I definitely remember some mode where PyMOL would show good/bad contacts with red/green dots, but I can't seem to figure it out now. It was in Warren's talk as he was manually docking in a ligand. I searched, but couldn't figure it out myself. Does anyone know how to put PyMOL into that mode?

Cheers,

-Michael

On Thu, Sep 3, 2009 at 12:04 PM, H. Adam Steinberg <adam@steinbergs.us> wrote:
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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_______________________________________

H. Adam Steinberg
Artist, Scientist
<http://adam.steinbergs.us>

Information Technology and Media Center
Department of Biochemistry
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