Re: [Jmol-users] selecting atom IDs such as 1h47

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

>>  * 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

Is it not the case that this violates the PDB recommendations?
I thought that they were supposed to put the digit in the front only in
the case where the atom name was more than 3 characters.

> This may cause great confusion with the PDB users.

The PDB causes great confusion for me.

>> Justification:
>>  * No reason to promote the pdb format
>>
> it is human readable

So is CIF, so is XML

>>  * 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

comma cannot be used because it is the 'or' operator in an expression
context.

>> 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. =22.=22 or =22;=22 should be fix=
ed in the
> long run.

The openrasmol use of ';' for model (chain?) will not be supported in Jmo=
l.

Jmol, like Chime, supports ';' as a statement terminator.


Miguel