> Jmol doesn't deal right with alternate locations This is the first time I have ever seen a file with 'alternate locations' ... I didn't know such a thing existed.
I just read the pdb spec and see that there is a column reserved for an 'alternate location specifier' > e.g. 1plc contains some > residues at the surface with two different conformations > http://www.imb-jena.de/cgi-bin/SCOPlnk3.pl?ASK=1plc > execute the script commands > restrict 71;wireframe 30; > you see, this does not look like a healthy residue, this is because > there are two alternative conformations of the [Glu]71 > the alternative conformation could be given for the whole residue or in > most cases only for the side chain part, e.g. [Ser]75 in 1plc OK > I noticed some further problems > 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. Oh ... I don't feel very good ... I think I am going to be sick. The RasMol documentation I worked from ... 2.6 ... does not mention alternate locations. I just looked at the 2.7.2 documentation which was recently posted on openrasmol.org and they *do* specify ; as the character for selecting alternate locations. This, of course, conflicts with Chime's use of ; as the statement separator character. 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. > picking the erroneously bound oxygen atoms, [Glu]71.OE1;A and > [Glu]71.OE1;B (in RasMol notation) > in the pdb1plc.ent file: > ATOM 1123 OE1AGLU 71 -3.634 19.815 16.036 0.50 28.03 > ATOM 1124 OE1BGLU 71 -3.850 18.852 17.241 0.50 27.59 > echoes (not in my TEXTAREA but) in the JavaConsole > notifyAtomPicked(1122,Atom: OE1 1123 GLU 71 Chain: ) > notifyAtomPicked(1123,Atom: OE1 1124 GLU 71 Chain: ) > there is no alternative location identifier There is not alternate location identifier because I didn't know such a thing existed :-) > a rule may be, draw bonds in between each alternative conformation and > don't bind an atom from the other conformation if the same type is > already bound but at the borders Rather than do that, we are just going to take the first confirmation. Miguel ------------------------------------------------------- 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
