Re: [PyMOL] Coordinates of ligand-binding site

[James S. <jms...@gm...>]

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
>>
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>