Difference between revisions of "dihed.pl"

Latest revision as of 02:47, 28 July 2009

Usage

usage:   dihed.pl [options] [refPDB [cmpPDB]]
options: [-l min:max[...]]
         [-list phi|psi|chi1|chi2|chi3|chi4|chi5|omega]
         [-atoms [chain]res:name [chain]res:name [chain]res:name [chain]res:name

Show source

Description

This script calculates phi, psi, and chi1 dihedral angles. If two structures are given as input it calculates the root mean square deviation for all residues as well as the fraction of angles in the second structure found within 40 degrees of the corresponding angle in the reference structure.

With the option -list followed by phi, psi, omega, or chiN and a single structure as argument a list of dihedral angles is written to standard output.

The option -l is available to restrict the comparison or list output to a residue subset.

It is also possible to specify an arbitrary set of four atoms with -atoms for which the dihedral angle is calculated.

Options

-help: usage information
-l min:max[...]: restrict calculation and output to residue subset
-list phi|psi|omega|chi1|chi2...: write out backbone dihedrals for all residues
-atoms [chain]res:name [chain]res:name [chain]res:name [chain]res:name: specify a set of atoms for calculating torsion angle

Examples

dihed.pl 1vii.exp.pdb 1vii.exp.min.pdb
calculates phi, psi, and chi1 dihedral deviations

phi: 33.270 ( 85.71 % ), psi: 41.244 ( 77.14 % ), chi1: 36.318 ( 70.97 % )

dihed.pl -list phi 1vii.exp.pdb
lists phi dihedral angles for all residues in the given protein structure

MET1:    0.000
LEU2:  -64.308
SER3:  -63.139
ASP4:  -33.485
GLU5:  -36.210
ASP6:  -47.252
PHE7:  -42.580
LYS8:  -35.823
ALA9:  -79.382
VAL10: -140.773

...

dihed.pl -l 10:21 1vii.exp.pdb 1vii.exp.min.pdb
compares dihedral angles only for residues 10 through 21

phi: 30.428 ( 75.00 % ), psi: 37.130 ( 75.00 % ), chi1: 34.822 ( 66.67 % )

dihed.pl -atoms 2:CA 3:CA 4:CA 5:CA 1vii.exp.pdb
calculate virtual dihedral for C-alpha residues from residues 2 through 5

-93.861236

@@ Line 11: / Line 11: @@
 found within 40 degrees of the corresponding angle in the reference structure.
 <BR>
 With the option <B>-list</B> followed by <font color=#508060>phi</font>, <font color=#508060>psi</font>,
-<font color=#508060>omega</font>, or <font color=#508060>chi1</font> and a single structure as argument a list of dihedral
+<font color=#508060>omega</font>, or <font color=#508060>chiN</font> and a single structure as argument a list of dihedral
 angles is written to standard output.
 <BR>
-The option <B>-l</B> is available to restricts the comparison or list output
+The option <B>-l</B> is available to restrict the comparison or list output
 to a residue subset.
+<BR>
+It is also possible to specify an arbitrary set of four atoms with <B>-atoms</B> for which the
+dihedral angle is calculated.
 == Options ==
 ; -help : usage information
+; -l min&#58;max[...] : restrict calculation and output to residue subset
+; -list phi|psi|omega|chi1|chi2... : write out backbone dihedrals for all residues
+; -atoms [chain]res&#58;name [chain]res&#58;name [chain]res&#58;name [chain]res&#58;name : specify a set of atoms for calculating torsion angle
 == Examples ==
@@ Line 30: / Line 38: @@
 <mmtsbToolExample cmd="dihed.pl" set="/apps/mmtsb/bench/dihed.pl-test/test3"></mmtsbToolExample>
+<mmtsbToolExample cmd="dihed.pl" set="/apps/mmtsb/bench/dihed.pl-test/test4"></mmtsbToolExample>