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GNM results files for 101M (in text format) Help

Filename	Description
101M_nodes.pdb GNM nodes	Structural data on GNM nodes, in PDB format.
101M_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.
101M.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 Γ_ij of Γ (i.e. -1 if i ≠ j, and coordination number or node degree if i = j).
101M.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.
101M.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.
101M.eigen Eigenvalues	The eigenvalues corresponding to the examined structure, organized in ascending order. The 1^st is the zero eigenvalue.
101M_entropy.txt Vibrational entropy	GNM-defined vibrational entropy (based on Karplus and Kuschik, 1981).
101M.slowmodes Slow modes	23 or more (to represent 40% of the spectrum) columns. 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.
101M.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. 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.
101M.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.
101M.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.
101M.fastmodes Fast modes 1-20	23 columns. 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.
101M.fast10av Fast mode average 1-10	4 columns. Columns 1-3 are same as above; column 4 lists the residue square fluctuations driven by 10 highest frequency modes.
101M.sloweigenvectors Slow eigenvectors	23 columns. 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.
101M.fasteigenvectors Fast eigenvectors 1-20	23 columns. 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.
101M_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.
101M.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.