Re: How to output CCC per residue from MDFF

From: Ryan McGreevy (
Date: Thu Apr 23 2015 - 22:15:49 CDT

Hi Michael, this is more of a question for vmd-l, but yes you can do such
an analysis. If you look at the Timeline plugin in VMD (under Analysis in
the extensions menu) there is a cross correlation option. VMD 1.9.2 uses a
newer, much faster multicore CPU and GPU parallel version of this
algorithm, but there is a known issue running this code on OSX and Windows
(so you may only get it to work on linux). VMD 1.9.1 has a much slower
algorithm, but one that should work on any operating system. That being
said, the default functionality is to calculate a per-secondary structure
CC (so each contiguous piece of secondary structure gets its own CC)
because per-residue is fairly computationally costly. There is also an
option to enter a custom atom selection list if you really need per residue
CC. You can find more information how how to run this analysis in the MDFF
tutorial: Please
note that the tutorial covers the 1.9.2 version of VMD, but most of the
information is still correct for 1.9.1 (except for how thresholds are

On Thu, Apr 23, 2015 at 10:01 PM Michael Yuchi <>

> Hi Everyone,
> Is there an easy way to plot per-residue CCC from a MDFF run? mdff check
> -ccc and mdff ccc seem to only give overall ccc values for specific
> selections.
> Thanks,
> Michael

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