pymol-users

Re: [PyMOL] molecular sculpting

[Lieven B. <li...@ul...>]

Pat...@gs... wrote:
> I would like to understand the molecular sculpting possibilities of pymol
> but haven't been able to figure it out yet.  When using the wizard, the
> first request is to click and atom but how to proceed from there?
>
> I have used the bit of script provided on the web page and deformed
> the benzene ring but have not been clever enough to see the
> possibilities
> from that.
>
> Could anyone provide just enough of a step-by-step push-this,
> click-that lead into the
> molecular sculpting to get me started?

I don't know about the script or the wizard (yet), but I did try the
sculpting demo in the Demo menu. You can then just drag atoms
by left-clicking them while holding down the control key. The
dragged atom moves, everything it is connected to is dragged along,
and the structure tries to minimize its energy. Great fun!

-- 
Lieven Buts
Department of Ultrastructure
Brussels Free University

RE: [PyMOL] molecular sculpting

[DeLano, W. <wa...@su...>]

Molecular sculpting works like a real-time energy minimizer, except that =
it isn't minimizing the energy.  Instead, its just trying to return =
local atomic geometries (bonds, angles, chirality, planarity) to the =
configuration the molecules possess when they were first loaded into =
PyMOL. =20

To actually use this feature:

1. load a PDB file

2. configure the mouse for editing (Mouse menu)
   or click in the mouse/key matrix box

3. select "auto-sculpting" from the Sculpting menu

4. select Sculpting from the Wizard menu

5. ctrl-middle-click on any atom in your protein to activate sculpting
   the green part will be free to move
   the cyan part will be a fixed cushion to provide context
   the grey part will be excluded

6. now perform any conformational editing operation in the green region
   such as:=20

     ctrl-left-click-and-drag on an atom

     ctrl-right-click on a bond, then ctrl-left-click-and-drag about =
that
     bond

You can adjust the radius and cushion using the blue pop-up menus.

Right now I'm not sure the sculpting feature is more than entertainment, =
but my expectation is that it will become part of PyMOL's =
crystallographic model building system in the future.

Warren

--=20
mailto:wa...@su...=20
Warren L. DeLano, Ph.D.=20
Informatics Manager=20
Sunesis Pharmaceuticals, Inc.=20
341 Oyster Point Blvd.=20
S. San Francisco, CA 94080=20
(650)-266-3606  FAX:(650)-266-3501=20
-----Original Message-----
From: Pat...@gs... [mailto:Pat...@gs...]
Sent: Thursday, July 18, 2002 4:04 AM
To: pym...@li...
Subject: [PyMOL] molecular sculpting



I would like to understand the molecular sculpting possibilities of =
pymol=20
but haven't been able to figure it out yet.  When using the wizard, the=20
first request is to click and atom but how to proceed from there?=20

I have used the bit of script provided on the web page and deformed=20
the benzene ring but have not been clever enough to see the =
possibilities=20
from that.=20

Could anyone provide just enough of a step-by-step push-this, click-that =
lead into the=20
molecular sculpting to get me started?

Thanks!=20
Trissa

Re: [PyMOL] molecular sculpting

[Lieven B. <li...@ul...>]

"DeLano, Warren" wrote:
> Right now I'm not sure the sculpting feature is more than entertainment, but 
> my expectation is that it >will become part of PyMOL's crystallographic model 
> building system in the future.

I agree. I think it has great potential there, as it allows for a more
"physical" or
"intuitive" way of manipulating the model than moving individual atoms
or turning
torsion angles.

-- 
Lieven Buts
Brussels Free University