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 >[email protected] >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 ------------------------------------------------------------------------- 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 [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
