twwistPDB
Overview
twwistPDB Help Output
twwistPDB Tutorial
(WEB PAGE PDF)
deviation Overview
twwistPDB transforms the coordinates of one PDB file to the reference frame of another pdb file. The transformed first PDB file is output as a new PDB file. The coordinate transformation is specified as 3 specific atoms from the first PDB file to be respectively mapped to 3 specific atoms of the second reference PDB file.
twwistPDB Help Output (“twwistPDB -h” output)
NAME
twwistPDB (version 1.3.0) -- maps pdb file1 to pdb file2
SYNOPSIS
twwistPDB [options] pdb1_fn pdb1_pt1 pdb1_pt2 pdb1_pt3 pdb2_fn pdb2_pt1 pdb2_pt2 pdb2_pt3
required (in order!):
pdb1_fn ....... pdb filename for first set of 3 points
pdb1_pt1 ...... number of first atom in first set
pdb1_pt2 ...... number of second atom in first set
pdb1_pt3 ...... number of third atom in first set
pdb2_fn ....... pdb filename for second set of 3 points
pdb2_pt1 ...... number of first atom in second set
pdb2_pt2 ...... number of second atom in second set
pdb2_pt3 ...... number of third atom in second set
CHARACTER OPTION___KEYWORD OPTION______DESCRIPTION____________________________DEFAULT____
-a <model#> .... --model1=<model#> ... MODEL number of pdb1ptX in pdb1_fn ... first model
-b <model#> .... --model2=<model#> ... MODEL number of pdb2ptX in pdb2_fn ... first model
-d ............. --list .............. list point values .................... no list
-e ............. --exact ............. process points in exact order ........ reorder
-m ............. --minimize .......... average new pdb1 to pdb2 distances ... no average
-o <filename> .. --output=<filename> . output filename for modified pdb1_fn . stdout
-x ............. --extend ............ extend pdb1_point3 and pdb2_point3 ... constrict
-h ............. --help .............. prints help (Enter 'twwistPDB -h' for help.)
<NO OPTIONS> ......................... shorter option synopsis (Enter 'twwistPDB'.)
--license ........... prints license terms for twwistPDB.
DESCRIPTION
twwistPDB maps pdb1_fn atom coordinates to pdb2_fn coordinates.
3 points must be specified, by ATOM # or HETATM #, for both pdb files.
For ambiguous ATOM # or HETATM #, one or more MODEL # must be provided.
Option '--model1=' ('-a') specifies the MODEL number of the specified pdb1_fn atoms.
Option '--model2=' ('-b') specifies the MODEL number of the specified pdb1_fn atoms.
By default, the first set of points is mapped onto the second set of points.
By using the option '--extend' ('-x'), pdb1_pt3 and pdb2_pt3 atoms will be
extended away from each other.
twwistPDB translates the coordinates of pdb1_fn to align the first points
and then rotates the coordinates of pdb1_fn to align the second and third
points. By default, twwistPDB reorders points to minimize alignment error,
such that the distance from point1 to point2 is the longest distance,
and the distance from point1 to point3 is the shortest distance.
Using option '--exact' ('-e') overrides this default behavior, causing
the points to be processed in the exact order listed.
Option '--minimize' ('-m') averages the distances between the new pdb1 points
and the existing pdb2 points.
Option '--output=' ('-o') specifies the output filename. If option '--output=' ('-o')
is not present, output will be written to stdout.
New "REMARK 250" lines will be added to the output PDB specifying execution details.
Errors and warnings go to stderr.
EXAMPLE
The twwistPDB command, below, maps the Streptococcus pneumoniae R6 (3H72)
neuraminidase atoms numbered 207, 1957, and 2569 to the influenza A (1W1X)
N6 neuraminidase atoms numbered 3302, 4122, and 4520, respectively,
resulting in a new pdb file, STRontoN6.pdb. This new output file consists
of the original Streptococcus (3H72) coordinates transformed to be in the
same orientation as the N6 neuraminidase (1W1X) coordinates; no relative
position within the 3H72 structure was changed.
With keyword options:
twwistPDB --output=STRontoN6.pdb 3H72.pdb 207 1957 2569 1W1X.pdb 3302 4122 4520
With character options:
twwistPDB -o STRontoN6.pdb 3H72.pdb 207 1957 2569 1W1X.pdb 3302 4122 4520
LICENSE INFORMATION
twwistPDB is a software program from Arthur Weininger (www.weiningerworks.com).
twwistPDB is subject to a license; use the keyword option '--license' in order to view
the license terms. Your use of this software contitutes an agreement to the license
terms. Do not use this software if you do not agree to the license terms.
twwistPDB Tutorial
twwistPDB Tutorial Page gives examples of using twwistPDB.
Picornavirus Monograph Superposition Shell Script gives examples of using twwistPDB.