On Mon, May 12, 2014 at 11:28 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> If this is indeed what they did, unfortunately CPPTRAJ does not break
> down eigenvectors in this way. One thing you could do that would be
OK - mea culpa - I was not completely correct when I said this. While
it's true that the 'projection' command can't break down eigenvectors
in this way, the 'modes fluct' and 'modes displ' analyses will break
down 1 or more eigenvectors by atom to calculate RMS fluctuation or
total displacement respectively. So e.g. for total displacement,
something like:
readdata 1rrb_vac_mwcovarmat_evecs.dat
modes displ name 1rrb_vac_mwcovarmat_evecs.dat beg 1 end 5 out test.dat
Will calculate total displacement for the first 5 modes from
1rrb_vac_mwcovarmat_evecs.dat and write the results or a per-atom
basis to test.dat. Note that currently I believe the displ/fluct/corr
functionality of 'modes' expects that the eigenvalues have been
converted to frequencies, so the units will only be correct if you
used a mass-weighted covariance matrix (the trends will be correct if
you used a plain covariance matrix but the units will be off).
I think this may be what you want. I don't think I was thinking very
clearly last week...
-Dan
> somewhat equivalent would be to generate pseudo-trajectories for
> desired modes with 'modes trajout' analysis in cpptraj, then
> subsequently calculate RMSF for each residue in the pseudo
> trajectories.
>
> Good luck,
>
> -Dan
>
> On Sun, May 11, 2014 at 1:10 PM, newamber list <newamberlist.gmail.com> wrote:
>> Dear Daniel
>>
>>>> Each of the dots in the principal component projection plots in Figs 3/4
>> represent the PC projection value for PCs 1 and 2 for a single frame.
>>
>> Sorry if I did not explain my problem correctly. I have problem, rather
>> could not understand, in obtaining a plot for EV1 vs Residue/Atom
>> displacement (Figure 3B) and what should be the matrix dimension
>> calculation/multiplication. (The thing is EV1 has 3N dimension and on x
>> axis I have just N atoms somehow averaged on F frames)
>>
>> Thanks again
>>
>>
>>
>>
>> On Thu, May 8, 2014 at 4:04 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>>> Hi,
>>>
>>> The projection of a coordinate frame along a certain eigenvector
>>> essentially tells you how much that frame contributes to that
>>> particular principal component. Each of the dots in the principal
>>> component projection plots in Figs 3/4 represent the PC projection
>>> value for PCs 1 and 2 for a single frame. In each frame you have N
>>> atoms, but 3N coordinates, which matches the dimensions of the
>>> covariance matrix.
>>>
>>> Also note that you have to be careful when comparing eigenvectors
>>> obtained from covariance matrices of different trajectories, as they
>>> are not guaranteed to be the same. I didn't see any discussion of this
>>> in my (admittedly brief) glance at the referenced paper. You can
>>> either check if the eigenvectors are aligned manually, or generate a
>>> covariance matrix from the combined trajectories, then calculate your
>>> projections for each trajectory separately.
>>>
>>> Hope this helps,
>>>
>>> -Dan
>>>
>>> On Wed, May 7, 2014 at 4:27 PM, newamber list <newamberlist.gmail.com>
>>> wrote:
>>> > Hi
>>> >
>>> >>> If you are referring to figures 3/4 in the above reference
>>> >
>>> > Yes, e.g. Fig 3A and 3B. I can get 3A as:
>>> >
>>> > crdaction crd1 projection modes evecs.dat out myproj.txt beg 1 end 2
>>> > :1-328.N. I have some confusion about calculation. Once you get
>>> > Eigenvectors for Covar Matrix of 3Nx3N dimension then you calculate new
>>> > data as e.g. just for EV1 and EV2 as:
>>> >
>>> > #Fx2 #2x3N
>>> >
>>> > |(xi1-Xi) (xk-Xk)| |EV1 in Row|
>>> > : : | |EV2 in Row|
>>> > : : |
>>> > |(xiF-Xi) (xiF-xk)|
>>> >
>>> > where x represents coordinate and X average. Does xi and xk would
>>> > necessarily mean the first and second dimension only (which happens to be
>>> > first two coordinates?) I know its wrong how xi and xj is chosen?
