Menu
▾
▴
Re: [PyMOL] using pymol from python script
|
From: Jason V. <jas...@sc...> - 2011-02-18 08:04:39
|
Hi John,
You don't actually need to ray trace before saying any more. That was
an older "feature".
Here's what worked for me:
# save this to examply.py
from pymol import cmd
cmd.load(sys.argv[1])
cmd.hide()
cmd.show("spheres")
cmd.set('sphere_scale',0.3)
cmd.set('orthoscopic',1)
cmd.png("printme.png")
using the command line:
pymol -qcr examply.py -- 1rsy.pdb
This quietly loads PyMOL, runs the commands, renders the image and
quits. The command,
pymol -qcr examply.py -- 1rsy.pdb
keeps PyMOL open, but still renders the image.
Did you ensure that you actually had the PDB file (or in your case
mymolecule.xyz) in the current working directory?
Cheers,
-- Jason
On Fri, Feb 18, 2011 at 2:46 AM, John Russo <lam...@gm...> wrote:
> I'm sorry to bother this mailing list so much but it
> seems that I cannot save images.
>
> This is the script examply.py
>
> from pymol import cmd
>
> cmd.load(sys.argv[1])
> cmd.hide()
> cmd.show("spheres")
> cmd.set('sphere_scale',0.3)
> cmd.set('orthoscopic',1)
>
> cmd.png("printme.png")
>
> which I execute like this:
>
> pymol -qrc examply.py -- mymolecule.xyz
>
>
> But I don't get the file printme.png. Executing the
> script interactively
>
> pymol -r examply.py -- mymolecule.xyz
>
> I can see that the molecule looks ok but still I don't get a png image.
> I have to type "png printme.png" in the pymol command line to get it.
>
>
> Does anybody now why is this?
>
> Thanks.
>
>
> 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...
>>>
>
>
> ------------------------------------------------------------------------------
> 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...
>
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) Jas...@sc...
(o) +1 (603) 374-7120
|
