Dear Daniel Roe,..
I have a question:
Why you named the average structure with "avgStruct.rst7", the number "7"
could be replaced or it is mandatory ?
can we named the average structure wit avgStruct.pdb ?
Thank you
Setyano Tri Wahyudi
On Mon, Apr 14, 2014 at 10:20 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I assume what you want is to calculate histograms of the projection of
> your coordinates along the first two PCs? If so, you just need to use
> the 'projection' action followed by 'hist' analysis. This can be done
> with the following commands:
>
> rms first :1-18.CA
> projection modes evecs-ca_10.dat start 1 stop 2 .CA myproj
> hist myproj:1 bins 200 out PC.hist.agr
> hist myproj:2 bins 200 out PC.hist.agr
>
> Modify the histogram commands as needed (e.g. put both data sets in
> the same command for a 2D histogram etc). Note that the coordinates
> (and mask you use) for the 'projection' command should be the same as
> when you generated the original covariance matrix, but the
> 'center'/'image' commands are not needed since the 'rms' command
> changes the coordinates of interest anyway.
>
> This entire procedure can actually be done in a single cpptraj run by
> saving the coordinates as a COORDS data set and making a few passes
> over it with 'crdaction' like so:
>
> rms first :1-18.CA
> average avgStruct.rst7
> createcrd crd1 # Creates COORDS data set crd1
> run
> reference avgStruct.rst7.1
> crdaction crd1 rms reference :1-18.CA
> crdaction crd1 matrix out matrix.dat name mymatrix covar .CA
> runanalysis diagmatrix mymatrix out evecs.dat vecs 10 name mymodes
> crdaction crd1 projection modes evecs.dat start 1 stop 2 .CA myproj
> hist myproj:1 bins 200 out PC.hist.agr
> hist myproj:2 bins 200 out PC.hist.agr
>
> Note that here I am RMS-fitting to an averaged structure, which should
> do a better job of eliminating global rotations (I assume you have a
> reason for making the fitting mask and matrix masks separate so I kept
> that in my example). Note that in the upcoming release of cpptraj you
> will actually be able to use the 'modes' data set generated by the
> 'diagmatrix' command directly with the 'projection' action rather than
> having to read it back in.
>
> Hope this helps,
>
> -Dan
>
> On Mon, Apr 14, 2014 at 5:45 AM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> > Hi List,
> >
> > I have calculated PCA using following to output file containing 10
> models.
> > center origin :1-18
> > # now image the whole system about the centered origin
> > image origin center
> > rms first :1-18.CA
> > matrix covar name covmat out covmat-ca_10.dat .CA
> > analyze matrix covmat out evecs-ca_10.dat vecs 10
> >
> > This seem like a trivial question. How do I read these models (PCA 1 to
> 2)
> > to define datasets in the hist (histogram) command in cpptraj?
> >
> > Many thanks,
> > Neha
> > _______________________________________________
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> 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 21 2014 - 01:30:03 PDT
