Rolf Huehne wrote:

>Bob Hanson wrote:
>  
>
>>Rolf Huehne wrote:
>>
>>    
>>
>>>Bob Hanson wrote:
>>> 
>>>
>>>      
>>>
>>>>OK, well, then, since they messed up there, I highly recommend you use 
>>>>"connect" just after loading. I've added the test for between-model 
>>>>bonding in Jmol 11.3.48
>>>>
>>>>   
>>>>
>>>>        
>>>>
>>>I don't fully trust the connect mechanism in Jmol (I saw for example
>>>hydrogen atoms bonded covalently with 2 other atoms in close proximity
>>>[a single model file]). Therefore I would prefer to display the
>>>"official" bonds.
>>>
>>> 
>>>
>>>      
>>>
>>specific example, please? It's true, that if two atoms are very close 
>>Jmol doesn't apply valence rules to only bond H to one of them. After 
>>all, there are plenty of situations where H is bonded to 2 atoms 
>>(boranes, for example).
>>
>>    
>>
>
>Sorry, I don't remember the ID. I noticed it while investigating the
>"Chemical Component Dictionary" of the wwPDB and it will be difficult to
>find it again within about 7000 structures. Since I have to use bonding
>information from the dictionary in order to be able to color the bond
>types individually I didn't pay much attention to it.
>But as far as I remember it were plain C-H bonds and one of the carbons
>had five bonds because of this. And the dictionary also showed different
>bonds. (The distance of the hydrogen to the carbons was nearly identical.)
>
>  
>
Well, it would be good to find that. Something almost certainly was odd 
about the positions of the H atoms in that file.


>Regards,
>Rolf
>
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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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