PCA depend of the number of frames?
Dear users I did a test with three sets of frames
(1) 13 frames From X-ray(2) 28 frames From X-ray(3) 1000 frames From MD
In each case translations and rotations were eliminated.then g_covar was
applied to obtain the covariance matrix
g_covar -f sample.xtc -s representative.tpr -o eig_sample.xvg -xpm
covar_sample.xpm For the case (1) and (2) the most representative structure was
used in the option -s ( One that has the lowest rmsd with respect to the
average of each cluster).In case (3) the initial structure of the MD was used
in the option -s.
When I look the eigenvalues for the case (1) and (2), I found that the
eigenvalue is zero only after index="number of frames" (see below)
In the case (3) the distribution is smoothI could expect a similar distribution
for the case (1) and (2), because the frames are representative of the dymanics
of the protein.
Why this difference?PCA depend of the number of frames?
A plot with the eigenvalues and cumulative number is available in this limk.
http://www.4shared.com/file/c4sQQd9U/cumulative.html?
In the plot Cluster (1) is case (1) Cluster (2) is case (2)
X1 is case (3)
Sincerely yours
Ricardo
caso (1)
@ title "Eigenvalues of the covariance matrix"@ xaxis label "Eigenvector
index"@ yaxis label "(nm\S2\N)"@TYPE xy 1 3.21824 2 1.59207
3 0.7186 4 0.603902 5 0.555743 6 0.479754
7 0.412325 8 0.345979 9 0.282516 10 0.269861 11
0.260193 12 0.209889 13 1.96752e-15 *IN THIS INDEX THE
EIGENVALUES IS CLOSE TO ZEROM COINCIDENT WITH THE NUMBER OF FRAMES 14
1.62777e-15 15 1.5654e-15 16 1.3087e-15 17 9.35402e-16
18 9.04299e-16 19 6.71342e-16 20 6.64882e-16
caso (2) Obtained from X-ray
@ title "Eigenvalues of the covariance matrix"@ xaxis label "Eigenvector
index"@ yaxis label "(nm\S2\N)"@TYPE xy 1 0.283967 2
0.0952257 3 0.0743586 4 0.0598192 5 0.0450539 6
0.0410722 7 0.0301708 8 0.0262085 9 0.0240471 10
0.0175948 11 0.0147602 12 0.0140895 13 0.011544 14
0.0107718 15 0.00884784 16 0.00851068 17 0.00748592
18 0.00662536 19 0.00645983 20 0.00609032 21 0.00516941
22 0.00404203 23 0.00373644 24 0.00336767 25
0.00299449 26 0.00227847 27 0.00156805 28 -3.86967e-05
*IN THIS INDEX THE EIGENVALUES IS CLOSE TO ZEROM COINCIDENT WITH THE NUMBER OF
FRAMES 29 1.04056e-07 30 -2.72851e-08 caso (3)
@ title "Eigenvalues of the covariance matrix"@ xaxis label "Eigenvector
index"@ yaxis label "(nm\S2\N)"@TYPE xy 1 3.03786 2 1.27271
3 0.53899 4 0.423554 5 0.27003 6 0.260328
7 0.220423 8 0.191197 9 0.168856 10 0.152404 11
0.128236 12 0.126204 13 0.110368 14 0.092775 15
0.0885705 16 0.0750595 17 0.0696554 18 0.0627624 19
0.0532074 20 0.0513393 21 0.0474214 22 0.0463299 23
0.0432387 24 0.0403574 25 0.0392867 26 0.0352699 27
0.0333476 28 0.0319553 29 0.0308987 30 0.0306235 31
0.027971 32 0.0268982 33 0.0258224 34 0.0249171 35
0.0234315 36 0.0221298 37 0.0217099 38 0.0202486 39
0.0196283 40 0.0191729 41 0.018719 42 0.0185378 43
0.0176382 44 0.0174487 45 0.0165635 46 0.0161611 47
0.015876 48 0.0155579 49 0.0147515 50 0.0139361...
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