Sorry, Frieda. That's my fault. It's just that this is precisely what I am working on right now, so you will see a few changes along the way. One change I just made -- comments appreciated -- involves solvent/sasurface/molecular distinctions and default values. The idea here is that if you say "isosurface solvent" or "isosurface sasurface" most likely you do NOT want to include file-designated solvent molecules within the surface. So for those two I have made "ignore(solvent)" implicit. -- You can certainly override that if you really want to include water by adding "ignore(none)"
I was playing with my new planar slice option along with clipboard clipping from the application -- perhaps these graphics will clarify the issue somewhat: http://www.stolaf.edu/academics/chemapps/jmol/docs/img/isosurface-options.jpg http://www.stolaf.edu/academics/chemapps/jmol/docs/img/isosurface-solvent.jpg http://www.stolaf.edu/academics/chemapps/jmol/docs/img/isosurface-vdw.jpg PROPOSED DEFAULTS: isosurface molecular -- a fairly slow calculation because of the smoothing -- no atoms ignored -- maps the van der Waals surface with some smoothing at atom junctions -- "smoothing" probe radius defined 1.4 Angstroms isosurface solvent [radius] -- a fairly slow calculation because of the smoothing -- defaults to ignore(solvent), but you can ignore(none) to override this -- maps the van der Waals surface with some smoothing at atom junctions -- uses a default radius of whatever is defined by "set radius" which defaults to 1.2 Angstroms -- using radius 0 gives a very fast calculation of the surface at the van der Waals radius with no smoothing isosurface sasurface [radius] -- a very fast calculation -- defaults to ignore(solvent), but you can ignore(none) to override this -- maps the (van der Waals + radius) surface with no smoothing at atom junctions -- defaults to 1.2 Angstroms beyond the van der Waals radius -- using radius 0 gives the surface at the van der Waals radius ("molecular" but with no smoothing) Note that the two: isosurface solvent 0 isosurface sasurface 0 produce identical results. I don't think these changes made it into 10.9.72, but expect them in 10.9.73 -- unless arguments can be made for different default values. Bob ------------------------------------------------------------------------- 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
