[gmx-users] Problems with g_anaeig

[James Starlight]

Mark,

By 'coverage' I mean the 1 value in the dot product of the comparing
eigenvectors sets (between 1 and 1, 2 and 2 and so on eigenvectors) (
that indicate that both eigenvector set are identical as I suppose).
In that case I had 2 identical pdp ensembles from which in 1 case I
obtained normal filter trajectory and in the second case- with broken
geometry.
In the picture below you can see the conformations of the protein
calculated in that 2 instances ( left conformation is fine and its
preserved in all filter trajectory but in the second case as you can
see all seven-helixes bulge of the protein was shrunken). I've tried
to re-make the cov.analysis ( changing number of structures in the pdb
ensemble as well as reference conformation but result was always the
same ).

http://img138.imageshack.us/img138/2717/7tmpca.png

James
>
> What do you mean by "coverage"?
>
> The eigenvectors are an orthonormal basis set for the observed variation.
> If the observed variation is a mess (because the structural ensemble you're
> treating as a black box is actually a mess, or your reference structure is
> an outlier), then the eigensystem will not lead to a sensible filter.
>
> Since you chose not to follow my hints last time:
> 1) Go and look at the X-ray ensemble. Is it one? Is your arbitrary choice
> of reference structure appropriate? Is there even an appropriate choice?
> 2) You can filter the trajectories based on the other's eigensystem. If the
> eigensystems are equivalent, then the filtered trajectories should look the
> same. If they don't, then your two ensembles differ.
>
> Mark
>
> James
>>
>> 2013/1/25 Mark Abraham <mark.j.abraham at gmail.com>:
>> > On Tue, Jan 22, 2013 at 8:22 PM, James Starlight <jmsstarlight at gmail.com
>> >wrote:
>> >
>> >> Dear Gromacs users!
>> >>
>> >>
>> >> There is some bug  with g_anaeig the souce of which I could not fully
>> >> understand.
>> >
>> >
>> > Good Advice: until you can almost write a code patch to fix it, be very
>> > hesitant in suggesting any software has a bug. The best people to help
>> > solve the issue are often those who wrote the code, and you don't want
>> them
>> > annoyed with you :-)
>> >
>> >   I have problems when I perform PCA of X-ray data set.
>> >> Below you can my workflow.
>> >>
>> >>
>> >> g_covar -f b2ar_xray_coors.pdb  -s ref.pdb  -o PCA_eigenval.xvg -v
>> >> PCA_eigenvec.trr -av PCA_average.pdb -last 8
>> >> g_anaeig -v PCA_eigenvec.trr -s ref.pdb  -f b2ar_xray_coors.pdb -rmsf
>> >> eigrmsfPCA.xvg -filt
>> >>
>> >>
>> >> here b2ar_xray_coors.pdb  is the trajectory made from 10 X-ray
>> >> structures of my protein (only main chain atoms are included)
>> >> ref_pdb is the first frame of that trajectory
>> >>
>> >>
>> >> As the result I've obtained reasonable eigenvalues and aigenvectors
>> >> from g_covar BUT when I check filter trajectory ( produced by
>> >> g_anaeig) fitted it to the ref.pdb or to the averaged structure in
>> >> both cases I've obtained very distorted geometry of the  protein in
>> >> thefiltered trajectory. I have no such problems in case of PCA of MD
>> >> trajectory ( when  -f trajectory.trr is from the md snapshots not from
>> >> x-ray structures)
>> >>
>> >>
>> >> How it could be fixed ?
>> >>
>> >
>> > How have you excluded the hypotheses that your reference structure is
>> not a
>> > valid representative of the middle of the range of variation? Or even
>> that
>> > the X-ray structural ensemble really is one?
>> >
>> > Mark
>> > --
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