Re: [PyMOL] Is it possible to pass command line arguments to a .pml file?

[Jordan W. <jwi...@gm...>]

It seems the difference I was looking for was 

pymol something.pml -- arg1 arg2 arg3

I was missing the --

Thanks
Jordan




On Jun 26, 2013, at 4:21 AM, lie...@vu... wrote:

> On Wednesday 26 June 2013 08:52:39 Jordan Willis wrote:
>> I'm looking to pass a .pml file, do some stuff, and then save it as a
>> session. Pymol -c My.pml looks like a good option.  I'm trying to write
>> hundreds of sessions each with different arguments. I was wondering if its
>> possible to pass command line arguments that can then be seen by the python
>> interpreter inside a .pml
>> 
>> While I'm at it, is it easy to pass objects, i.e. variable names, between
>> the python enviroment and the pml enviroment inside a .pml script? Is
>> cmd.extend the best option? Is there a way to go backwards (from the .pml
>> to the python interpreter)?
> 
> This .pml sequence works for me:
> 
> stored.a = 5
> python
> import sys
> print sys.argv
> print stored.a
> stored.a = 10
> python end
> print stored.a
> 
> Cheers,
> 
> -- 
> Lieven Buts, Postdoctoral Fellow
> Structural Biology Brussels, Vrije Universiteit Brussel
> Department of Structural Biology, VIB
> 
> 
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