crops-renumber options

Cropping and Renumbering Operations for PDB structure and Sequence files (CROPS) v.1.0.2 This script will renumber a structure file in agreement with the residue positions in the sequence file corresponding to that structure.

Non-polymer elements are numbered starting right after the final (TER) residue.

WARNING: If the input sequence and the input structure files are not from the same source (e.g. RCSB PDB) a source conflict might occur making the renumbering operation unsuccessful even if the program does not crash.

usage: crops-renumber [-h] [-r] [-f] [-p Oligoseq_ids [Oligoseq_ids ...]]
                      [-o Output_Directory] [--version]
                      Sequence_filepath Structure_filepath

Positional Arguments

Sequence_filepath
	Input sequence filepath.
Structure_filepath
	Input structure filepath or dir. If a directory is inserted, it will act on all structure files in such directory.

Named Arguments

-r, --remove_ligands
	Remove ligands and water molecules from structure to prevent certain errors during renumbering. Default: False
-f, --force_alignment
	Use Needleman-Wunsch algorithm to try to bypass small disagreements between fasta and pdb sequences. Default: False
-p, --preselect
	From all the sequences in the input sequence file, just print out this preselected subset.
-o, --outdir	Set output directory path. If not supplied, default is the one containing the input sequence.
--version	show program’s version number and exit