hi Jan, at 11:00 am EDT on (Thursday) 20 November 2003 jr said:
> Hi Miguel, > if you simply reduce data you don't get compatible with RasMol script > language. And I am very unhappy with such a decision and I think all > the biomacromolecular structure people dealing with PDB files are. > Parsing a PDB header is a pain and not really necessary for a molecule > display applet, but parsing the structure data is prerequisite, so all > features of an ATOM or HETATM (CONECT, TER) should be represented in > the Jmol atom object, and they all should be addressable by script > selection commands. > I agree completely. (but that pesky semicolon... ;-) > > > > restrict [Glu]71;A would in RasMol select only one of them and not > > > [Glu]71;B, but on the command line, the ";" is not interpreted as > > > alternative conformation separator. [...] > > > > There is currently not a good mechanism in Jmol to support alternate > > locations. Therefore, I will modify the .pdb reader to take the first > > conformation it sees and discard the others. > > > > I have filed a bug report so that we don't lose the fact that we are > > not supporting alternate conformations. > > hi Miguel, <cringe> I would put this fairly high on the priority list, actually. is it just the semicolon that makes it difficult, or some larger issue? > This is the moment to repeat my description of already existing atom > selecting primitives in RasMol 2.7.2 > > Primitive: [Gly]1:E.Ca;B/1 > Residue name: Gly, ATP, [SO4], As? > Residue number: 1,16,12,9-20 > Insertion code: not implemented! > Chain: :E > Atom name: *.Ca, *.C??? > Alternate location indicator: *;B (no wildcard) > Model: */1 (no wildcards but /0) > Wildcards: **:*.????/0 > > The Insertion code is really important and I'm very sad about the lack of a primitive for it, but RasMol in contrary to Jmol > is able to deal with it (there must be an internal primitive). I am having trouble determining exactly what is the Insertion code? regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/> usa:north carolina:wake forest ------------------------------------------------------- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
