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.
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>
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:
|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|
January 11, 2007.
Developed at suggestion of Eric Dawson.