cmd.hide() > cmd.show("spheres") > mymodule.dosomething() > > > Note, that pymol has to be able to find mymodule, which if you're > using a Delano Scientific/Schrodinger binary can be annoying, but it > looks like that is already working for you. > > Also, http://pymolwiki.org/index.php/Python_Integration makes it look like > pymol -l examply.py -- mymolecule.xyz > > may work, but I've never done it, so no idea how the behavior differs. > > -David > > > On Thu, Feb 17, 2011 at 3:05 AM, John Russo<lam...@gm...> wrote: >> Thanks, that is what I was looking for! I just made a simple >> script out of it which looks like this >> >> #!/usr/bin/env python >> >> import pymol >> from pymol import cmd >> import mymodule >> >> pymol.finish_launching() >> >> cmd.load("mymolecule.xyz") >> cmd.hide() >> cmd.show("spheres") >> mymodule.dosomething() >> >> >> I've noticed something strange though. The dosomething() function just >> colors atoms according to some order parameter. If I execute in the script >> above it is quite slow, I can see individual atoms being colored. Instead if >> I execute dosomething() from within the pymol interpreter it is much faster. >> Any reason for this? >> >> >> >> >> >> >> On 02/17/2011 04:33 PM, Tsjerk Wassenaar wrote: >>> Hi John, >>> >>> Is this what you're looking for?: >>> >>> http://www.pymolwiki.org/index.php/Launching_From_a_Script >>> >>> Cheers, >>> >>> Tsjerk >>> >>> On Thu, Feb 17, 2011 at 8:19 AM, John Russo<lam...@gm...> wrote: >>>> Hi, >>>> I'm sorry for making such beginner's questions but searching the manual, >>>> google >>>> or the wiki didn't help me. >>>> >>>> I know how to extend pymol by writing python functions (through the >>>> extend command). >>>> But is it possible to do the opposite? I want to write a script that >>>> loads a molecule, does something >>>> to it and then displays the pymol window or outputs a png file. I want >>>> to this without having to >>>> enter commands in the pymol command line, since I need to put these >>>> operations in a script, >>>> without interactive control on pymol. >>>> >>>> Example. I want to write a script examply.py with which I can do >>>> >>>> ./examply.py mymolecule.xyz >>>> >>>> And for output I want to get mymolecule.png or the pymol window with all >>>> the operations >>>> already done. >>>> >>>> Any hints? Thank you. >>>> >>>> >>>> John >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: >>>> Pinpoint memory and threading errors before they happen. >>>> Find and fix more than 250 security defects in the development cycle. >>>> Locate bottlenecks in serial and parallel code that limit performance. >>>> http://p.sf.net/sfu/intel-dev2devfeb >>>> _______________________________________________ >>>> PyMOL-users mailing list (PyM...@li...) >>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> Archives: http://www.mail-archive.com/pym...@li... >>>> >>> >> >> ------------------------------------------------------------------------------ >> The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: >> Pinpoint memory and threading errors before they happen. >> Find and fix more than 250 security defects in the development cycle. >> Locate bottlenecks in serial and parallel code that limit performance. >> http://p.sf.net/sfu/intel-dev2devfeb >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> |