Re: [PyMOL] using pymol from python script

[John R. <lam...@gm...>]

Hi,
your program looks exactly like mine, but I don't get the
png image if I don't raytrace it before. I think everything
else is working because if I run interectively the molecule
is loaded properly, and by just adding the cmd.ray command
gives me a correct image (but raytraced).

I'm running version Version 1.2r2.

   John



On 02/18/2011 05:04 PM, Jason Vertrees wrote:
> 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
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
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>>>> 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
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>>
>> ------------------------------------------------------------------------------
>> 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...
>>
>
>