prody pca


Running prody pca -h displays:

usage: prody pca [-h] [--quiet] [--examples] [-n INT] [-s SEL] [-a] [-o PATH]
                 [-e] [-r] [-u] [-q] [-v] [-z] [-t STR] [-j] [-p STR] [-f STR]
                 [-d STR] [-x STR] [-A] [-R] [-Q] [-J STR] [-F STR] [-D INT]
                 [-W FLOAT] [-H FLOAT] [--psf PSF | --pdb PDB] [--aligned]

positional arguments:
  dcd                   file in DCD or PDB format

optional arguments:
  -h, --help            show this help message and exit
  --quiet               suppress info messages to stderr
  --examples            show usage examples and exit
  --psf PSF             PSF filename
  --pdb PDB             PDB filename
  --aligned             trajectory is already aligned

  -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")

  -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
  -j, --projection      write projections onto PCs

output options:
  -p STR, --file-prefix STR
                        output file prefix (default: pdb_pca)
  -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
  -J STR, --projection-figure STR
                        save projections onto specified subspaces, e.g. "1,2"
                        for projections onto PCs 1 and 2; "1,2 1,3" for
                        projections onto PCs 1,2 and 1, 3; "1 1,2,3" for
                        projections onto PCs 1 and 1, 2, 3

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 pca --examples displays:

This command performs PCA (or EDA) calculations for given multi-model
PDB structure or DCD format trajectory file and outputs results in NMD
format.  If a PDB identifier is given, structure file will be
downloaded from the PDB FTP server.  DCD files may be accompanied with
PDB or PSF files to enable atoms selections.

Fetch pdb 2k39, perform PCA calculations, and output NMD file:

  $ prody pca 2k39

Fetch pdb 2k39 and perform calculations for backbone of residues up to
71, and save all output and figure files:

  $ prody pca 2k39 --select "backbone and resnum < 71" -a -A

Perform EDA of MDM2 trajectory:

  $ prody eda mdm2.dcd

Perform EDA for backbone atoms:

  $ prody eda mdm2.dcd --pdb mdm2.pdb --select backbone