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
