The most recent proposal for Jmol bonding behavior for .pdb files was:
- respect CONECT records
- apply auto-bonding to those atoms not mentioned in CONECT records
Unfortunately, I don't think this is going to work. Following up on
Geoff Rowland's reference on double bonds (details below), we see that
only the double bonds are specified. Therefore, the atoms that are
specified in these CONECT records still go through the auto-bonding
process for the rest of their connectivity.
Geoff's other reference is quite valuable for reference. But I am under
the impression that we don't want to mimic this behavior.
http://www.umass.edu/microbio/rasmol/rasbonds.htm
Miguel
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http://www.umass.edu/microbio/rasmol/faq_em.htm#doublebonds
Double and triple bonds
Beginning with RasMol 2.6 beta-2 (and also in Chime 2) the PDB file
needs to specify CONECT records only for the double or triple bonds (not
for all bonds in the entire molecule as in the previous version of
RasMol), ... Here is a sample PDB file with three double bonds,
fumarate.pdb.
----
fumarate.pdb
REMARK The first atom in each CONECT record (line) is connected to each
of REMARK the other atoms in the record. The 2nd through Nth atoms in
each REMARK record are not connected to each other by that record.
CONECT 1 2 2
CONECT 4 5 5
CONECT 6 7 7
END
REMARK A double bond can also be specified with two CONECT records, e.g.
REMARK CONECT 1 2
REMARK CONECT 1 2
REMARK In this case, both must be specified in the same direction. That
REMARK is, this doesn't work:
REMARK CONECT 1 2
REMARK CONECT 2 1
PDB file with three double bonds, fumarate.pdb.
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