Monday, June 30, 2008

Is there a program that prints out the coordinates of the grid representing surface?

I recently came across your programs that calculate solvent accessible surfaces. I am interested in a program that would print out the coordinates of the grid representing that surface. The msms program by Senner does something like that but it prints the solvent excluded surface. I briefly looked at your programs but I see that they will only output the surface, but not the grid. I wonder if you have or know where to get such a program?


It will output the entire volume grid if you specify EZD format. Which can be converted to CCP4 and is viewable in UCSF Chimera and PyMol. I would be happy to modify the program to suit your needs, if possible.

If you just want a bunch of points representing the SA surface, my program deals with volumes, not surfaces. The MSMS program outputs coordinates for triangles (texels) representing the surface. My program deals with voxels (3D pixels).

The solvent accessible solvent is actually relatively easy to generate mathematically, the solvent excluded on the other hand is quite tricky. So, if you just want a bunch of points representing the SA surface, I have a perl script that will do that by just creating a bunch of spheres (VDW + probe radius) and then asking whether or not the points are inside another sphere. This works great for SA surfaces, but not SE surfaces.

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