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? > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys -- and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://workshops.proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.proteinexplorer.org PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List (molvis-list): http://bioinformatics.org/mailman/listinfo/molvis-list - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
