Re: [Jmol-users] Aromatic Bond Tests - 11.3.30

[Bob H. <ha...@st...>]

Jmol 11.3.31:

O=S and O=P are now in; N=C should also be fixed when N and C are both 
trivalent and not doubly bonded;

Bob


Rolf Huehne wrote:

>Bob Hanson wrote:
>  
>
>>Wow, I didn't know about that site. I like it!
>>
>>Thanks VERY much, Rolf. I'm pleased that so many were right on target. 
>>My goal at this point is to do what it looks like we've achieved -- 
>>generally correct structures given the data present in the file.
>>
>>Rolf Huehne wrote:
>>
>>    
>>
>>>Entries with differences:
>>>
>>> http://remediation.wwpdb.org/pyapps/ldHandler.py?query=017
>>>   Dictionary: Sulfur 2 non-aromatic double bonds to 2 oxygens
>>>   Jmol      : Sulfur 1 double, one single bond
>>>
>>> 
>>>
>>>      
>>>
>>Of course, there's even debate in the community whether those double 
>>bonds belong there or not. That's a story unto itself. But one can 
>>certainly lock those in, I think with a simple select/connect double 
>>sequence. Should this be part of the algorithm? Should we let the user 
>>worry about that? It's a simple command:
>>
>>select _S or _O and connected(1);connect double modify
>>
>>I would only want to implement that if it's a sure bet.
>>
>>    
>>
>
>I am a biologist and not a chemist. So it is not up to me to decide
>that. I just wanted to point out the differences and get a general idea
>of the quality of the data in the "Chemical Component Dictionary" before
>we integrate it into the "JenaLib".
>
>  
>
>>So those are great tests. I'd like to see what some nitroso and nitro 
>>compounds look like as well.
>>
>>    
>>
>
>The following three examples don't show any differences:
>
>  http://remediation.wwpdb.org/pyapps/ldHandler.py?query=NBE
>  http://remediation.wwpdb.org/pyapps/ldHandler.py?query=LMZ
>  http://remediation.wwpdb.org/pyapps/ldHandler.py?query=NW1
>
>In the next example Jmol shows the nitro group with 2 single bonds while
>the dictionary shows 1 non-aromatic double bond and 1 non-aromatic
>single bond:
>
>  http://remediation.wwpdb.org/pyapps/ldHandler.py?query=BIQ
>
>Regards,
>Rolf
>
>-------------------------------------------------------------------------
>This SF.net email is sponsored by: Splunk Inc.
>Still grepping through log files to find problems?  Stop.
>Now Search log events and configuration files using AJAX and a browser.
>Download your FREE copy of Splunk now >> http://get.splunk.com/
>_______________________________________________
>Jmol-users mailing list
>Jmo...@li...
>https://lists.sourceforge.net/lists/listinfo/jmol-users
>  
>


-- 
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