[Jmol-developers] Re: lpc jmol

[Miguel <mi...@jm...>]

>> 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?


Miguel