[Jmol-developers] [ jmol-Bugs-888841 ] Incorrectly displays connections between atoms

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Bugs item #888841, was opened at 2004-02-01 19:36
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https://sourceforge.net/tracker/?func=detail&atid=379133&aid=888841&group_id=23629

Category: Graphics
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Nobody/Anonymous (nobody)
Summary: Incorrectly displays connections between atoms

Initial Comment:
Hi,

I have noticed in a number of pdb files that Jmol (which 
is an absolutely brilliant vis tool... WELL DONE) arbitrarily 
draws a connecting line between atoms making non-
sensicle structures.  Initially thought it was because the 
pdb's were old and had poor format but i have noticed it 
with new files also.  Loaded up the same moleculae in 
Rasmol and the structure loads fine.  So it seems to be 
something related to the default connect algorithm 
between atoms that Jmol uses.  Here are some of the 
files/pdbs that this occurs with.  None of these 
anomolies occur in Rasmol

5cpa.pdb - numerous erroneous atomic connections
1e8a.pdb - forms what looks like a spider wec in a beta 
turn between residues 63-68. 
6adh.pdb
5rsa.pdb

If you can tell me where in the code i could find the 
connect algorithm, i'll fix it for you if you like.

Thanks, keep up the brilliant work !

Dave Chandler
eg...@ii...

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