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 <a...@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
> University of Wisconsin-Madison
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> 608/265-4982
> _______________________________________
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>
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--
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
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