>> THE BIG QUESTION
>> ----------------
>> What do I do when I see a .pdb file that has 200 atoms and 20 CONECT
>> records?
>>
>
> build the connections for the 20 Atoms referred by the CONECT records
> form the CONECT information and than start calculation for the rest of
> the molecule but don't calculate any bond between two of the 20 atoms
> again.
OK, so your recommendation is to do 'both':
Within a single .pdb file
1. apply the CONECT records
2. apply the bonding algorithm to atoms that were not
mentioned in the CONECT records
To me, this seems consistent with the .pdb file format specification. (I
honestly do not like it, but I will have to live with it :-)
That leads to:
THE SECOND BIG QUESTION
-----------------------
If we follow these rules, will we ever have a situation where we will
automatically create bonds when the end-user did not want one?
As long as an atom was mentioned in a CONECT record the Jmol will not
touch it.
But, will people have molecules with single atoms floating around that
could get auto-linked together?
(Sebastian, what do you think?)
Miguel
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