On 9 Oct 2006 at 7:03, Bob Hanson wrote: > 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.
OK then. So, it's just a question of different defaults for ignore and radius, not different parameter options. I can then use "isosurface ignore(solvent) molecular 1.2" if I want, right ? > 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, It is better for anyone; I don't like "solvent" since I must remember whether it means solvent- accesible or solvent-excluded. I know that you perceive it also as a "solvent" surface, but that's not (yet) intuitive to me. No problem, one has to learn the syntax and that's all. My surface doc page is still growing but I'm near the end of it. The format is sophisticated for the Wiki, so I will keep it in my server, of maybe put it into Jmol-web --opinions? how to integrate it? > and it makes no sense then to ignore water. OK > But in biomolecular work, obviously you want to ignore solvent in > the case of "solvent" and "sasurface" -- otherwise the calculation is > meaningless. Agree. > My thinking is that biomolecule-oriented applications would just stick > to "solvent" and "sasurface", because that's what is relevant there. Well --or use "ignore(solvent) molecular" :) > That make sense? Indeed. Let's hear others. > >The addition of surfaces to the pop-up menu is a great idea! > I'm thinking about a "models" menu that updates depending upon the > models. I don't know exactly what it should show, though. Tricky. The only ID I can think of are sequential numbers, not too useful. Has anyboody checked extensively the frame animation controls lately? I recall having some trouble that looked like a bug --sorry, didn't wrte it down or filed it, my fault. > >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. Suprising! If the command language imposes it, don't worry too much about fixing it. ------------------------------------------------------------------------- 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
