Miguel wrote:
...
I observe that the PDB file calls is '1HG1' and the mmCIF file calls it
'HG11'.
Please comment on the following proposal:
* Jmol will support the 'HG11' version
* The Jmol pdbReader code will convert atom names that
match the following format:
<digit> H <alpha> <digit> -> H <alpha> <digit> <digit>
the example I posted shoes that 1HB -> HB2
This may cause great confusion with the PDB users.
Justification:
* No reason to promote the pdb format
it is human readable
* No reason to promote poor/incorrect nomenclature
* I think this is a practical solution
an alternative operator for IUPAC atom naming
RasMol> select *.1HB;A
Jmol> select *,HB2%A
I think that the alternative is to do nothing ... the parser is not going
to be fixed in the short term.
a parser which ignores context of e.g. "." or ";" should be fixed in the
long run.
Regards, Jan
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