Sorry --- it was on another list. That should have read: For the generation of isosurfaces, Jmol can now (11.1.18) read three-dimensional scalar data from two formats:
CUBE files created using Gaussian's CubeGen program (molecular orbitals) http://local.wasp.uwa.edu.au/~pbourke/dataformats/cube/ "multigrid" OpenDX files created using APBS (Adaptive Poisson-Boltzmann Solver, MEP - molecular electrostatic potential) http://apbs.sourceforge.net/doc/user-guide/index.html#opendx-format Both of these formats define a three-dimensional grid of points in space. At each point is a number (a "scalar value"). This set of point values is then used by Jmol to define an "isosurface" -- the surface separating points having values greater than a given cutoff from those that have a value less than a certain cutoff. A typical application is molecular orbitals. The PHASE parameter of the ISOSURFACE command allows bicolor rendering -- one color for "points greater than x" and another color for "points less than -x". Generally a MEP data set is not used for the isosurface itself. Rather, it is used to map color onto another isosurface, usually some representation of the "molecular surface". In addition, Jmol can read and write JVXL files (Jmol Voxel Format) http://www.stolaf.edu/academics/chemapps/jmol/docs/misc/JVXL-format.pdf These files represent a SINGLE mapped or unmapped isosurface. They can be remapped with color, but they cannot be used to generate OTHER isosurfaces. Examples: Molecular orbital contained in the loaded file load "myfile.spartan" select * isosurface MO 3 # only the selected atoms MO 3 # same thing, but all atoms and not so many options, such as you get ONE per file Writing and loading JVXL files (from the app): write isosurface "myfile.jvxl" isosurface delete isosurface "myfile.jvxl" isosurface delete isosurface colorscheme rwb "myfile.jvxl" [I see there is a bug in not being able to use "reverse" in a JVXL context -- I will fix that.] Bob Angel Herraez wrote: >I'm afraid I missed the original message, but this sound interesting. >Can anyone explain what a DX file is? > > > >------------------------------------------------------------------------- >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 >[email protected] >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 [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
