Hi, jmol has come a long way since I have first used it - this is truly a tool with a lot of potential.
I'd just like to ask two small questions re: usability where perhaps I've missed something (they seem like simple enough steps but cost me an awful lot of fiddling): * 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?) * 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. My current "best workaround" is to use OpenBabel to convert xyz to pdb; OpenBabel gets the format right but fails at identifying the numerical identifiers of the backbone peptides, and specifically the designations of the C atoms "CA" and "CB" . 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) (2) the pdb file assigns the peptide number to each atom (3) there is a MAIN at the end of each line of the pdb file (4) "CA" and "CB" are properly identified. Is this so? Since jmol is able to create the correct wireframe geometry for all these 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). Is something like this possible / am I missing a shorter way here? thanks again for a great and intuitive tool! VB PS: again, I am not a java programmer, but would be well willing to test if someone were to point out the relevant functionality to me ------------------------------------------------------------------------- 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
