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. > http://remediation.wwpdb.org/pyapps/ldHandler.py?query=033 > Dictionary: all rings aromatic, > Sulfur 2 non-aromatic double bonds to 2 oxygens > Jmol : only 1 carbonyl double bond (others all single) > > > 11.3.31 added O and S support for furans and thiophenes. So when I load this one using load "http://remediation.wwpdb.org/data/0/033/033_ideal.pdb"; select *;connect aromatic modify;calculate aromatic It looks OK, except for the single bond to O for S. > http://remediation.wwpdb.org/pyapps/ldHandler.py?query=062 > Dictionary: 3 double bonds in the heteroaromatic ring > (double bond between N1/C2) > Jmol : only 2 double bonds in the heteroaromatic ring > > > Pyridine N-oxides would need formal charge +1 on the N. If that is done, then the bonding should be fine: load "http://remediation.wwpdb.org/data/0/062/062_ideal.pdb"; select *;connect aromatic modify;select (*.N1 or _O);connect single modify {*.N1}.formalcharge=1 This is using 11.3.31 capability now for setting that formal charge. In principle we might be able to fit this into the algorithm. Is it worth it? Is there a simple rule? > http://remediation.wwpdb.org/pyapps/ldHandler.py?query=107 > Dictionary: see http://www.fli-leibniz.de/ImgLibPDB/tmp/107-dict.png > Jmol : see http://www.fli-leibniz.de/ImgLibPDB/tmp/107-jmol.png > > This again is the thiophene issue. Jmol does all the aromatic bonding correctly in 11.3.31. command: load "http://remediation.wwpdb.org/data/1/107/107_ideal.pdb"; select *;connect aromatic modify;calculate aromatic So those are great tests. I'd like to see what some nitroso and nitro compounds look like as well. The question is whether we want to add some logic to the algorithm for SO2 groups to have them be automatically shown as O=S=O. My guess is that it doesn't matter. What do you think? And pyridine N-oxides and nitro groups are additional special cases. That's a bit tricky. Again, is it worth it? Or is it acceptable to leave it to the user to define formal charges to force those issues? What a great database! Bob -- 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
