Calculates pairwise sequence identity, similarity and normalized similarity score of proteins in a multiple sequence alignment.

Assess models previously generated with modeller with the DOPE method

Extract chains' and polypeptides' sequences from PDB or mmCIF files.

Given a set of protein sequences filters out these with non-standard residues. If not input file given it reads from the standard input and if not output file given it writes to standard output.

Scramble peptide sequences in FASTA format.

Compare a set of images and report a structural similarity index (ssim) matrix, in CSV and Mega-compatible formats.

Take a selection of chains from a set of structures and save them as new structures.

Superimpose a set of protein structures and report a RSMD matrix, in CSV and Mega-compatible formats.

Superimpose a set of protein structures and report a RSMD matrix, in CSV and Mega-compatible formats, using Pymol as a module

Calculate the pairwise distances (euclidean and rmsd) between a set of electrostatic maps, contained in Gaussian cube files, and report these distances in CVS and a Mega compatible formats.

Substract two electrostatic maps, contained in Gaussian cube files, and generate a new electrostatic map with the difference.

Split fasta or other sequences files into individual sequences.

Extract rosetta commons fragments from PDB

Reduce PDF file size without noticeable quality loss.

Unattended video transcoder to H265 and ACC codecs, in MKV containers.

Print basic stats from sequence files.

Remove duplicated protein/nucleic acid sequences, keeping the first occurrence.

Unattended video transcoder to H264 and ACC codecs, in MKV containers.

Unattended video transcoder to XVID and MP3 codecs, in AVI containers.