|Author||Andrew Magis, University of Florida
Developed in the Department of Physiology and Functional Genomics,
Peter Sayeski, Ph.D.
|Description||Sphere_select allows the user to select spheres in several different ways. MOL2 coordinate files can be used as inputs to select spheres around a known binding ligand, as with the original sphere_selector. Sphere_select also reads coordinate files in PDB format, and automatically detects the file format. Spheres can also be selected around a specific atom in either the MOL2 or PDB coordinate file. This is somewhat different than selecting spheres based on a ligand. In this case, the user knows or suspects a binding site, but lacks a MOL2 ligand coordinate file with which to select spheres. In this case the original PDB (or MOL2) file of the receptor can be provided as a coordinate file, and an atom can be specified around which to select spheres. The atom number exists in column 1 of the TRIPOS MOL2 format and column 2 of the PDB file format. Finally, the user can specify a specific sphere around which to select other spheres. In this case the coordinate file is ignored. This might be useful in a situation where the user knows or suspects a binding site that has been populated with spheres, and simply picks a sphere in approximately the correct place to select a group of spheres for DOCKing calculations.|
|Platform||Linux CentOS 4.1, Solaris, Cygwin (Windows linux emulator)|
|Instructions||included in download|
|Added code to site||08-01-06|