Bob Hanson wrote: >Angel, I took a look at this, and I did make an update that at least >colors dots properly. So 10.9.47 has that in it. But as I was doing >that, I found that the dots ON/OFF business is a bit complicated. If we >want dots OFF to work like labels and such, then it will take some >reworking. There is a single "ON/OFF" flag for all dots. I like the idea >of changing this to specific atoms, but we need to be sure that's what >people want. > >Q: Anyone object to having DOTS turn on and off in response to the >currently selected set of atoms? > > I checked different versions of Jmol (>=10.00). From 10.00 until at least 10.00.36 Jmol only switches off the dots of selected atoms, not all. This was changed somewhere between 10.00.36 to 10.00.47 (I don't have any version in between).
I would expect that the 'dots' command considers the current selection and would rather like this change to be reverted. >Q: When this is done, should the dot set be recalculated so that places >where there was overlap with now-invisible atoms are filled in? Or >should there be no additional calculation and only dots that were >present before present after? > I think both options would be useful. Before you stated otherwise a few mails ago, I just took the 'dots' rendering as a kind of transparent spacefill rendering. For this purpose a recalculation would be needed. >Q: Should the presence of dots and no other aspect of an atom count as >"visible" for that atom? That is, if: > > restrict 1-10; wireframe off;spacefill off; dots on; > >would you then expect > > select visible > >to include all residues 1-10? > > > Generally I would expect any rendering type, including dots, to be considered for visibility. Maybe, if this would be easily possible, you could make the renderings that affect the visibility flag configurable by a script command. Regards, Rolf ------------------------------------------------------------------------- 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 [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
