> Concerning a questian raised by Tim concerning what is the naming
> used in mmCIF, I had a look at 1L2K both in PDB and mmCIF format
> (http://www.rcsb.org/pdb/cgi/explore.cgi?
> job=download;pdbId=1L2K;page=0;pid=171361130167582&opt=show&format=PDB&p
> re=1 and http://www.rcsb.org/pdb/cgi/explore.cgi?
> job=download;pdbId=1L2K;page=0;pid=171361130167582&opt=show&format=mmCIF
> &pre=1) ;
> here are the records of a given H atom :
> in PDB = ATOM 10 1HG1 VAL A 1 -3.462 15.657 17.717 1.00
> 27.83 H
> in mmCIF = ATOM 10 H HG11 . VAL A 1 1 ? -3.462 15.657 17.717
> 1.00 27.83 ? ? ? ? ? 1 VAL A 1HG1 1
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>
Justification:
* No reason to promote the pdb format
* No reason to promote poor/incorrect nomenclature
* I think this is a practical solution
I think that the alternative is to do nothing ... the parser is not going
to be fixed in the short term.
Miguel
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