Richard, Jmol has built-in tables for formal charges. Each element/charge pair has its own vdw radius and bonding radius.
The tables are in org/jmol/viewer/JmolConstants.java If someone tries to assign a charge that it invalid then 'rolls-back' to having no charge. A reminder ... I am not a chemist and I have no personal stake in how this works. I may well have misunderstood how this is supposed to work. So if it is broken then we will fix it. > Br which attaches to the alkene should have a +1 charge, In the tables that I have, +1 is not a valid charge for Br. The valid charges for Br are -1, +5, and +7 Therefore, when you try to assign a charge of +1 to Br it will refuse to accept the charge. > and in > http://undergrad-ed.chemistry.ohio-state.edu/reactions/sn1.html the C atom > should have a +1 charge when the Cl leaves). According to my tables, C can only have charges of -4 and +4. Therefore, when you try to assign a charge of +1 to C it will refuse to accept the charge. > I have tried using various > formats for the positive charge (i.e. +1, 1+ or 1) > but none of them seem to work. The pdb specification calls for 1+, but that doesn't really matter in this case. > Any ideas on would is wrong? (All of the data files are in > http://undergrad-ed.chemistry.ohio-state.edu/reactions/) All of the support for charges was added at the request of Philip Barak. Phil may have been using it for some special purpose that may not be geneneralizable to what other people want to do. This is the second "complaint" I have heard about this in the past few months. So, it is pretty clear that we need to review this and see if we can come up with another mechanism that can avoid confusion and can prevent people from wasting time. According to the comment that I put in JmolConstants.java a year or two ago: * This data is from * Handbook of Chemistry and Physics. 48th Ed, 1967-8, p. F143 * (scanned for Jmol by Phillip Barak, Jan 2004) As I write this it occurs to me that perhaps there is some difference between "ions" and "charge" that I have misunderstood. The data that I have is for 'ionic radii' and contains radii for elements in various ionization states. As I said above, other 'ionization states' are not allowed and revert to be uncharged (I *think* this is logged to the error log). I thought that ionization state and formal charge were the same things. If you folks tell me that they are not, then you can educate me and we can change the implementation. Regardless, we need to do *something* so that people don't waste time on this and/or so that I don't have to keep explaining it. Let's keep talking. Miguel ------------------------------------------------------- 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_idv37&alloc_id865&op=click _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
