GNM Application

Perform GNM calculations and output the results in plain text NMD, and graphical formats.

prody_gnm(pdb, **kwargs)

Perform GNM calculations for pdb.

Parameters:

• altloc – alternative location identifiers for residues used in the calculations, default is 'A'
• cutoff – cutoff distance (A), default is 10.0
• extend – write NMD file for the model extended to “backbone” (“bb”) or “all” atoms of the residue, model must have one node per residue, default is ''
• figall – save all figures, default is False
• figbeta – save beta-factors figure, default is False
• figcc – save cross-correlations figure, default is False
• figcmap – save contact map (Kirchhoff matrix) figure, default is False
• figdpi – figure resolution (dpi), default is 300
• figformat – figure file format, default is 'pdf'
• figheight – figure height (inch), default is 6.0
• figmode – save mode shape figures for specified modes, e.g. “1-3 5” for modes 1, 2, 3 and 5, default is ''
• figsf – save square-fluctuations figure, default is False
• figwidth – figure width (inch), default is 8.0
• gamma – spring constant, default is '1.'
• kirchhoff – write Kirchhoff matrix, default is False
• membrane – whether to include the explicit membrane model, default is False
• model – index of model that will be used in the calculations, default is 1
• nmodes – number of non-zero eigenvectors (modes) to calculate, default is 10
• nproc – number of processors, default is 0
• npzmatrices – write matrix to compressed ProDy data file, default is False
• numdelim – number delimiter, default is ' '
• numext – numeric file extension, default is '.txt'
• numformat – number output format, default is '%12g'
• outall – write all outputs, default is False
• outbeta – write beta-factors calculated from GNM modes, default is False
• outcc – write cross-correlations, default is False
• outcov – write covariance matrix, default is False
• outdir – output directory, default is '.'
• outeig – write eigenvalues/vectors, default is False
• outhm – write cross-correlations heatmap file, default is False
• outnpz – write compressed ProDy data file, default is False
• outscipion – write continuousflex modes directory and sqlite, default is False
• outsf – write square-fluctuations, default is False
• prefix – output file prefix, default is '_gnm'
• select – atom selection, default is "protein and name CA or nucleic and name P C4' C2"
• zeros – calculate zero modes, default is False