reformatms

Author: Renee DesJarlais

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:

 

(3I5, I2, 3F9.3, 4F7.3, I2)

 

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

area solvent-accessible area

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)

UC Regents 1998
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