[Chimera-users] Display of qpack color output

Eric Dawson eric.dawson at vanderbilt.edu
Tue Nov 1 09:37:21 PST 2005

In the older UCSF MidasPlus incarnation of your software, there was a
feature that allowed an interface with Gregort & Cohen's QPACK software
for coloring according to molecular packing density using a sphere growth
method. Per residue packing scores were applied with a color range after
running qpack with the special option, '-m'.


In the primary literature report of QPACK, it was suggested by the authors
that they would work to make this feature available in UCSF MidasPlus and
'its successors'. Since this is a very fast and convenient way to evaluate
the quality of models, I would like to recommend/request that this feature
be enabled (or added) to Chimera. In MidasPlus, it was a command line
option. The user simply entered qpack; there was a .midasrc file that
contained the explicit local path to the qpack binary as well as a command
line script to launch the package with the '-m' option.

Thanks for your consideration of this suggestion.  

Best regards,


Eric S. Dawson, Ph.D.
CSB Computation, Education & Outreach
Research Instructor, Biochemistry
Center for Structural Biology (CSB)
Vanderbilt University
Nashville, TN 37232-8755
Tel: (615)-936-5579 (MRB III)
Tel: (615)-322-3303 (5119 SC)
Fax: (615)-936-2211

"All that is gold does not glitter, not all those who wander
  are lost." J.R.R. Tolkien - Fellowship of the Ring

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