Timothy Driscoll wrote:
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?
If by "can" you mean "could" -- Yes, absolutely. I modified the
prototype last night; it was quite simple, so there's no reason not to
fix up 10.2 as well.
Go ahead and try it yourself at
http://fusion.stolaf.edu/chemistry/jmol/xtalx.
It all has to do with recognizing what's a number and what's not.
Currently, Jmol 10.2 recognizes "3.X" where X is a letter A-Z as "not a
number". But it only looks ahead one character after the decimal, so it
considers "3.1" a number and throws that error. I simply adjusted it so
it would look ahead TWO characters -- "3.1H" then is "not a number".
While at it, I fixed it so that "?" is counted toward "not a number" the
same way A-Z is. Now, if we can have 3.11HG as well, that's more of a
pain, but if not, maybe not worth the trouble to generalize this. Can
you ever have two numerical digits at the beginning of an atom name?
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