psiblast.pl

Usage

usage:   psiblast.pl [options] [seqFile]
options:             [-nr] [-pdb] [-db name]
                     [-eshow value] [-ekeep value]
                     [-n alignments] [-i iterations]
                     [-gap initial extension]
                     [-matrix BLOSUM45|BLOSUM50|BLOSUM62|BLOSUM80|PAM250|PAM70|PAM30]
                     [-verbose] [-log file]
                     [-readlog file] [-no value]
                     [-csblast]

Show source

Description

Options

-help: usage information

Examples

mutate.pl -seq 10:ADEF 1vii.exp.min.pdb
mutates residues 10 through 13 from VFGM in the original structure to ADEF.

ATOM      1  N   MET     1       3.075  -9.691  -2.062  0.00  0.000         
ATOM      2  CA  MET     1       1.835  -9.001  -2.351  0.00  0.000         
ATOM      3  C   MET     1       0.889  -9.260  -1.188  0.00  0.000         
ATOM      4  O   MET     1       0.838 -10.371  -0.644  0.00  0.000         
ATOM      5  CB  MET     1       1.181  -9.487  -3.654  0.00  0.000         
ATOM      6  CG  MET     1       1.921  -9.123  -4.938  0.00  0.000         
ATOM      7  SD  MET     1       1.107  -9.774  -6.420  0.00  0.000         
ATOM      8  CE  MET     1       0.002  -8.437  -6.776  0.00  0.000         
ATOM      9  N   LEU     2       0.128  -8.242  -0.786  0.00  0.000         
ATOM     10  CA  LEU     2      -0.806  -8.363   0.321  0.00  0.000         

...