From: Miguel <mi...@jm...> - 2004-03-31 14:29:44
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>>I see the picture, but I don't understand how it is supposed to >>work. >> >>Tim, can you help explain it to me? >> > > I'll try. :-) Sculpt was stand-alone energy minimization software that > MDL incoporated into Chime a while ago - but ONLY the Windows version of > Chime. > > Sculpt is able to perform overall energy calculations "on-the-fly". you > can pick up and move parts of a structure relative to other parts, > stretching and breaking bonds, changing rotations, etc. Sculpt > continuously calculates the energy in the current conformation and > privdes visual feedback cues. for example, areas where Sculpt > calculates high energy (i.e., unfavorable interactions) are shown as red > shells. I believe Sculpt will also automatically break or form covalent > bonds depending on bond distances and atom properties. > > IIRC, Sculpt mode in Chime also allows for performing energy > minimization, too. in other words, drag parts of the structure to forkm > a new conformation, and Sculpt will 'tweak' the structure to the lowest > possible overall energy state. OK, that sounds pretty cool ... but it also sounds somewhat complicated. > it is an intense and, as Ewen says, a wonderful teaching tool. Ewen ... this will not make it into Jmol within the next 6 months. Sorry. But I have filed a feature request so that it doesn't get lost. Miguel |
From: Christoph S. <c.s...@un...> - 2004-03-31 14:50:48
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>>IIRC, Sculpt mode in Chime also allows for performing energy >>minimization, too. in other words, drag parts of the structure to fork= m >>a new conformation, and Sculpt will 'tweak' the structure to the lowest >>possible overall energy state. >=20 >=20 > OK, that sounds pretty cool ... but it also sounds somewhat complicated. It is - and it's a real killer feature not only for educational=20 applications. It pure fun (at least for a chemist :)) to watch the thingy work. It almost feels as if you had a model in your hand, but one which knows=20 how to snap into chemically "right" positions. On the long run, we could use our current energy minimization code for th= is. Cheers, Chris --=20 Dr. rer. nat. habil. Christoph Steinbeck (c.s...@un...) Groupleader Junior Research Group for Applied Bioinformatics Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z=FClpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |
From: Miguel <mi...@jm...> - 2004-03-31 15:48:54
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Christoph wrote: >> OK, that sounds pretty cool ... but it also sounds somewhat complicated. > > It is - and it's a real killer feature not only for educational > applications. > It pure fun (at least for a chemist :)) to watch the thingy work. > It almost feels as if you had a model in your hand, but one which knows > how to snap into chemically "right" positions. > > On the long run, we could use our current energy minimization code for > this. You are right. We should use CDK to do the calculcations ... with Jmol doing the rendering. Miguel |