On May 7, 2006, at 2:47 a, Jan wrote:
Miguel wrote:
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
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 agree, better than nothing.
hi,
I'm a bit confused by the evolution of this thread, and I suspect
that for some reason, I may not have received all of the relevant
messages. but I wanted to respond in some way, so...
:-)
can Jmol support both versions (HG11 and 1HG1) without converting
between them? in my estimation, pdb is still the standard. mmCIF
has yet to see widespread use, despite being promoted by the RCSB,
and despite being a more flexible format. so I think pdb still has
to be considered the primary format for macromolecules, while it
should not necessarily be promoted, it should be supported. (someone
please feel free to correct me, of course.)
I'm pretty sure that is what Miguel is saying above; I just wanted to
add my comments.
best,
tim
--
Timothy Driscoll em: [EMAIL PROTECTED]
molvisions - see. grasp. learn. ph: 919-368-2667
<http://www.molvisions.com/> im: molvisions
usa:virginia:blacksburg tx: [EMAIL PROTECTED]
"Anyone who considers arithmetical methods of producing random digits
is, of course, in a state of sin." - J von Neumann
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