[Jmol-developers] Jmol improvements in PDB element type recognition

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

Per Jan's suggestion, the PdbReader in Jmol now uses FORMUL records to
decide which atom types are present in the group.

When FORMUL records are present, only element names that are present in
the FORMUL record will be used for

Q: Jan, can you find me an entry with FORMUL records that include a
continuation onto a second line? If it is not easy to do then do not do
it.

> We know at least one another such example in the pdb file 3DFR.

This fixes the problem in 3DFR.

>> Jmol seems to have a problem with defining bonds, eg
>>
>> Contacts of the ligand COA1350C in PDB entry 1EBL

However, this does not explain the problem with 1EBL. This entry had the
element type in the appropriate columns. Therefore, the
'ambiguous-atom-name' problem was not the cause.

David, I do not understand what type of problem you are/were having with
1EBL near [coa]1350 ... it looks OK to me, even in older versions of Jmol.
I am not a chemist, so you need to give me a simple explanation.



Miguel