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%". 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. > (without necessarily doing any rendering of such). Why not? It is the calculation that takes time, not the rendering, isn't it? A little research into what other programs do: == 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). == 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. == 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. == 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 http://biomodel.uah.es/pruebas/jmol/surface/inicio.htm _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
