Re: [PyMOL] Coordinates of ligand-binding site

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

Hi James,

the "get_extent" command in PyMOL will give you the corners of the 
selected region, from which you easily can calculate center and edge 
lengths.

http://pymolwiki.org/index.php/Get_extent

Example:
box = cmd.get_extent('sele')
print 'Center:', [(a+b)/2.0 for (a,b) in zip(*box)]
print 'Size:', [(b-a) for (a,b) in zip(*box)]

Regarding your issue (1-): Coordinates should not change unless you 
align to some other molecule.

Cheers,
   Thomas

On 07/18/2012 09:37 AM, James Starlight wrote:
> Jordan,
>
> Thank you for advise.
>
> I've tried to do the same already but
>
> 1- In Resulted pbd file ( with ligand and surrounded residues only)
> the coordinates of ligand and residues have been changed  in
> comparison to the initial pdb/ How to prevent it?
>
> 2- The resulted pdb consist of coordinates of each atoms but how to
> define the proper coordinates of ligand-binding BOX based on that
> point coordinates?
>
> James
>
> 2012/7/18 Jordan Willis <jwi...@gm...>:
>> I'm thinking a good work around is simply this.
>>
>>
>> Select the binding site of the amino acids and ligand in pymol.
>>
>> Then copy those selected aa's and atoms to another object:
>>          save -> model -> copied_object as output.pdb
>>
>> output.pdb will then contain all the x,y,z coordinates of only what was selected.
>>
>> Then just get those columns and upload them to swiss dock.
>>
>> Jordan
>>
>>
>> On Jul 18, 2012, at 2:23 AM, James Starlight wrote:
>>
>>> Dear PyMol users!
>>>
>>>
>>> Some of docking servers (e.g swiss dock) which I'm using need in
>>> explicit definition of the coordinates (in XYZ) of the docking region
>>> as well as coordinates of its COM. How I could obtain such coordinates
>>> of intrested pdb file based on the knowing protein-ligand interaction
>>> sites ( e.g if i visualize ligand binding site by means of Pymol
>>> itself ).
>>>
>>>
>>> Thx for help
>>>
>>>
>>> James

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