prody gnm


Running 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]

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

  -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

  -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)

  -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 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

  $ 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