pdbPCA

pdbPCA is Eos's Command for calculating specified axis of atom model. By using Principal Component Analysis(PCA), it calculates 3 orthogonal axis. 1st Principal Component expresses longest direction of molecule.

List of option

Main option

Option	Essential/Optional	Description	Default
-i	Optional	Input: PDB	stdion(Standard Input if not set)
-o	Optional	Output: calculated result outputs: ASCII	stdout(Standard output by default)
-oU	Optional	Output:Unit Vector: ASCII(Array)	NULL(not output if not set)
-oM	Optional	Output:Unit Vector: ASCII(Marix3D)	NULL(not output if not set)
-oPDB	Optional	Output: Atom model rotated by Unit : PDB 　　　　　　　1st, 2nd, 3rd Principal Axis is x, y, z-axis	NULL(not output if not set)
-c	Optional	ConfigurationFile	NULL
-m	Optional	Mode	0
-h	Optional	Help

-m details

Value	Description
0

Execution example

 $ pdbPCA -i 1VOM.pdb 
 Program Start
 (0,0):=1149624.289131
 (0,1):=-118627.789270
 (0,2):=315483.835955
 (1,0):=-118627.789270
 (1,1):=2010078.268384
 (1,2):=-1021173.592972
 (2,0):=315483.835955
 (2,1):=-1021173.592972
 (2,2):=2127164.855685
 nrot for PCA: 11
 Result
 C: covariance matrix
 2 3 3 
  1149624.250000  -118627.789062   315483.843750 
  -118627.789062  2010078.250000 -1021173.562500 
   315483.843750 -1021173.562500  2127164.750000 
 u: unit vector
 2 3 3 
        0.154886       -0.671246        0.724871         # 1st Principal ComponentのEigenvector
        0.767707        0.543582        0.339330         # 2nd Principal ComponentのEigenvector
       -0.621801        0.503931        0.599514 　　　　# 3rd Principal ComponentのEigenvector
 lambda^2: lambda^2
 1 3 
  3140204.500000  1205074.000000   941588.812500 
　#1st Principal Component　　　#2nd Principal Component　　　# 3rd Principal Component

Input file details

Gravity Centre(CA) Atom far from Centre(CA) Atom far from Centre(CA, Axis)

6.727136e+01 3.631518e+01 -2.983928e+01 5.314867e+01 40.92 41.49 48.47

Case: Options only essential

-o 's data

Result
C: covariance matrix
2 3 3 
 1149624.250000  -118627.789062   315483.843750 
 -118627.789062  2010078.250000 -1021173.562500 
  315483.843750 -1021173.562500  2127164.750000 
u: unit vector
2 3 3 
       0.154886       -0.671246        0.724871 
       0.767707        0.543582        0.339330 
      -0.621801        0.503931        0.599514 
lambda^2: lambda^2
1 3 
 3140204.500000  1205074.000000   941588.812500 
Averege: Center Position
1 3 
      66.530304       36.237804      -29.722399 

-oU 's data

2 3 3 
       0.154886       -0.671246        0.724871 
       0.767707        0.543582        0.339330 
      -0.621801        0.503931        0.599514 

-oM 's data

       0.154886       -0.671246        0.724871 
       0.767707        0.543582        0.339330 
      -0.621801        0.503931        0.599514 
       0.000000        0.000000        0.000000 

-oPDB 's data

Gravity Centre(CA) Atom far from Centre(CA) Atom far from Centre(CA, Axis)

-3.558668e+01 6.125959e+01 -4.141817e+01 5.314899e+01 48.12 36.21 35.41