Running :command:`prody align -h` displays:
usage: prody align [-h] [--quiet] [--examples] [-s SEL] [-m INT] [-i INT] [-o INT] [-p STR] [-x STR] pdb [pdb ...] positional arguments: pdb PDB identifier(s) or filename(s) optional arguments: -h, --help show this help message and exit --quiet suppress info messages to stderr --examples show usage examples and exit atom/model selection: -s SEL, --select SEL reference structure atom selection (default: calpha) -m INT, --model INT for NMR files, reference model index (default: 1) chain matching options: -i INT, --seqid INT percent sequence identity (default: 90) -o INT, --overlap INT percent sequence overlap (default: 90) output options: -p STR, --prefix STR output filename prefix (default: PDB filename) -x STR, --suffix STR output filename suffix (default: _aligned)
Running :command:`prody align --examples` displays:
Align models in a PDB structure or multiple PDB structures and save aligned coordinate sets. When multiple structures are aligned, ProDy will match chains based on sequence alignment and use best match for aligning the structures. Fetch PDB structure 2k39 and align models (reference model is the first model): $ prody align 2k39 Fetch PDB structure 2k39 and align models using backbone of residues with number less than 71: $ prody align 2k39 --select "backbone and resnum < 71" Align 1r39 and 1zz2 onto 1p38 using residues with number less than 300: $ prody align --select "resnum < 300" 1p38 1r39 1zz2 Align all models of 2k39 onto 1aar using residues 1 to 70 (inclusive): $ prody align --select "resnum 1 to 70" 1aar 2k39 Align 1fi7 onto 1hrc using heme atoms: $ prody align --select "noh heme and chain A" 1hrc 1fi7