chimera and hydrophobic potentials
Hi, I would like to display the hydrophobic potential of a protein onto its MSMS surface. One program that calculates such potentials is GRID (from Molecular Discovery: http://www.moldiscovery.com/ ) GRID can produce the map in different formats. One of them is like delphi (grasp mode) map. This has the drawback that the map has to be 65x65x65 grid points and the grid points separation has to be an integer starting with 1 Ansgtroem. Hence, it's not appropriate for medium-big proteins. The GRID format hasn't those limitations. I can __sometimes__ read in chimera (throught the DelphiViewer) the delphi maps produced by GRID. Sometimes they are unreadable (and this seems to me more a problem with GRID than with chimera: something wrong in the header) But even when they are readable I'm not sure they are covering the region they are supposed to be covering. Does anyone know if chimera can read any other of the GRID map formats: GRID (this would be the optimal) Chem-X Frodo Insight Molcad Quanta Sybyl Otherwise: does anybody how to the kind of representation I'm looking for in any other way? Thank you for any advice! Miguel -- Miguel Ortiz Lombardía email: mol@ysbl.york.ac.uk http://www.ysbl.york.ac.uk/~mol ----------------------------------------------------------------------- Our business in life is not to succeed, but to continue to fail in good spirits. R.L. Stevenson
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 produces. 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. Tom
participants (2)
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Miguel Ortiz Lombardía -
Thomas Goddard