Miguel wrote:
this mostly addresses nucleotidic HET groups (large HET)Jmol seems to have a problem with defining bonds, eg
Contacts of the ligand COA1350C in PDB entry 1EBL
Yes, unfortunatly Jmol (in differance with Chime plug-in) does not recognises atoms marked in pdb as AC, BC, as carbon; AN, BN, as nitrogen; and AO, BO as oxygen. Because of this, Jmol considers as covalently bonded to this atoms atoms at considerably larger distances. Because of the same reason, JMOL colors this atoms differently from colors for carbon, nitrogen and oxygen.
We know at least one another such example in the pdb file 3DFR.
That is a correct assessment of the problem.
[complain]
Jmol would have recognized the element type if the PDB had bothered to follow their own file format specification of 1996 and had filled in columns 77-78 with the element symbol.
[/complain]
If you feel that it is truly justified, I could try mapping ?C, ?N and ?O to carbon, nitrogen, and oxygen.
However, we will be unable to map AC because:
AC = Ac = actinium
Do you have any recommendations as to how we can address this problem?
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_62.html
' - In large het groups it sometimes is not possible to follow the convention ...'
so if there is a
select hetero and nucleic
the N,A,B which confused element detection (and are part of all atom names) must be striped off.
and element composition is mentioned in FORMUL record! http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_41.html
by the way, why does hetero not select all HETERO groups, this must be a Jmol bug
Regards, Jan
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