Angel Herraez wrote: >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 ? > > ignore(solvent) is fine; the "1.2" isn't allowed right now. The "1.2" refers to the solvent probe radius which, again, in my conceptualization of this as a general command, isn't always applicable. Or maybe it is; I don't know. I do want "molecular" to mean what biomolecular folks think it should mean; I made it 1.4 simply because I'm seeing that a lot more than 1.2 in current discussions. Do you have a feeling for that -- does half the world use 1.2 and the other 1.4, or is 1.2 "old school"? I just wanted a simpler alternative to "solvent [radius]" but if you think that's splitting hairs and just making it confusing, I could change the default to 1.2 and allow for "molecular [radius]".
Then the only difference between "solvent" and "molecular" would be "ignore(solvent)" and "ignore(none)" as the defaults. Would that be too confusing? > > >>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. > > > > no, it's just the way it's implemented. Obviously "color value" and "translucency" should be independent. > >------------------------------------------------------------------------- >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
