timothy driscoll wrote: > at 12:12 pm EDT on (Thursday) 20 November 2003 jr said: > > > > > > > > > > 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). Try 1hag > > > > http://www.imb-jena.de/cgi-bin/SCOPlnk3.pl?ASK=1hag > > > > Jmol wouldn't load the molecule, and if, how do I select between > > > > ATOM 20 CA GLY E 1F 20.593 14.133 18.600 1.00 50.00 > > > > 1HAG 213 > > > > ATOM 30 CA GLY E 1D 18.774 17.420 21.596 1.00 50.00 > > > > 1HAG 223 > > > > the insertion code is the char (here F and D) in column 27 of the ATOM > > or HETATM record > > > > > > > > > > > How was it marked again to be two complementary, alternative > locations? > > > > This aren't alternative locations, this is for compatibility in residue > > number e.g. the homologous molecule in different species or think of a > > splice variant ... > > > so the insertion code identifies atoms from a homologous structure? I > grow more confused. if this is true, don't they belong in a separate > structure file altogether?
no, it should make it easier for humans to compare different but related structures, e.g. for the Trypsin-like serin protease prethrombin2 in 1hag the numbering is done like in chymotrypsin it may become clearer if you read the REMARKs REMARK 4 CHYMOTRYPSIN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS 1HAG 74 REMARK 4 USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE 1HAG 75 REMARK 4 STRUCTURE OF CHYMOTRYPSIN (W.BODE ET AL., 1989, EMBO J. 8, 1HAG 76 REMARK 4 3467-3475). 1HAG 77 Regards, Jan ------------------------------------------------------- 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
