Hi Volker > * After a fairly complex series of scripted commands in a large molecule, I > do > not see a simple way to "save" the current state of jmol - i.e. whenever I'd > like to go back and reproduce my work, "all is lost" and I end up starting > from scratch. Is that correct? (with the recent addition of "show set", a > save option might not be too far off?)
Well, this was not possible if former versions, but the latest 11.1.x (maybe even 11.0) can do exactly what you want. Please read "save STATE" at http://www.stolaf.edu/academics/chemapps/jmol/docs/?ver=11.1#save What it does not do is saving to a file, but you can "show state" and copy the output from the console. > * I noticed that many of the useful protein animation features (ribbons etc) > work only from a pdb file. > > That is slightly problematic when working from an xyz file where the atoms > are > not ordered / named in the usual pdb sequence. The reason for that is that only PDB format provides the residue information. I know that, for ex., the keyword "protein" interprets the atom IDs, not the amino acid residue names, but mostly everything is based on standard PDB atom IDs, like CA and CB. But maybe some of your proposals can be implemented. > 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) Yes, I guess that's one of the keys. > (2) the pdb file assigns the peptide number to each atom Same > (3) there is a MAIN at the end of each line of the pdb file I don't think this is relevant. > (4) "CA" and "CB" are properly identified. 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). 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? ------------------------------------------------------------------------- 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
