[Chimera-users] chimera and hydrophobic potentials

Thomas Goddard goddard at cgl.ucsf.edu
Thu Apr 8 11:22:35 PDT 2004

Hi Miguel,

  The only Chimera tool for coloring a molecular surface using data values
from a 3 dimensional grid is the DelphiViewer extension.  It can read
Delphi and GRASP grid files.  As you say the GRASP format requires the
grid size to be 65x65x65.  The Delphi format which is almost the same
allows any grid size but apparently GRID cannot produce that format.

  To determine if a GRASP grid is covering your molecule, open it in
Chimera with File/Open using file type "Delphi or GRASP potential".
This will display an isosurface and a white bounding box showing the
extent of the grid.  You can open your molecule and visually see how well
it covers.

  Chimera can read several other volumetric data formats (CCP4, MRC,
CNS, XPLOR, SPIDER, DOCK, PRIISM, ...) but these cannot be used to
color an MSMS surface.  You can display isosurfaces, or translucent
solid representations with the Volume Viewer tool.  I don't know
if any of the GRID output formats for Chem-X, Frodo, Insight, Molcad
Quanta or Sybyl are equivalent to any of the formats Chimera knows.

  We are interested in making it possible to color an MSMS surface
using any of the volumetric data formats Chimera can read.  I could
add something to Chimera that does this.  But it looks like it would
also be necessary to add some file reader for some format that GRID

  I saw that GRID has a K2A program that outputs the grid data in ascii.
A relatively simple program might convert that to Delphi format for use
with the current Chimera DelphiViewer extension.


More information about the Chimera-users mailing list