AMBER Archive (2009)

Subject: [AMBER] Question regarding PCA analysis.

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Tue Sep 01 2009 - 22:53:10 CDT

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. 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

--------------------------------------------------------------------------------------------------------------------

_________________________________________________________________
Show them the way! Add maps and directions to your party invites.
http://www.microsoft.com/windows/windowslive/products/events.aspx
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber