Re: [PyMOL] molecular sculpting

[Lieven Buts]

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

Re: [PyMOL] molecular sculpting

[Lieven Buts]

patricia.a.elk...@gsk.com 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, Warren]

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.  

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: 

 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

-- 
mailto:war...@sunesis.com 
Warren L. DeLano, Ph.D. 
Informatics Manager 
Sunesis Pharmaceuticals, Inc. 
341 Oyster Point Blvd. 
S. San Francisco, CA 94080 
(650)-266-3606  FAX:(650)-266-3501 
-Original Message-
From: patricia.a.elk...@gsk.com [mailto:patricia.a.elk...@gsk.com]
Sent: Thursday, July 18, 2002 4:04 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] molecular sculpting



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?

Thanks! 
Trissa