Hi all, I tested the new aromatic bond computing capabilities of Jmol 11.3.30. For the tests I used several entries of the "Chemical Components Dictionary" available at the wwPDB (converted from mmCIF to CIF format, since Jmol cannot read the entries directly).
Another related observation first: "select ISAROMATIC" always selected all atoms In Jmol the following command sequence was applied to each entry to manipulate the aromatic bonds: select *;connect aromatic modify; calculate aromatic; The original single/double aromatic/non-aromatic bond annotation from the mmCIF files was used to build a script coloring aromatic bonds purple and setting them specifically to "aromaticSingle" or "aromaticDouble". Entries without any differences (besides the choice of double bond position inside rings): http://remediation.wwpdb.org/pyapps/ldHandler.py?query=003 http://remediation.wwpdb.org/pyapps/ldHandler.py?query=008 http://remediation.wwpdb.org/pyapps/ldHandler.py?query=039 http://remediation.wwpdb.org/pyapps/ldHandler.py?query=041 http://remediation.wwpdb.org/pyapps/ldHandler.py?query=042 http://remediation.wwpdb.org/pyapps/ldHandler.py?query=047 http://remediation.wwpdb.org/pyapps/ldHandler.py?query=061 http://remediation.wwpdb.org/pyapps/ldHandler.py?query=072 http://remediation.wwpdb.org/pyapps/ldHandler.py?query=073 http://remediation.wwpdb.org/pyapps/ldHandler.py?query=084 http://remediation.wwpdb.org/pyapps/ldHandler.py?query=094 http://remediation.wwpdb.org/pyapps/ldHandler.py?query=112 http://remediation.wwpdb.org/pyapps/ldHandler.py?query=143 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 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) 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 http://remediation.wwpdb.org/pyapps/ldHandler.py?query=075 Dictionary: Sulfur 2 non-aromatic double bonds to 2 oxygens Jmol : Sulfur 1 double, one single bond http://remediation.wwpdb.org/pyapps/ldHandler.py?query=093 Dictionary: Sulfur 2 non-aromatic double bonds to 2 oxygens Jmol : Sulfur 1 double, one single bond 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 ---- Test System ---------------- Jmol: 11.3.30, application Java: 1.5.0_12 OS : Linux, OpenSuSE 10.2 --------------------------------- 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
