Re: [PyMOL] listing distance measurements

[Dan K. <dw...@bi...>]

Maybe I'm understanding the question wrong, but here is a solution for 
getting a list of all atom-atom distances between a ligand and a protein.
Just change the pdb id, and the definitions of the protein and ligand to 
your case.  A list of these distances will then be in the dist_list 
object, which you can do anything you want with.  In the example I 
simply printed them out.

To run example below (if saved as distlist.py) from pymol:
run distlist.py

~ Dan

---
Dan Kulp
Biophysics Graduate Student @ UPenn
dw...@ma...
http://dwkulp.homelinux.net/tiki/tiki-index.php
---


------------------------------------------------------------
import cmd

cmd.load("1O2K.pdb")

cmd.select("protein","not resn 656 and not resn HOH")
cmd.select("ligand", "resn 656")

dist_list = {}
pro_atoms = cmd.get_model("protein")
lig_atoms = cmd.get_model("ligand")

for l_at in lig_atoms.atom:
    for p_at in pro_atoms.atom:
        
dist_list[str(l_at.resi)+":"+l_at.name+";"+str(p_at.resi)+":"+p_at.name] 
= cmd.dist("foo", "index "+str(l_at.index),"index "+str(p_at.index))
        cmd.delete("foo")


print "LIST OF ATOM-ATOM PROTEIN-LIGAND DISTANCES"
for d in dist_list.keys():
    print "Distance of "+d+" is "+str(dist_list[d])
----------------------------------------------------------



Warren DeLano wrote:

>Stephanie,
>
>This is a very reasonable request, but unfortunately it is not one that
>PyMOL can meet at present --  it will require some significant changes
>within the C code for the "distance" command. 
>
>Thank you for the suggestion.
>
>Cheers,
>Warren
>
>--
>Warren L. DeLano, Ph.D.                     
>Principal Scientist
>
>. DeLano Scientific LLC  
>. 400 Oyster Point Blvd., Suite 213           
>. South San Francisco, CA 94080 USA   
>. Biz:(650)-872-0942  Tech:(650)-872-0834     
>. Fax:(650)-872-0273  Cell:(650)-346-1154
>. mailto:wa...@de...      
> 
>
>  
>
>>-----Original Message-----
>>From: pym...@li... 
>>[mailto:pym...@li...] On Behalf Of 
>>Stephanie Endsley
>>Sent: Wednesday, May 18, 2005 3:38 PM
>>To: pym...@li...
>>Subject: [PyMOL] listing distance measurements
>>
>>Hi there,
>>
>>I can get MacPyMol to find distances between a ligand and 
>>protein, but I want to output a list of all of these 
>>distances.  I have looked everywhere on how to do this, and I 
>>saw another posting with the same question, but it wasn't answered.
>>
>>Does anyone out there know how to get a list of the distances 
>>that PyMol calculates?  Please help.
>>
>>Thanks
>>
>>Steph
>>
>>
>>
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