[PyMOL] Creating a single PDB from two PDB - ala docking by hand

[Mark Benson]

Dear All,

I am trying to build a single PDB file from two different PDB 
files.  One PDB has a small organic ligand, and the second PDB 
contains amino acid side chains from an active site.

I load both PDB files, but I want to "freeze" the orientation of 
the amino acid side chains PDB ( not move it), and then place and 
orient the ligand PDB in a certain pose with respect to the amino 
acid side chains.

Ideally, I would then like to save the coordinates for both the 
amino side chains and the ligand coordinates to a single PDB 
file.

In the long run, I want to run a simple minimization on an 
possible active site cluster and I want to get a feel for the 
energetics of the ligand in the active site.  I don't like working 
with MOLDEN or some of the other suites out there and I wanted to 
try this with PyMOL.  I've gone through the manual, the web, 
pymolwiki, the "masking" and "protecting" options, and I've tried 
examining the use of frames and split_states, but I haven't come 
up with anything.

I've heard about a demo that Warren DeLano put on for the ACS 
where, as part of the demo, he showed off some toy example where 
he docked a ligand in by hand, complete with having PyMOL show 
red/green dots for steric clashes/matches.

Any ideas?

-Mark


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Re: [PyMOL] Creating a single PDB from two PDB - ala docking by hand

[H. Adam Steinberg]

Bring up both pdb files in one session,
orient the ligand by going to editing mode and using the shift key with 
the left mouse button (3 button mouse mode) to move just the ligand.
Once you have it in the position you want,
type select all in the command line and then hit enter,
In the A menu for the (sele) you just created pick copy to object.
PyMOL will create a new pdb with all of the coordinates of the two pdb 
files as they are positioned on screen.
Rename it if you'd like, and save the new pdb out from the File 
menu/save molecule.


Mark Benson wrote:
> Dear All,
>
> I am trying to build a single PDB file from two different PDB 
> files.  One PDB has a small organic ligand, and the second PDB 
> contains amino acid side chains from an active site.
>
> I load both PDB files, but I want to "freeze" the orientation of 
> the amino acid side chains PDB ( not move it), and then place and 
> orient the ligand PDB in a certain pose with respect to the amino 
> acid side chains.
>
> Ideally, I would then like to save the coordinates for both the 
> amino side chains and the ligand coordinates to a single PDB 
> file.
>
> In the long run, I want to run a simple minimization on an 
> possible active site cluster and I want to get a feel for the 
> energetics of the ligand in the active site.  I don't like working 
> with MOLDEN or some of the other suites out there and I wanted to 
> try this with PyMOL.  I've gone through the manual, the web, 
> pymolwiki, the "masking" and "protecting" options, and I've tried 
> examining the use of frames and split_states, but I haven't come 
> up with anything.
>
> I've heard about a demo that Warren DeLano put on for the ACS 
> where, as part of the demo, he showed off some toy example where 
> he docked a ligand in by hand, complete with having PyMOL show 
> red/green dots for steric clashes/matches.
>
> Any ideas?
>
> -Mark
>
>
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> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
> trial. Simplify your report design, integration and deployment - and focus on 
> what you do best, core application coding. Discover what's new with 
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
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>   

-- 
___

H. Adam Steinberg
Artist, Scientist


Information Technology and Media Center
Department of Biochemistry
University of Wisconsin-Madison
433 Babcock Drive
Madison, WI 53706
608/265-4982
___



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