I have a pretty good understanding of what sequence of events is causing the undesirable hbond behavior that we are observing.
It is not clear to me how to resolve the issue, so I would like your thoughts/assistance. The 'hbonds' command is used both to set the size of hbonds *and* to calculate hbonds. Prior to the introduction of 'connect hbonds ...' hbonds were either author-provided in the file or they were calculated. In addition, since there was no way to delete hbonds, once they were calculated the system thought that it never needed to calculate them again. (It isn't clear to me whether or not the 'hbond calculation' code was ever properly respecting the author-supplied hbonds ... I have not looked back that far.) The introduction of 'connect hbond ...' gave us a new way to create hbonds. When we set the size on an hbond, the hbond calculation code is being run because it has never run before. Once the hbond calculation code has been run, it will never run again ... even if we do a 'connect delete hbond ...' because the hbond code does not currently know that hbonds can be deleted. My thoughts: * we need to separate hbond size control from hbond autocalculation * doing so will break compatibility with existing scripts that use 'hbond on' run the hbond autocalc code * it doesn't seem to me that this will be much of a problem for many people ... but I don't really know * it seems to me that this should be something like 'hbond calculate' ... or something similar. * this would be distinct from 'hbond on/off/<size>' ... which would only affect the display of current hbonds Thoughts/feedback/assistance appreciated. Miguel ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid0944&bid$1720&dat1642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
