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GNM results files for your structure (in text format) Help

Filename Description
temp_nodes.pdb
GNM nodes
Structural data on GNM nodes, in PDB format.
temp_connectivity.txt
Network topology
The type of connectivity (topology) in the examined structure. The file is organized in three columns: the first two are the indices of the connected nodes, and the third designates the type of connection. Designations 1, 2 and 3 refer to amino acid pairs, nucleotides pairs and amino acid – nucleotide pairs, respectively. If the file contains multiple chains, nodes indices are assigned starting from 1 for chain A, and continuing sequentially with chains B, C, etc as listed in the PDB file.
temp.kdat
GNM Kirchhoff matrix
The GNM Kirchhoff matrix Γ written in three columns. The first two are the indices i and j of contact-making (or connected) nodes, and the third is the corresponding element Γij of Γ (i.e. -1 if i ≠ j, and coordination number or node degree if i = j).
temp.cont
Coordination number of nodes
The file consists of four columns: (i) residue type, (ii) chain identifier, (iii) node index, and (iv) coordination number of the corresponding node.
temp.bfactor
B-factor profiles
Theoretical and experimental B-factors organized in 5 columns: (i) chain identifier, (ii) residue type, (iii) node index, (iv) GNMbpredicted B- factor, and (v) X-ray crystallographic B factor.
temp.eigen
Eigenvalues
The eigenvalues corresponding to the examined structure, organized in ascending order. The 1st is the zero eigenvalue.
temp_entropy.txt
Vibrational entropy
GNM-defined vibrational entropy (based on Karplus and Kuschik, 1981).
temp.slowmodes
Slow modes
23 or more (to represent 40% of the spectrum) columns. The columns 1-3 list the chain identifier, residue type and node index, respectively; columns 4-23 (or more) are the corresponding displacements in modes 1-20 (or more) starting from the slowest (first) mode.
temp.slow2av
Slow mode average 1-2
Cumulative contribution of the slowest two modes to the mobility of residues. The file is organized in 4 columns. The columns 1-3 columns list the chain identifier, residue type and corresponding node index; and column 4 is the square displacement driven by the these slowest two modes.
temp.slow3av
Slow mode average 1-3
Same as the above file, except for the last column which describes the cumulative effect of slowest three modes.
temp.slow10av
Slow mode average 1-10
Same as the above file, except for the last column which describes the cumulative effect of slowest ten modes.
temp.fastmodes
Fast modes 1-20
23 columns. The columns 1-3 list the chain identifiers, residue types and node indices, respectively; columns 4-23 are the fastest mode shapes starting from the highest mode. Since these modes are highly localized columns 4-23 have only a few non-zero elements.
temp.fast10av
Fast mode average 1-10
4 columns. The columns 1-3 are same as above; column 4 lists the residue square fluctuations driven by 10 highest frequency modes.
temp.sloweigenvectors
Slow eigenvectors
23 columns. The columns 1-3 are same as above; columns 4-23 are the elements of eigenvectors associated with the 20 slowest (lowest frequency) modes, starting from the slowest mode.
temp.fasteigenvectors
Fast eigenvectors 1-20
23 columns. The columns 1-3 are same as above; columns 4-23 are the elements of eigenvectors associated with the 20 fastest (highest frequency) modes, starting from the highest mode.
temp_cc_all.txt
Orientational cross-correlations
Orientational cross-correlations between residue fluctuations. The values vary from -1 (fully anticorrelated motions) to +1 (fully correlated). The file is provided for structures having no more than 1,000 nodes.
temp.collectivity-slow
Degree of collectivity
The degree of collectivity is listed for N/10 (N is the total number of nodes) or at least 20 slowest modes.

ANM results files for your structure (in text format)

Filename Description
temp_ANM.slowevs
Slow eigenvectors
21 columns. The 1st column list the node index; columns 2-21 are the elements of eigenvectors associated with the 20 slowest (lowest frequency) modes, starting from the slowest (first) mode. Each node has three rows for x, y and z dimensions.
temp_ANM.slwmodes
Slow modes
21 columns. The 1st column list the node index; columns 2-21 are the corresponding displacements in modes 1-20 starting from the slowest (first) mode.
temp_ANM.xyz
ANM motions
The ANM motion of the 20 slowest modes in xyz format, starting from the slowest mode.
temp_ANM.eigenval_all
Eigenvalues
The eigenvalues corresponding to the examined structure, organized in ascending order. The first six values are the zero eigenvalue.

PRS results files for your structure (in text format)

Filename Description
temp_prs_all.txt
PRS matrix
All elements in the GNM-based PRS matrix; the index of rows and columns are indices for those nodes triggered by others and nodes trigger the responses (accept perturbation), respectively.
temp_mean_prs_all.txt
Mean profiles
5 columns. The columns 1-3 list the chain identifiers, residue types and node indices, respectively; columns 4 and 5 are the elements of average response of effectors (triggered by others) and sensors (triggered by themselves), respectively.

Hitting time results files for your structure (in text format)

Filename Description
temp_hit_hitting.txt
Hitting time matrix
All elements in the hitting time matrix; the index of rows and columns are indices for those residues receiving signals and residues broadcasting signals, respectively.
temp_hit_hitting_all.txt
Mean hitting times
7 columns. The columns 1-3 list the chain identifiers, residue types and node indices, respectively; columns 4 and 5 are the elements of average hitting time of receivers (receiving signals efficiently, perturbation sites) and broadcasters (sending signals efficiently, response sites), respectively; columns 6 and 7 are the elements of the standard deviation of average hitting time of receivers and broadcasters, respectively.
temp_hit_hitting_norm.txt
Hitting rate matrix
All elements in the hitting rate matrix; the index of rows and columns are indices for those residues receiving signals and residues broadcasting signals, respectively.
temp_hit_hitting_all_norm.txt
Mean hitting rates
7 columns. The columns 1-3 list the chain identifiers, residue types and node indices, respectively; columns 4 and 5 are the elements of average hitting rate of receivers (receiving signals efficiently, perturbation sites) and broadcasters (sending signals efficiently, response sites), respectively; columns 6 and 7 are the elements of the standard deviation of average hitting rate of receivers and broadcasters, respectively.