reformatms converts an ms file of qcpe format to an ms file of the format read by sphgen . reformatms requires a Brookhaven Protein Data Bank coordinate file as well as the QCPE ms file as input. The program is interactive.
The qcpe ms file must be in the long format: The Fortran format for this file and the information contained in it are listed below:
n1, n2, n3, shape, x, y, z, area, xn, yn, zn, buried
n1 atom number of atom that surface point is on or closest to
n2 other atom that probe touches (0 for convex)
n3 third atom that probe touches, n3>n2 (0 for convex and saddle)
shape 1: convex, 2: saddle, 3: concave
x, y, z coordinates of surface point
xn, yn, zn components of the unit vector normal
buried 0: exposed, 1: buried, blank: not determined
The lines must be sorted by n1.
The ms format that sphgen reads and the information that it contains are listed below:
(A3, I5, 2X, A3, 3(F8.3, X), X, A3, 4F7.3)
resnm, nres, atnm, x, y, z, srftag, area, xn, yn, zn
resnm residue name of the closest atom, or the atom itself (if srftag = A)
nres residue number of the closest atom, or the atom itself (if srftag = A)
atnm name of the closest atom, or the atom itself (if srftag = A)
x, y, z coordinates of the point or atom
srftag A: atom, SR0: reentrant point, SS0: saddle point, SC0: convex point
area solvent-accessible area (blank if srftag = A)
xn, yn, zn components of the unit vector normal (blank if srftag = A)