Thanks Daniel. I suspected the answer was what you explained, but since I
wanted the fluctuations of the CM I was secretly hoping someone would prove
me wrong :D
Jose Borreguero Calvo
Neutron Data Analysis and Visualization Division
Oak Ridge National Laboratory
PO BOX 2008 MS6454
OAK RIDGE TN 37831-6454
Work/Cell: 678-793-6463
work: borreguerojm.ornl.gov , http://neutrons.ornl.gov/ndav,
http://camm.ornl.gov
personal: borreguero.gmail.com , http://www.borreguero.com
On Mon, Apr 13, 2015 at 11:49 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Fri, Apr 10, 2015 at 4:44 PM, Jose Borreguero <borreguero.gmail.com>
> wrote:
> > Is it the fluctuations of the center of mass of the first residue, or
> the
> > average of the atomic fluctuations for the atoms in the first residue? I
> > could not get a clear cut answer from the manual.
>
> Sadly this is sometimes the case, although I promise you we are
> constantly working to make the manual better!
>
> Here your second guess is correct; when 'byres' is specified the
> mass-weighted atomic fluctuations of each atom in the residue are
> averaged like so:
>
> ResidueFluct = SUM[ AtomFluctX * massX ] / TotalMass
>
> 'bymask' is similar except the averaging occurs over the entire atom mask.
>
> Hope this helps, and thanks for pointing out the omission in the manual.
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Mon Apr 13 2015 - 09:30:02 PDT
