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
(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>
No, please! I strongly disagree with Jmol taking the role of fixing PDB
files!
PDB and CIF files will be different; that's the way it is, folks.
The prototype now reads both these properly. There is no reason the main
branch can't do it.
Justification:
* No reason to promote the pdb format
* No reason to promote poor/incorrect nomenclature
* I think this is a practical solution
Absolutely not. This is a can of worms.
I agree, better than nothing.
I think that the alternative is to do nothing ... the parser is not
going
to be fixed in the short term.
why not? It was 3 lines of code. Check the commit for bob200603.
---
I thought * is replacing the whole field, while ? replaces a single
char in the field
*.?H??
should match any hydrogen and e.g. Rh or Th
*.*H
throws an error, because there is no ; before the alternate location
indicator ;H (RasMol notation)
wild cards in Jmol can only be used as whole-field wild cards. If you want
*.*H
use
*.H or *.?H or *.??H
(whichever suits, or the combination)
Bob
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