> I have just been at the ABINIT group - very nice to see another active > opensource group in action. I commended Jmol to them (of course some of > them already use it as it can read some abinit output.)
I do not think that Jmol v10 can read abinit output yet. > One topic was tools for displaying isosurfaces (3D contours) or (say) > charge density, etc. overlaid on atoms. Is Jmol able to (a) produce (b) > display isosurfaces? The short answer is ... No, not yet. The longer answer is ... isosurfaces has been one of the 'untouchable' areas for me because it was specifically listed on an NSF grant that I applied for. However, given that I learned last week that the grant was turned down, I am now free to work on these things. This week I have been working on ribbons. The ribbons are curved surfaces that require shading/lighting calculations. So, in some sense, they provide foundation work for iso-surfaces. Regarding 'production' of iso-surfaces ... Jmol can properly calculate a solvent-accessible-surface using vdw radii a probe sphere. This can be seen today using the 'dots' display. The protein folks would like to see this rendered as a real surface with charge coloring. But this is not really an isosurface that is defined by a mathematical model. Q: Is this the kind of surface that you want, or do you have a 'field' that is defined by a mathematical equation? It would be helpful for me to understand what types of isosurfaces (what shapes) you and others (including the abinit crowd) are interested in. ... I am going to need some tutoring. Miguel ------------------------------------------------------- This SF.Net email is sponsored by: SourceForge.net Broadband Sign-up now for SourceForge Broadband and get the fastest 6.0/768 connection for only $19.95/mo for the first 3 months! http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
