Dear all, I am drawing the SOLVENT isosurface around a protein, and used the MAP keyword to colour using a cube file which consists of a grid over the active site with values for the 'depth' from the protein 'surface' (i.e. deep within the active site, the SOLVENT isosurface should be blue, and closer to the surface, it should be red).
So far, so good. In fact, so far so very good - I didn't think it would work, as I thought there would need to be an explicit 1:1 correspondance between the points on the SOLVENT isosurface and the points in my cube file. I was very impressed by the result. However, I am unsure as to how Jmol assigns the colors to the SOLVENT isosurface for points which are outside the cube file. Looking at the results, I assume it is doing some sort of interpolation (I should say extrapolation really) based on the nearest grid points, despite these grid points being very far away. My preferred behaviour would be for Jmol to not show the SOLVENT isosurface for points which are not within my cube file. What do you think? I know that conceptually the MAP is only supposed to provide colors, but I don't think it is sensible to allow Jmol to guess the colours for points outside the grid. These are practically guaranteed to be incorrect, and worse, misleading (as Jmol doesn't complain that some isosurface points are outside the MAP). Regards, Noel ------------------------------------------------------------------------- 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
