Thanks, Angel, comments below.
Angel Herraez wrote: >El 15 Jun 2006 a las 17:41, Bob Hanson escribió: > > >>Yes, well, now that I'm more informed as to what a "solvent-accessible >>surface" really is, I see that what I have been calling such is really >>the "molecular surface", and that the "solvent-accessible surface" is >>really a FAR easier thing to depict and work with. >> >> > >I'm not an expert in this, just finding out the definitions. I will >summarize to check that I got things right. It seems that: > >1.- solvent-accesible surface ~= VdW surface expanded by probe >radius. I see why Bob says this is easy to do; we already have >"spacefill N%", and I had never tried, but N>100 is allowed; so, what >is needed is to calculate 100%+2R for each element; by default R is >1.2 (or 1.4 in other programs). It would also be interesting to have >"dots N%". > > > I think the real issue isn't visualization. That's trivial. What people are interested in is calculated measures -- atomic volumes, surface areas, etc. >2.- solvent-excluded surface =? molecular surface ~= surface >reached by the probe center. Unlike the former, this is a smooth >surface (i.e no sharp corners) --what we see with the new "isosurface >solvent" in Jmol. > > > >>1) Should I change the rhetoric in documentation and web pages to >>refer >>to this thing we have worked so hard to calculate as the "molecular >>surface"? >> >> > >That makes sense. Rasmol 2.7.3.x has new "surface molecule" and >"surface solvent" commands, defined as SES and SAS. Although the >result is not quite the same as Jmol new surface (more on this >below). > > > >>2) Should we also depict the true solvent-accessible surface? >> >> > >If easy to do, that will be fine. To me, it is of no use, though. >What I am interested in is a nice-looking surface that simplifies >protein shape and gives the user an idea of the "real" shape and >contact surface; that is, SES. > > > >>3) What format for output would be desireable if we wanted to, say, >> show calculation solventAccessibleSurface >> >> > >I would say any format that can be read back and rendered by Jmol. >Another business,so it seems, is the measurement of such a surface, >which has analytical value but is difficult and time-consuming. >That's for specialist users. > > > This would be a tabulated numerical set of data -- like for a spreadsheet, not for Jmol. >>(without necessarily doing any rendering of such). >> >> > >Why not? It is the calculation that takes time, not the rendering, >isn't it? > > > The point is that I was asked for a "report" format, not rendering. So that's what I'm asking about here. Again, the rendering part is not such a big deal -- especially if dots suffice (That's done, essentially, we just have to show the dots at solvent center instead of at the VDW radius. I think I could do that in 30 minutes. >A little research into what other programs do: > > > this is VERYMUCH appreciated! >== Chime == >(but not Rasmol 2.6) renders rather wonderful surfaces, quite similar >to Jmol isosurfaces, pretyy quickly. The command is "surface <name> ><color> <spacing> <radius> <smoothing>". It is poorly documented. >Default probe radius is 1.4, despite being 1.2 for "set solvent on; >dots on". Semitransparency allowed (similar to Jmol "translucent" in >other elements). > > Can Chime do this for, say, a 20kD protein? What's its practical limit? >== Rasmol 2.6 & 2.7.x, Chime and Jmol 10.0-10.2 == >"set solvent on; dots on" generates dot "surfaces" which look as SES >(smoothed corners). Dot density is customizable. > > > right, same as Jmol but a bet better, probably. >== Rasmol 2.7.3 == >All defined as "Lee-Richards moelcular surfaces": > >"surface molecule <radius>", defined as SAS. Generates (time >consuming to calculte but especially to move around) smooth surfaces, >although less smoothed than Jmol or Chime. Radius value is required. > >"surface solvent <radius>" , defined as SES. Generates (fast) >cornered surfaces, with a >100% VdW aspect. Radius value is required. > > > Do you have SAS and SES reversed there? "solvent-accessible" should be the one with the sharp corners and the surface at VWD+1.4. "solvent excluded" I think is >== RasTop 2.0 - 2.1 == >(a Windows GUI for Rasmol, with some extra functionality) >Defines "complete Richards - Connolly surfaces". Present in the menu, >not in the command language, as "Connolly"; uses "set solvent on; >dots on", hence is rendered only as dot surfaces, like in >Rasmol/Chime. Dot density and dot size is customizable. > >Screenshots at >http://biomodel.uah.es/pruebas/jmol/surface/images.htm > > This is wonderful! Thank you. I can tell you right now that the "surface molecule 1.2" is bogus. It's just a fake. There should be no sharp edges whatsoever. No way is this a molecular surface. Jmol is better! Same goes for "surface solvent". Chime is more believable. I'm quite impressed with those surfaces and the speed. Be interesting to se what these would look like with JVXL. >http://biomodel.uah.es/pruebas/jmol/surface/inicio.htm > > This must be 10.2, right? because it's got the gaps. Please try this in 10.x.14 and tell me what you think. See http://www.stolaf.edu/people/hansonr/jmol/test/proto/isosurface.htm; click "load any PDB file" and choose 1HEL. then restrict protein;set solvent on;dots the yellow dots are the ones missing in 10.2, pretty much. for the 10.x.14 SES right now, either: restrict protein;set solvent on;dots;set testflag3 or isosurface solvent except that has computational limitation issues, I think. Looks like a crash -- but it's just working. Bob >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
