(resending was too big >40kb) Hi,
----- Ursprüngliche Mail ----- Von: "Robert Hanson" < [email protected] > An: [email protected] Gesendet: Mittwoch, 24. November 2010 19:02:53 Betreff: Re: [Jmol-users] obj surface files exported from pymol > Alexander, > > Glad to hear it is that simple. I do think you should report it as a > bug to PyMol, that they are outputting surface data that depends upon > model rotation. Does it also depend upon zoom?? That seems rather > inappropriate to me. It depends on rotation, but not on zoom - would be funny though. I filed a bug report, but got no answer yet. > in Jmol, the following gets you there: > > load xxxx.pdb > isosurface OBJ xxxxx.obj offset @{ {*}.xyz } nice and works it also after loading isosurface ID "foo" OFFSET { 1 1 1 } that was possible all along, right? but not documented > That is, move the isosurface to the protein, not the protein to the > isosurface. > > It should be interesting for you to compare PyMOL's surfaces to > Jmol's. I don't think that's ever been done. From what I can see, the > closest to that in Jmol would be > > isosurface select {protein} ignore {not protein} molecular > > that is, a surface at the van der waals radius that is a rounded out > form of > > isosurface select {protein} ignore {not protein} sasurface 0 > > But they aren't exactly that, either, so perhaps PyMOL is adding > hydrogen atoms first, then doing the calculation? no, definitely not > I have no idea how PyMOL creates the troughs for the molecular > surfaces. Anyway, it's not a typical solvent-accessible surface, which > would be considerably larger. I did not thought much about it when I named my file with 'sas' for solvent-accessible surface, sorry for the confusion > What's the PyMOL command that gives this? > I guess you showed me the PyMOL command -- show surface. > > http://www.pymolwiki.org/index.php/Surface says that's the Connolly surface. > I don't believe it, though. It's too rounded. It must be a molecular surface > with troughs. > Actually, I think the troughs are a bit better than Jmol's. Jmol's are a bit > deep. you guessed right, it's PyMOL> show surface with the default solvent radius of 1.4 A it looks to me like the solvent-excluded surface ( = Connolly surface ???) PyMOL> set surface_solvent, 1 PyMOL> set solvent_radius, 1.4 this is the solvent-accessible surface I'll look some more into it when I have time and report back. Alex ------------------------------------------------------------------------------ Increase Visibility of Your 3D Game App & Earn a Chance To Win $500! Tap into the largest installed PC base & get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
