Angel recently shared with me a preprint of an article: T. Can et al. / Journal of Molecular Graphics and Modelling 25 (2006) 442–454, about surface rendering. Although I couldn't understand the article (either :)), it gave me a few ideas. I realized that even though they are pitching an "even better" method than what other programs use, one of the "not so good" methods seemed better than what we have, so I implemented it and am happy to say the solvent-type surface rendering in Jmol just took a leap forward --- like 200-10000% faster, with the capability to do molecular surfaces for small whole proteins, partial surface rendering of anything, and solvent-accessible surfaces for just about anything as well.
This article refers to cases where there are interior cavities, so I thought it might be neat to depict those as well in color in an automatic sort of way. With slab mode in Jmol, of course, one can take a look inside the surfaces. Take a look at a couple of JPEGs I produced: <http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/img/2ptn-molecular+hydrogens.jpg> <http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/img/2ptn-molecular+hydrogens2.jpg> The commands used here (with a local prototype) were: load 2ptn.cif isosurface delete ignore(solvent) colorscheme "sets" addHydrogens molecular It's colorscheme "sets" that tells Jmol to color the isosurface by which surface set the triangles are in. I think there might be some neat possibilities here for someone interested in this sort of thing. Up to 100 colored surface sets can be automatically colored this way. I note that these workers use the "unified atom" method, which Jmol doesn't support. This technique fakes hydrogen atoms by increasing the size of groups that would have them. That's probably an ok solution, but Jmol can supply the hydrogens -- that's what is done here. They have the interesting finding that there are several pockets in this particular protein. I may not have gotten the exact same solvent radius and such, and the hydrogens certainly make a difference, but it is perhaps interesting that Jmol finds different pockets. I suspect that this kind of thing is very sensitive to parameters. ------------------------------------------------------------------------- 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
