> 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. >
from the Jmol application (not applet): write state "somefile.spt" then, at your leisure: script "somefile.spt" should get you back EXACTLY where you left off. If it doesn't I want to know! > >> 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. >> (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. > 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
