Angel Herraez wrote: >On 8 Oct 2006 at 21:22, Bob Hanson wrote: >[snip] > > >>PROPOSED DEFAULTS: >> >>isosurface molecular >> >>-- a fairly slow calculation because of the smoothing >>-- no atoms ignored >> >> > >I find it easier to handle that all three have the same default, i.e. >ignore(solvent). No need to >remember different defaults. If one wants to start specifying things, >"solvent" should be used. > > > >I assume that "isosurface molecular" is a convenient quick command. Is should >take no- >options (if it also accepts "ignore" we get complicated). > > > all isosurface commands need to take all options in the sense of other keywords, I think. So I'd rather not start using logic like "if this is 'isosurface molecular' command, then don't allow 'ignore'." That starts to be exceptionally complicated when notifying a user of errors.
I added "molecular" because there are wider applications of this than biomolecular work, where "solvent" makes no particular sense -- as in inorganic and organic crystallography. There it seemed to me that "molecular" was a better term, and it makes no sense then to ignore water. But in biomolecular work, obviously you want to ignore solvent in the case of "solvent" and "sasurface" -- otherwise the calculation is meaningless. My thinking is that biomolecule-oriented applications would just stick to "solvent" and "sasurface", because that's what is relevant there. That make sense? >Therefore, I propose > >isosurface <ID> molecular = isosurface <ID> ignore(solvent) solvent 1.4 > > >(BTW, something is wrong with >http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/isosurface.htm >Iam getting an empty page since yesterday) > > > right -- fixed. >The addition of surfaces to the pop-up menu is a great idea! > > > People who use molecular orbitals are in for a real treat -- the menu updates to display all orbitals in highest to lowest energy order depending upon which model is selected. I'm thinking about a "models" menu that updates depending upon the models. I don't know exactly what it should show, though. One problem I see is that, at least on a PC, the menu doesn't seem to smartly scroll. Is this a Swing option I'm missing? >I find that changing color via Color > Surface forces opauqe color, removes >previous >translucency; it should not. > > > yes, I saw that, too, and I don't know a way around it. These should be independent things, but "color orange" involves an implicit "color opaque orange" -- I'll see what I can do. >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys -- and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
