A few more questions on the same topic: 1. Are "isosurface vdw 1.4" and "set solventProbe 1.4; isosurface molecular" exactly the same thing?
2. What I need is the locus of points at a distance of vdw(X) + 1.4 Angstroms of at least one atom X and at least as large as vdw(Y) + 1.4 Angstroms for any atom Y. I think that's the usual definition of the "surface accessible area", but I may be wrong. Are the two commands suggested, namely "isosurface vdw 1.4" and "set solventProbe 1.4; isosurface molecular", compatible with the above description? 3. I have a pqr file which contains the radius of each atom in the molecule. Is it possible to replace vdw(atom) + 1.4 with radius(atom) + 1.4, where each atom can have a different radius? Note that atoms at different positions in the molecule can have different radii, even if they have the same atomic number. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