>>> >
>>> > Still for Figure 3B I don't understand how its calculated as Eigenvector
>>> > has a dimension of 3N but I have NxF atoms (where N is number of atoms
>>> and
>>> > F is Number of frames)
>>> >
>>> > thanks
>>> > Jiom
>>> >
>>> >
>>> >
>>> >
>>> > On Wed, May 7, 2014 at 3:52 PM, Daniel Roe <daniel.r.roe.gmail.com>
>>> wrote:
>>> >
>>> >> On Tue, May 6, 2014 at 10:21 PM, newamber list <newamberlist.gmail.com>
>>> >> wrote:
>>> >> > Its working now but I am not sure if this is how people
>>> calculate/present
>>> >> > their results. Usually in papers they show displacements along one
>>> >> > eigenvector (e.g.
>>> >> >
>>> >>
>>> http://pubs.rsc.org/en/Content/ArticleLanding/2014/MB/c4mb00177j#!divAbstract
>>> >>
>>> >> If you are referring to figures 3/4 in the above reference, then what
>>> >> you want to calculate is the projection of your coordinates along
>>> >> certain eigenvectors - see the 'projection' command in CPPTRAJ. The
>>> >> 'modes displ' just calculates total XYZ displacement for all
>>> >> eigenvectors.
>>> >>
>>> >> -Dan
>>> >>
>>> >> > )
>>> >> >
>>> >> > I get displX, Y and Z but I was expecting some net displacement which
>>> >> > simply I think should be sqrt(x^2+y^+z^2) and also for each individual
>>> >> > eigenvector I should do something like this:
>>> >> >
>>> >> > modes name evecs.dat displ out dis1.dat beg 1 end 1
>>> >> > modes name evecs.dat displ out dis2.dat beg 2 end 2
>>> >> >
>>> >> > 2)
>>> >> >>> If the only goal is to get two structures that look the least like
>>> each
>>> >> > other, one way is to calculate the 2D RMSD
>>> >> >
>>> >> > This is nice suggestion indeed. I was following some previous amber
>>> >> archive
>>> >> > mails to generate procupine plots which needs two extreme pdbs in
>>> >> > discussion it was not mentioned how one can get two extremes.
>>> >> >
>>> >> > best regards
>>> >> >
>>> >> >
>>> >> > On Wed, May 7, 2014 at 4:27 AM, Daniel Roe <daniel.r.roe.gmail.com>
>>> >> wrote:
>>> >> >
>>> >> >> On Tue, May 6, 2014 at 8:13 PM, newamber list <
>>> newamberlist.gmail.com>
>>> >> >> wrote:
>>> >> >> > runanalysis diagmatrix myCovar out evecs.dat vecs 15
>>> >> >> > readdata evecs.dat
>>> >> >> > modes displ out dis.dat name myCovar beg 1 end 3 :1-328.N
>>> >> >> ###
>>> >> >>
>>> >> >> The problem here is that you are trying to use 'myCovar' (which is a
>>> >> >> matrix) as your modes data set, which by default will be called
>>> >> >> 'evecs.dat' since you did not supply a name. Try using 'modes name
>>> >> >> evecs.dat ...'.
>>> >> >>
>>> >> >> > 2) Also how one can obtain two extreme configurations of system for
>>> >> whole
>>> >> >> > traj? Just by using lowest and highest rmsd with respect to average
>>> >> >> > structure or something one can do with PCA?
>>> >> >>
>>> >> >> If the only goal is to get two structures that look the least like
>>> >> >> each other, one way is to calculate the 2D RMSD and find the pair of
>>> >> >> frames with the largest RMSD. You will probably want to use the
>>> >> >> 'nosquare2d' option with standard data output to make searching
>>> >> >> easier, e.g.
>>> >> >>
>>> >> >> 2drms .CA out rms2d.dat
>>> >> >> datafile rms2d.dat nosquare2d
>>> >> >>
>>> >> >> Hope this helps,
>>> >> >>
>>> >> >> -Dan
>>> >> >>
>>> >> >> >
>>> >> >> > thanks
>>> >> >> > JIom
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> > On Tue, May 6, 2014 at 6:24 PM, Daniel Roe <daniel.r.roe.gmail.com
>>> >
>>> >> >> wrote:
>>> >> >> >
>>> >> >> >> Hi,
>>> >> >> >>
>>> >> >> >> On Mon, May 5, 2014 at 5:23 PM, newamber list <
>>> >> newamberlist.gmail.com>
>>> >> >> >> wrote:
>>> >> >> >> > 2) Also in many papers there are Principal component plots. If
>>> am
>>> >> not
>>> >> >> >> > wrong these are same obtained from 'projection modes' as shown
>>> >> below
>>> >> >> >> > (myproj.txt). Or its something else?
