GNM version 1.3.0
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Output File Descriptions (for Fortran and C Versions)
Filename
Description
(PDB
Code).bfactor
This file is the theoretical and experimental B-factor (temperature
factor) file and contains three columns. The first column is the
residue index, the second is GNM calculated theoretical B-factors
and the last column is the x-ray crystallographic b-factors taken
from the PDB file.
(PDB
Code).ca
Experimental data. 5 columns, comprising residue indices, x-, y- and
z- coordinates of alpha-carbons, and corresponding temperature
factors.
(PDB
Code).cc
The file contains the cross-correlations between residue
fluctuations. The values are between +1(perfect concerted motion)
and -1(perfect anti-correlated motions).
(PDB
Code).cont
It
lists the number of neighbors are in contact with a specific residue
within a cutoff 7.3Å
(PDB
Code).eigen
This lists N-1 eigenvalues in the decreasing order
(PDB
Code).sloweigenvectors
22
columns. The first column refers to residue indices. Columns 3-22
are the elements of eigenvectors associated with the 20 slowest
(lowest frequency) modes, starting from the slowest (first) mode
(column 3). The dimension of each element in these vectors is
Angstroms.
(PDB
Code).fasteigenvectors
22
columns. The first column refers to residue indices, columns 3-22
are the elements of eigenvectors associated with the 20 fastest
(highest frequency) modes, starting from the highest mode (column 3)
. The dimension of each element in these vectors is Angstroms.
(PDB
Code).slowmodes
22
columns. The first column refers to residue indices, columns 3-22
are slow mode shapes associated with the 20 slowest (lowest
frequency) modes, starting from the slowest (first) mode. The
dimension in each row of columns 3-22 is in Angstrom square, giving
the fluctuations resulting from these independent modes.
(PDB
Code).fastmodes
22
columns. The first column refers to residue indices, columns 3-22
are fast mode shapes associated with the 20 fastest (highest
frequency) modes, starting from the highest mode. The dimension in
each row of columns 3-22 is in Angstrom square, giving the
fluctuations resulting from these independent modes. Since the last
modes reflect localized fast motions in the protein, these modes
have few non-zero elements.
(PDB
Code).slowav
2
columns. The first column refers to residue indices, column 2 is the
residue mean-square fluctuations driven by the joint contribution of
the slowest two modes.
(PDB
Code).fast10av
3
columns. The first column refers to residue indices, column 2 lists
the residue mean-square fluctuations driven by the highest frequency
mode, column 3 shows the result from the weighted contribution of
the fastest modes.
In order to visualize the output files, open them in a graphing or
visualization program and set the indices and axes appropriately. (We use Kalediograph and Microsoft Excel most commonly for this purpose).
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