Hi Jeff > 1. In the lastest versions of Jmol, including 12.0.18, there are two > different colors for helices, most of them magenta as before but some, > mostly short helices, a shade of purple. What is the significance of > the two colors? Are the purple ones variant (e.g. 3-10) helices? Does > this have to do with the introduction of DSSP? I can't find anything in > the documentation.
Yes to all! Bob's doc is probably not yet updated, but I wrote something last weekend. Please read http://wiki.jmol.org/index.php/Protein_Community#Secondary_structure The colors will be illustrated in the main Jmol website (Documentation > Colors) when it is next updated by Nico. For now, you can see them at http://biomodel.uah.es/Jmol/colors/jmol_colors.en.htm#Secondary_struct ure > 2. In Rasmol beta turns are colored blue. The Jmol documentation says > that turns are colored blue in Jmol as well, but this doesn't seem to be > the case. The command "select turn" always returns zero atoms. Is > there a way to select beta turns in Jmol? All that is right, but Jmol may not see turns (it seems that PDB does not specify them**). After you recalculate using DSSP, they are there; I've seen a lot of them these last few days. (**) I thought it did, but I cannot find any mention of them in the pdb format spec. Rasmol must be doing tis own analysis. ------------------------------------------------------------------------------ Download new Adobe(R) Flash(R) Builder(TM) 4 The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly Flex(R) Builder(TM)) enable the development of rich applications that run across multiple browsers and platforms. Download your free trials today! http://p.sf.net/sfu/adobe-dev2dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
