just to confirm after one more test (for what it's worth - apologies, I'll stop sending large amounts of mail after this) - all the below is correct in 11.1.25:
* with just the residue number and all CA's identified, ribbons et al work. No "ALA", "CB", "MAIN" needed. Thanks again, VB On Wednesday 21 March 2007 19:21, [EMAIL PROTECTED] wrote: > >> (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. > > >> (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. > ------------------------------------------------------------------------- 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
