QPACK Interface
January 11, 2007
QPACK is described in
Gregoret, L.M. and Cohen, F.E.
"A Novel Method for the Rapid Evaluation of Packing in Protein Structures"
J. Mol. Biol.
211:959-974 (1990).
To use this tool, you must obtain the
QPACK distribution
from the Cohen group, and compile and install the qpack
and cofm programs.
If you are using Chimera versions prior to 1.2332, you will also need
to put this file, findExecutable.py,
into the chimera/share/CGLutil folder (see the
installation instructions for
more information).
Installing
this extension
adds an entry Qpack to
the Tools->Structure Analysis menu, as well
as a qpack command.
Usage
|
The graphical interface enables the user to select a molecule for analysis,
executes the QPACK program, assigns the computed packing radii
and ratio to ideal packing radii as atom attributes, and optionally
invokes the Render by Attribute tool to color the molecule
using the attributes. Other options include specifying the location
of the QPACK and COFM executables, and providing a file listing the
ideal radii to use in the QPACK calculation.
Only one molecule may be selected since the QPACK algorithm
may not be applicable for inter-molecular packing.
Selecting Okay will start the QPACK calculation, and,
if the Open Render/Select by Attribute button is checked,
the Render by Attribute dialog will appear when the
calculation is finished.
|
|
QPACK may also be invoke from the command line.
The qpack command syntax are:
qpack <options> spec <atom-spec>
qpack <options>
where <options> are space-separated name-value pairs
that correspond to options in the graphical interface.
The second form is provided as a shortcut for the case
where only one molecule is open; if more than one molecule
is open, an error is reported.
Supported option names are:
| Name |
Value |
Default |
| qpack |
path to qpack executable file |
automatically detected |
| cofm |
path to cofm executable file |
automatically detected |
| radii |
path to ideal radii file |
none |
| rba |
whether to invoke Render by Attribute after QPACK computation |
true |
Purpose
January 11, 2007.
Developed at suggestion of Eric Dawson.