Re: [Jmol-users] Chime Sculpt mode?

[Eric M. <em...@mi...>]

Sculpt used to be a very cool stand-alone molecular mechanics program with 
some electrostatics, that does energy minimization. You can attach forces 
(rubber bands") to atoms and pull them into new conformations, with live 
energy minimization. I used Sculpt to animate the release (and played 
backwards) simulate the binding of an HIV protease inhibitor to the HIV 
protease protein, and of ten water molecules coalescing into a "droplet", 
as seen here:
http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/morfdoc.htm#sims

Sculpt is a commercial program developed by Mark Surles, which he started 
while in the group of David and Jane Richardson at Duke. He founded his own 
business around Sculpt. Later, MDL acquired it and Mark began working at MDL.

The Sculpt mode of Chime is a limited functionality "teaser" that attempted 
to interest people in buying Sculpt. About all I've seen it do is, for 
small molecules (too slow for big proteins) if you "shake" the molecule by 
a jiggle-drag of the mouse, it energy minimizes one step for each jiggle. 
It is quite spectacular, conveying flexibility of molecules and real-time 
energy minimization in Chime -- but of limited use in Chime. It is the 
stand-alone Sculpt program that is useful.

Because MDL owns Sculpt, I doubt that any of the Sculpt code would be 
released into the open-source domain by MDL for use in Jmol. Sculpt appears 
to be an active component in MDL's suite of commercial software. (It is, 
after all, MDL's consistent refusal to open the source of Chime that 
fostered Jmol's evolution into a Chime replacement!)

However, it will be interesting to hear Mark's response to this discussion, 
so I have copied this message to him. (Mark, please correct any 
inaccuracies I may have stated above!)

The old URL for Sculpt at MDL (the link from my site above) is broken. 
Searching for "sculpt" at MDL leads you to the current page, 
http://www.mdl.com/products/predictive/sculpt/index.jsp
The price is now $1,496/license seat. That price has gone way up! The 
description at the above URL is very different from mine above, so probably 
a lot has been added to Sculpt to integrate it with other MDL products.

Personally, I think that adding energy minimization to Jmol is going too 
far. I fear it would greatly increase the bulk and cumbersomeness of the 
Jmol applet -- unless it can be somehow a separate module that is not 
downloaded or interpreted by the client unless explicitly needed. In any 
case, if people wish to integrate an optional energy minimization module, I 
agree that it would have to start from an open-source base. Not knowing 
anything about open-source energy-minimization software, I'll defer to others.

-Eric

At 10/6/06, Bob Hanson wrote:
>So what IS the sculpt mode of Chime, and how is it useful?
>
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Eric Martz, Professor Emeritus, Dept Microbiology
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