Re: [PyMOL] execute a set of pml files on a set of pse files iteratively and saving without opening the Pymol GUI

[Thomas H. <sp...@us...>]

Hi Sajeewa,

paste this into a python script (script.py):

from pymol import cmd
for i in range(1, 240+1):
     cmd.reinitialize()
     cmd.load('%d.pse' % i)
     cmd.do('@%d.pml' % i)
     cmd.sync()
     cmd.save('%dnew.pse' % i)


Run it with PyMOL in batch mode:

pymol -cqr script.py

See also: http://pymolwiki.org/index.php/Command_Line_Options

Cheers,
   Thomas

On 03/21/2012 08:48 AM, Sajeewa Pemasinghe wrote:
> Hi everyone,
>
> I have a set of (240 files) of pse files like
>
> 1.pse
> 2.pse
> .
> .
> .
> 240.pse
>
> I also have a set of(240 files) pml files like
>
> 1.pml
> 2.pml
> .
> .
> .
> 240.pml
>
> I want execute the pml files iteratively on the corresponding pse files
> and save the new pse files as 1new.pse,2new.pse, so on. from the command
> line of pymol(without opening the GUI). Can anyone suggest me a way to
> do this?
>
> Thank you
>
> Sajeewa

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen