pymol-users

[PyMOL] distance between two atoms in all the pdb files in a directory

[pkb b. <pks...@gm...>]

Hello Pymol users,

I am new to pymol scripting and I want to calculate the distance between two
points of all the pdb file in a directory.
I tried to write the script but seems its not working.
PLease help me.

from pymol import cmd
from glob import glob

lst = glob("*.pdb")
lst.sort()

for fil in lst:
        cmd.load(fil,"tmp")
        dst=cmd.distance('/tmp//A/LYS`203/NZ','/tmp//A/GLU`145/OE2')
        print lst

Re: [PyMOL] distance between two atoms in all the pdb files in a directory

[Tsjerk W. <ts...@gm...>]

Hi pkb bioinfo (which I do hope is not your real name),

Did you actually paste the script or did you retype it?

> from pymol import cmd
> from glob import glob
>
> lst = glob("*.pdb")
> lst.sort()
>
> for fil in lst:
>         cmd.load(fil,"tmp")
>         dst=cmd.distance('/tmp//A/LYS`203/NZ','/tmp//A/GLU`145/OE2')
>         print lst

You set dst to be the distance, and then you print lst...

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Re: [PyMOL] distance between two atoms in all the pdb files in a directory

[Tsjerk W. <ts...@gm...>]

O, and just when I pressed send (which also made firefox crash for
some reason), it struck me that you only load files, which means that
you're only appending states. But you don't specify a state to
calculate the distance, which means the first is taken again and
again. You might want to add a line 'cmd.delete("tmp")', or you could
load all files in separate states and use iterate_state.

Cheers,

Tsjerk

On Wed, Sep 9, 2009 at 8:51 AM, Tsjerk Wassenaar<ts...@gm...> wrote:
> Hi pkb bioinfo (which I do hope is not your real name),
>
> Did you actually paste the script or did you retype it?
>
>> from pymol import cmd
>> from glob import glob
>>
>> lst = glob("*.pdb")
>> lst.sort()
>>
>> for fil in lst:
>>         cmd.load(fil,"tmp")
>>         dst=cmd.distance('/tmp//A/LYS`203/NZ','/tmp//A/GLU`145/OE2')
>>         print lst
>
> You set dst to be the distance, and then you print lst...
>
> Cheers,
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623