>
> Dear Sir/Madam,
>
> After running PCA, I got two files (xxx.pev and xxx.ppj). I could like to
> ask if I want to calculate % of total protein motions described by the
> first eigenvector, what should I do? What is the meaning of the numbers
> in these two files?
>
>
> With reference to previous answers of the related question, I know in the
> xxx.pev file:
>
>
>
> the first line" Eigenvectorfile: COVAR" is the tilte
>
> the second line "1695 = number of atoms * 3"
>
>
>
> However, I still cannot figure out what is 73.10704 42.51491.....0.0009,
> they are not in the decending order.
Apology if my response here is over-elementary, but I sense you are
needing to get oriented in the output as first order of business.
The first numbers you are seeing are the coordinates of the atoms in the
systemat their mean positions from the ptraj run. As long as you removed
translation and rotation correctly before creating your covariance
matrix,these coordinates would correspond to the coordinates of the system
at a local mimum around which a typically more challenging Normal Mode
calculation (diagonalization of Hessian matrix) were being performed.
You will find the eigenvalues and eigenvectors after these coordinates.
grep --after=10 --before=1 "\*\*" ptraj.output.file | less
could yield something like this. You see the the last of the coordinates.
Then a "1" indicates the "first" Eigenvector and a 0.56814 for the
Eigenvalue.
Note that the units of the Eigenvalues varies depending on whether you do
Mass-weighted output or not. The units are discussed elsewhere in
documentation or on the reflector.
Numbers after that are the first eigenvector, the harmonic approximations
of the amplitude of the motion of the atom coordinates x,y,z; x,y,z; etc.
Hope the above helps more than it hurts.
27.16307 37.16769 52.95533 27.24810 37.52958 53.27943 27.16547
****
1 0.56814
0.00180 0.00127 0.00087 0.00207 0.00124 0.00050 0.00188
0.00137 0.00086 0.00174 0.00134 0.00046 0.00140 0.00107
0.00200 0.00198 0.0
What is the first eigenvector and
> eigenvalue in this analysis? I want to calculate the % of motion
> described by the first eigenvector, does it equal to [73.10704 / sum
> (73.10704......0.0009)]*100%
>
>
>
> Then, what is the mean of the values in xxx.ppj files?
>
>
> Best regards & many thanks,
>
> Cat
>
>
>
>
> The xxx.pev files starts with
>
> ---------------------------------------------------------------------------
>
>
>
>
>
>
>
>
> Eigenvector
> file:
> COVAR
>
>
>
>
>
> 1695
> 1695
>
>
>
>
>
>
> 73.10704
> 42.51491
> 65.46974
> 73.51263
> 45.08371
> 64.03552
> 75.46584
>
> 44.06115
> 61.03077
> 76.46655
> 46.93481
> 58.74557
> 76.09958
> 45.09636
>
>
>
>
>
>
>
> 55.40839
> 76.08002
> 48.42934
> 53.48851
> 79.68982
> 49.11898
> 54.59358
>
> 81.03393
> 45.72585
> 53.53507
> 82.31487
> 44.6972
> 50.12527
> 79.7907.....................................................................................0.0009
> --------------------------------------------------------------------------
>
> The xxx.ppj files starts with
>
> -----------------------------------------------------------------------------------
>
>
>
>
>
>
>
>
> Projection
> of
> snapshots
> onto
> modes
>
>
>
>
>
>
>
>
>
> Snapshot
> Mode1
> Mode2
> Mode3
> Mode4
> Mode5
> Mode6
> Mode7
> Mode8
> Mode9
> Mode10
>
>
> 1
> -26.927
> 24.853
> 5.978
> -0.671
> -3.39
> 16.009
> 2.134
> 1.791
> -6.824
> 0.177
>
>
> 2
> -27.408
> 24.742
> 3.341
> -0.199
> -4.45
> 17.883
> 0.757
> 3.522
> -7.053
> -1.57
>
>
> 3
> -27.11
> 26.452
> 3.71
> 0.511
> -3.956
> 17.529
> 0.793
> 1.711
> -6.518
> -0.177
>
>
> 4
> -27.994
> 25.609
> 4.671
> 0.121
> -3.586
> 16.577
> 0.261
> 2.362
> -5.53
> 0.835
>
>
> 5
> -26.922
> 26.545
> 6.5
> -0.496
> -4.567
> 16.954
> 2.366
> 2.107
> -4.384
> 1.03
>
>
> 6
> -28.509
> 24.969
> 8.291
> 0.139
> -3.417
> 16.243
> 1.178
> 2.262
> -4.706
> 0.511
>
>
> --------------------------------------------------------------------------------------------------------------------
>
>
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Received on Thu Sep 03 2009 - 07:30:11 PDT