>>> >> >> >>
>>> >> >> >> The plots you refer to are actually histograms generated using the
>>> >> >> >> 'hist' command of the principal component projections obtained
>>> from
>>> >> >> >> the 'projection' command, see the bottom of the script in
>>> >> >> >>
>>> >> >> >>
>>> >> >>
>>> >>
>>> http://pubs.acs.org/doi/suppl/10.1021/ct400862k/suppl_file/ct400862k_si_001.pdf
>>> >> >> >> .
>>> >> >> >>
>>> >> >> >> > trajin 1trj.nc
>>> >> >> >> > trajin 2trj.nc
>>> >> >> >> > rms first :1-328.N
>>> >> >> >> > average Avg.rst7 ncrestart
>>> >> >> >> > createcrd crd1
>>> >> >> >> > run
>>> >> >> >> >
>>> >> >> >> > reference Avg.rst7.1 [avg]
>>> >> >> >> > crdaction crd1 rms ref [avg] :1-328.N
>>> >> >> >> > crdaction crd1 matrix covar :1-328.N name myCovar
>>> >> >> >> > runanalysis diagmatrix myCovar out evecs.dat vecs 15
>>> >> >> >> >
>>> >> >> >> > readdata evecs.dat
>>> >> >> >> > crdaction crd1 projection modes evecs.dat out myproj.txt beg 1
>>> end
>>> >> 3
>>> >> >> >> :1-328.N
>>> >> >> >>
>>> >> >> >> The last 'projection' command will create 3 data sets
>>> (corresponding
>>> >> >> >> to projections for PCs 1, 2, and 3) which you can then histogram,
>>> >> >> >> either with cpptraj or your favorite program. It will be probably
>>> be
>>> >> >> >> easier to histogram within cpptraj if you name the 'projection'
>>> data
>>> >> >> >> sets, e.g.:
>>> >> >> >>
>>> >> >> >> crdaction crd1 projection P1 modes evecs.dat out myproj.txt beg 1
>>> >> end 3
>>> >> >> >> :1-328.N
>>> >> >> >> runanalysis hist P1:1,*,*,*,100 out pca.hist.agr norm name P1-1
>>> >> >> >>
>>> >> >> >> etc. See the manual for more details on the 'hist' command (or
>>> >> >> >> alternatively the 'kde' command to use a kernel density estimator
>>> >> >> >> instead).
>>> >> >> >>
>>> >> >> >> Hope this helps,
>>> >> >> >>
>>> >> >> >> -Dan
>>> >> >> >>
>>> >> >> >> >
>>> >> >> >> > Thanks
>>> >> >> >> > _______________________________________________
>>> >> >> >> > AMBER mailing list
>>> >> >> >> > AMBER.ambermd.org
>>> >> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
>>> >> >> >>
>>> >> >> >>
>>> >> >> >>
>>> >> >> >> --
>>> >> >> >> -------------------------
>>> >> >> >> 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)
>>> >> >> >>
>>> >> >> >> _______________________________________________
>>> >> >> >> AMBER mailing list
>>> >> >> >> AMBER.ambermd.org
>>> >> >> >> http://lists.ambermd.org/mailman/listinfo/amber
>>> >> >> >>
>>> >> >> > _______________________________________________
>>> >> >> > AMBER mailing list
>>> >> >> > AMBER.ambermd.org
>>> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >> --
>>> >> >> -------------------------
>>> >> >> 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)
>>> >> >>
>>> >> >> _______________________________________________
>>> >> >> AMBER mailing list
>>> >> >> AMBER.ambermd.org
>>> >> >> http://lists.ambermd.org/mailman/listinfo/amber
>>> >> >>
>>> >> > _______________________________________________
>>> >> > AMBER mailing list
>>> >> > AMBER.ambermd.org
>>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>>> >>
>>> >>
>>> >>
>>> >> --
>>> >> -------------------------
>>> >> 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)
>>> >>
>>> >> _______________________________________________
>>> >> AMBER mailing list
>>> >> AMBER.ambermd.org
>>> >> http://lists.ambermd.org/mailman/listinfo/amber
>>> >>
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>>
>>> --
>>> -------------------------
>>> 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)
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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)
--
-------------------------
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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 19 2014 - 10:00:02 PDT
