Re: [PyMOL] using pymol from python script

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

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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>
>