Thanks for all the feedback! On Wednesday 21 March 2007 19:21, [EMAIL PROTECTED] wrote:
> >> Now, after some experimental work with jmol (I am not a java > >> programmer), I > >> find that some laborious hand conversion of my OpenBabel generated pdb > >> files > >> will suddenly activate all the nicer features in jmol if > >> (1) the pdb file contains the peptide identifier (ALA or the likes) > > Jmol does not use the ALA names -- these are too unpredictable. It uses > the names of the atoms -- CA, N, O, etc. Particularly important is to > label the alpha carbon CA. > > > Yes, I guess that's one of the keys. > > > >> (2) the pdb file assigns the peptide number to each atom > > I think it IS important that the residues be numbered, yes. 1 for all the > atoms in the first residue, 2 for the next, etc. That field is critical. > > >> (3) there is a MAIN at the end of each line of the pdb file > > > > I don't think this is relevant. > > right, not relevant. correct, restested that. > >> (4) "CA" and "CB" are properly identified. > > CA is critical. > > > Likely > > > >> Since jmol is able to create the correct wireframe geometry for all > >> these > > > > But wireframe, i.e. bond assignation, is only based on interatomic > > distance. > > > >> molecules, it should not be too far a stretch to be able to identify the > >> longest connected line in a wireframe, see whether the sequence > >> is -CCN-CCN-CCN- ... in a certain segment, and attempt to auto-recognize > >> a > >> peptide backbone (and activate all the nice eye-candy). > > All that is needed is N and CA for this. > > > As I said, as far as I know the backbone is assigned based not on > > elements, but on proper IDs. I guess there could be trouble with > > nonprotein molecules having -CCN-CCN-, maybe? > > > >> Is something like this possible / am I missing a shorter way here? > > > > I don't think there's any shorter way, it's just that XYZ was not > > meant for proteins. Why do you have xyz files of proteins? > > Just use the PDB format, and you will be OK. Residue numbers, CA/N and C,O > if you want cartoons, and you will be all set. Yes. I guess what I was trying to say was that this can be done but (for large molecules) this ends up being a lot of mechanical work to be done/verified by hand. I have xyz files because they come from a general app, not specifiec to proteins (it would be a separate programming task to implement .pdb there just for the case that someone is actually dealing with peptides). What I found tantalizing is that jmol must have almost all necessary information already avainalbe internally - that is, via wireframe connectivity, the knowledge what _could_ be a backbone; then, by simply counting -CCN-'s along the supposed backbone, the numbers of each residue, and the correct CA / CB / N assignment ... it sounds like a very short step. (Of course one can extend this by all sorts of things like checking whether the N is bonded to a H, one C is bonded to an O, the other C has a meaningful side group, etc, but that's not even what I am after ... it's only that a very good guess for the backbone information must almost be avaliable internally, and would make available a lot of functionality to mere coordinate based files that is now only available after hand-editing a largish file.) In any case, no harm intended, hand-editing works too ... it was just a long road to find all this out experimentally, which is why I decided to mention it. Perhaps simply documenting just what information is essential to access things like ribbons, cartoon etc would already be helpful. best VB > > Bob Hanson > > > > ------------------------------------------------------------------------- > 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 -- Dr. Volker Blum Theory Department Fritz Haber Institute of the Max Planck Society Faradayweg 4-6 D-14195 Berlin Germany Phone: +49 30 8413-4846 Fax: +49 30 8413 4700 email [EMAIL PROTECTED] "A physicist is the atoms' way of thinking about atoms." ------------------------------------------------------------------------- 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
