If you want a structure representative for your trajectory, rather
than the average, I suggest using g_cluster to cluster your frames
and take the cluster center from the largest cluster.
/Erik
20 sep 2007 kl. 17.18 skrev Arneh Babakhani:
Great, got it, thanks for the suggestion, appreciate the input,
Arneh
Arneh Babakhani wrote:
Hi,
When outputting the average structure from g_rmsf using the -ox
option,
some of my residues in that average structure pdb have awkward
coordinates
(when you visualize it in VMD, it looks very strange). Sometimes
atoms
are placed very close to each other, with really bad bond angles. I
suppose this is a facet of the averaging scheme in g_rmsf.
Yes. If you ask for an not-necessarily-physical result, you
usually get
one... see http://wiki.gromacs.org/index.php/Average_Structure
Is there a way to correct for this, and to obtain an
averagestructure.pdb
that looks more reasonable coordinates and bond angles? (I ask b/
c I'd
like to use this averagestructure.pdb in further studies, such as
docking.)
"Correcting for" is not quite the right phrasing here... :-) It's
already correct according to the algorithm you used... it's not the
algorithm's fault you actually wanted a physical structure. One
approach
you can use is to select the structure with the smallest RMSD from
the
average, kind of like selecting the median as the central measure
rather
than the mean of a numerical data set. Or you can take the
nonphysical
structure and do EM on it... One needs to apply brain, of course!
Mark
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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
[EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys
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