Monica
Also consider that there is a quite short space of min-max distance between the vertex point and the closest atom
@zeffii > Maybe use a proxy mesh, all vertices of which represent the cloud of atoms from the .pdb, the indices of the vertices will reflect the kind of atom....
@zeffii > OK, before starting to write code can you elaborate on which conditions this imposes? The surface mesh is defined as 'Solvent Excluded Surface', also called 'Connolly surface', defined...
Yes, this info is in the columns 14-15 (atom) and 18-20 (aminoacid) of the PDB file. Then there is the fi values library
If this BBinfo can be used, it might be easy to substitute the Temp factor (last 0.00, column 61-66) with fi value, and then its easy to retrieve.
If I understand the number on each atom is the fi value associated, right? If this works, I will test it on a few molecules on which the MLP is...
@zeffii > passing a maximum search radius (probably maximum vdwaals radius in the pdb) maximum search radius is = max VdW radius + probe radius
Just a sec. I am making a figure that will explain better
 Aplogies for the low qaulity of the drawing. Please note that the molecular surface defined is not by the center of the probe, but by its surface. The radius...
Hi, sorry for not follwing yesterday. I was in Bologna at ameeting , with very poor connection, barely enough to check the mail occasionally. I see there is quite some...