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Difference between revisions of "dihed.pl"
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found within 40 degrees of the corresponding angle in the reference structure. | found within 40 degrees of the corresponding angle in the reference structure. | ||
<BR> | <BR> | ||
| + | |||
With the option <B>-list</B> followed by <font color=#508060>phi</font>, <font color=#508060>psi</font>, | 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> | + | <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. | angles is written to standard output. | ||
<BR> | <BR> | ||
| − | The option <B>-l</B> is available to | + | |
| + | The option <B>-l</B> is available to restrict the comparison or list output | ||
to a residue subset. | to a residue subset. | ||
Revision as of 02:41, 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
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.
Options
- -help
- usage information
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 % )