> Jan's observation that > > connect 1.2 2.0 HBOND (carbon) (hydrogen) > > may not have any observable effect, because HBONDS are by default > OFF, suggests that there is a more general problem with connect.
I don't believe that hbonds are off by default ... I certainly do not think that they should be off by default). (Note that the display of hbonds is distinct from the calculation of hbonds) > Specifically, what determines the displayed > radius of the bond being created? > > Answer: HBONDS 0, others: wireframe Seems like a bug. Default radius for hbonds should be the same as the default radius for wireframe. > To address this issue, I'va added an optional parameter that allows > the radius to be specified: > > connect > <min-dist> <max-dist> <type> <radius> (source set) (target set) > > All parameters are optional except (target set). If ONLY one distance > is given, and a radius is also given, that radius must follow an > explicit <type>. (Otherwise, the two numbers would be taken to be > minimum and maximum distances.) > > This is now at > > <http://www.stolaf.edu/people/hansonr/jmol/test/json/express.htm> > > > examples: > > connect 1.2 (carbon)(hydrogen) > #make single C-H bonds if < 1.2 angstroms apart > > connect 1.2 single 0.1 (carbon)(hydrogen) > #make 0.1-radius single C-H bonds if < 1.2 angstroms apart > > connect 1.2 2.0 HBOND 2 (carbon) (hydrogen) > #a 2-pixel-radius HBOND > > connect 1.2 2.0 2 HBOND (carbon) (hydrogen) > #a 2-pixel-radius HBOND > > connect 1.2 2.0 HBOND 0.01 (carbon) (hydrogen) > #a 0.01-angstrom radius HBOND > > connect 1.2 2.0 HBOND (carbon) (hydrogen) > #a default HBOND (off) > > connect 1.2 2.0 SINGLE (carbon) (hydrogen) > #a default SINGLE bond (based on wireframe) > > connect 1.2 2.0 DOUBLE 0 (carbon) (hydrogen) > #a DOUBLE bond, but not shown, because it has no radius > > Notice that there is a difference between "SINGLE 0" and "DELETE". > The first creates or modifies the bond but does not display it (yet); > the second actually removes the bond. > > Sound OK? No comment at this time. 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-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
