The dots not changing color is certainly a bug that will be fixed in 10.9.47 (later today).
As for the action of restrict, this is intentional. (That is, a feature, not a bug.) Let's discuss what we really mean by dots. Here's the deal: Note that dots do not simply surround an atom. They take into account neighboring atoms. Thus, unlike spacefill, dots are not just "displayed", they are the result of a rather complex calculation -- essentially the solvent-accessible-surface calculation. (They are not quite the solvent-accessible surface, because they do not take into account all the other atoms around the selected set. "isosurface sasurface" takes this into account, but "dots" does not. In fact, "select *;dots +1.2" IS the solvent-accessible surface.) (Oh, I do so hate "restrict"!) I'll look into whether restrict could properly restrict to part of the dot surface, but the thinking on the part of Miguel and me up until now is that since dots depend upon neighbors, and restrict changes neighborhoods, dots should be completely removed if a restrict command is given. The basic problem is that the following two will be different (which might be OK): select *; dots on; restrict (atomno < 10); # this would be a partial surface, like the action of sasurface? restrict (atomno < 10); dots on; # this would be a continous surface around those atoms. Bob > First, any restrict command (including "restrict not none" and "restrict > all", which do not affect any renderings that I know of except dots) hides > ALL dots. It seems to me that using "restrict" to hide a subset of atoms > should not hide ALL dots -- it should hide dots only for the set hidden -- > just as it does for spacefill, etc. > > Second, "dots off" hides ALL dots, even when preceded with "select none". > > Working around these bugs in FirstGlance in Jmol has required adding a lot > of messy javascript. It would be great to have them fixed! > > Thanks, -Eric > > > ---- > Eric Martz, Professor Emeritus, Dept Microbiology > University of Massachusetts, Amherst MA US > http://www.umass.edu/molvis/martz > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
