Those are hydrogen bonds. PDB specs read:
* If more than four fields are required for non-hydrogen and nonsalt-bridge
bonds, a second CONECT
record with the same atom serial number in columns 7 - 11 will be used.
There is a vague reference thre to hydrogen bonds and salt bridges. They are
not specified well, but they are indicated after the first four columns.
Must be a very old throw-back.
Bob
2010/11/11 Angel Herráez <angel.herr...@uah.es>
> I just tested this file (mentioned in a different thread)
>
> http://q4md-forcefieldtools.org/Tutorial/P2N/Metal-
> complex/Mol_red1.p2n
>
> in Jmol 12.1.15, which reads it as pdb format.
>
> I'm curious: how is it that Jmol draws from the central cobalt 4
> regular single bonds and 2 dashed, partial bonds?
> What is the algorithm deciding this?
> (The file provides no specification of partial bonds. Also, there's
> no difference in bond distance)
>
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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