Bugs item #1292907, was opened at 2005-09-16 09:40 Message generated for change (Comment added) made by migueljmol You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1292907&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: File Input/Output Group: None >Status: Closed >Resolution: Fixed Priority: 5 Submitted By: Nobody/Anonymous (nobody) Assigned to: Miguel (migueljmol) Summary: CML file "formalCharge" read incorrectly Initial Comment: see http://www.stolaf.edu/people/hansonr/jmol/test/aceticacid.cml which is a hacked up cml file with formalCharge atom attributes. Something is very strange there -- only some charges are read, and then even for the same charge differently for different atoms in the collection. Bob Hanson ---------------------------------------------------------------------- >Comment By: Miguel (migueljmol) Date: 2005-12-17 11:00 Message: Logged In: YES user_id=1050060 fixed in 10.00.45 charges are no longer verified ---------------------------------------------------------------------- Comment By: Miguel (migueljmol) Date: 2005-11-28 10:59 Message: Logged In: YES user_id=1050060 Formal charges are checked for validity. For example, -3 is not a valid formal charge for Carbon. See the formal charge data structures in JmolConstants.java If an invalid formal charge is presented then Jmol will assume no charge. I am not sure that this is the *best* behavior, but it is all that I could come up with. I have no data for what a ficticious -3 C would look like in terms of bonding radius and vdw radius. If you have any ideas/info about this then let me know. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1292907&group_id=23629 ------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
