Running :command:`prody gnm -h` displays:
usage: prody gnm [-h] [--quiet] [--examples] [-n INT] [-s SEL] [-c FLOAT] [-g FLOAT] [-m INT] [-a] [-o PATH] [-e] [-r] [-u] [-q] [-v] [-z] [-t STR] [-b] [-k] [-p STR] [-f STR] [-d STR] [-x STR] [-A] [-R] [-Q] [-B] [-K] [-M STR] [-F STR] [-D INT] [-W FLOAT] [-H FLOAT] pdb positional arguments: pdb PDB identifier or filename optional arguments: -h, --help show this help message and exit --quiet suppress info messages to stderr --examples show usage examples and exit parameters: -n INT, --number-of-modes INT number of non-zero eigenvectors (modes) to calculate (default: 10) -s SEL, --select SEL atom selection (default: "protein and name CA or nucleic and name P C4' C2") -c FLOAT, --cutoff FLOAT cutoff distance (A) (default: 10.0) -g FLOAT, --gamma FLOAT spring constant (default: 1.0) -m INT, --model INT index of model that will be used in the calculations output: -a, --all-output write all outputs -o PATH, --output-dir PATH output directory (default: .) -e, --eigenvs write eigenvalues/vectors -r, --cross-correlations write cross-correlations -u, --heatmap write cross-correlations heatmap file -q, --square-fluctuations write square-fluctuations -v, --covariance write covariance matrix -z, --npz write compressed ProDy data file -t STR, --extend STR write NMD file for the model extended to "backbone" ("bb") or "all" atoms of the residue, model must have one node per residue -b, --beta-factors write beta-factors calculated from GNM modes -k, --kirchhoff write Kirchhoff matrix output options: -p STR, --file-prefix STR output file prefix (default: pdb_gnm) -f STR, --number-format STR number output format (default: %12g) -d STR, --delimiter STR number delimiter (default: " ") -x STR, --extension STR numeric file extension (default: .txt) figures: -A, --all-figures save all figures -R, --cross-correlations-figure save cross-correlations figure -Q, --square-fluctuations-figure save square-fluctuations figure -B, --beta-factors-figure save beta-factors figure -K, --contact-map save contact map (Kirchhoff matrix) figure -M STR, --mode-shape-figure STR save mode shape figures for specified modes, e.g. "1-3 5" for modes 1, 2, 3 and 5 figure options: -F STR, --figure-format STR pdf (default: pdf) -D INT, --dpi INT figure resolution (dpi) (default: 300) -W FLOAT, --width FLOAT figure width (inch) (default: 8.0) -H FLOAT, --height FLOAT figure height (inch) (default: 6.0)
Running :command:`prody gnm --examples` displays:
This command performs GNM calculations for given PDB structure and outputs results in NMD format. If an identifier is passed, structure file will be downloaded from the PDB FTP server. Fetch PDB 1p38, run GNM calculations using default parameters, and results: $ prody gnm 1p38 Fetch PDB 1aar, run GNM calculations with cutoff distance 7 angstrom for chain A carbon alpha atoms with residue numbers less than 70, and save all of the graphical output files: $ prody gnm 1aar -c 7 -s "calpha and chain A and resnum < 70" -A