Running :command:`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] dcd 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 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") 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 -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) figures: -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 :command:`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