Investigation of the unforseen hbond interactions has led me to the conclude that for the 10.1 release we should not allow the creation and deletion of hbonds using the 'connect' command.
In addition, we will roll back the default display behavior ... which is to *not* display hbonds even if they are present in the .pdb file. I believe that this is best the Jmol installed-base because it does not introduce incompatibiilities for existing scripts and does not break the expected behavior for current Jmol users. We will figure out the interactions and come up with a plan after the 10.1 release. The only other alternative that I see would be to remove the 'connect' functionality entirely from the 10.1 release. Bob fixed an hbond calculation bug that is included in the 10.1 release. More details on this is below. Miguel ========== The following hbond-related bug fix is included in the 10.1 release. It was originally r4556 and r4557. This was reintroduced in r4848: NOTE: the log entry for 4848 is incorrect ... the numbers were r4556 and r4557 [EMAIL PROTECTED] viewer]$ svn log -r 4848 ------------------------------------------------------------------------ r4848 | migueljmol | 2006-03-30 12:45:45 -0500 (Thu, 30 Mar 2006) | 5 lines reintroduced hbond calculation fixes done by Bob in r4456 & r4457 Note that these patches contained other changes that were not related to hbond calculations ------------------------------------------------------------------------ [EMAIL PROTECTED] viewer]$ [EMAIL PROTECTED] trunk200603]$ svn log -r 4556:4557 ------------------------------------------------------------------------ r4556 | hansonr | 2006-03-08 16:22:38 -0500 (Wed, 08 Mar 2006) | 2 lines fix for too long hydrogen bonds ------------------------------------------------------------------------ r4557 | hansonr | 2006-03-08 21:25:08 -0500 (Wed, 08 Mar 2006) | 6 lines fixed error in RasMol HBond calculation. (N-H bond was being calculated 25% too long as the C-O distance instead of the RasMol 1.0 Angstroms). ------------------------------------------------------------------------ [EMAIL PROTECTED] trunk200603]$ ========== The problems with hbond calculations are summarized as follows: * the 'hbonds' command is used to control display of hbonds AND to control the calculation of hbonds * the secondary structures (helix & sheet determination) can also trigger calculation of hbonds * adding 'connect hbond' and 'connect delete hbond' introduced other interactions * displaying hbonds with a default of 1 pixel has the undesired impact of showing the hbonds after secondary structures are generated. ========== ------------------------------------------------------- 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
