Michael,
Assuming you have a PyMOL 1.2 build with the Tcl/Tk user interface
displayed:
Load a small-molecule or peptide structure or simply type "fab AAAA"
then
(1) activate the builder by clicking on the "Builder" button on the
upper window
(2) click the "Bumps" checkbox
(3) click the Sculpt button
Now CTRL-click-and-drag atoms around in the 3D viewer. You'll see the
little disks appear when the van der Waals radii overlap. When done,
click the Clean button to minimize the structure into a nearby local
energy minimum.
Cheers,
Warren
________________________________
From: Michael Lerner [mailto:mglerner+sourcefo...@gmail.com]
Sent: Friday, September 04, 2009 6:15 AM
To: a...@artforscience.com
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Creating a single PDB from two PDB - ala
docking by hand
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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Madison, WI 53706
608/265-4982
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