v3.16.2 (2026.2)

New functions

• Added description of ligands/HETatms when available

• Added –no_network to prevent network usage when not available

Extended functions

• water

  • Added support for selective removal of water molecules according to contacts

Bug fixes

• sequences

  • Fixed missing initial fragment, structure sequence header

• backbone

  • Fixed accumulated display of modified residues after consecutive reconstructions

• input

  • Fixed –limit management to avoid useless structure loading

v3.15.6 (2025.1)

Extended functions

• input

  • Added transparent support for .gzipped sequence and structure files

Bug fixes

• input

  • Updated default PDB server

  • Fixed non json serializable np.floats

  • Fixed Str to Seq conversion, forced by Bio.seqrecord

  • Fixed io folder to a safer name

  • Fixed clash distance for severe clashes too short

v3.13.5 (2024.4)

Bug Fixes

• backbone

  • Fixed interactive behaviour when missing sequences

• mutateside

  • Fixed bug. Mutated residue was deleted when using –rebuild

v3.13.4 (2023.3)

Bug Fixes

• sequences

  • Fixed key error bug fix in sequencedata.match_sequence_numbering

v3.13.3 (2023.2)

Extended functions

• input

  • Added assembly download from wwpdb.

  • Added –overwrite_cache to refresh cached structures.

  • improved recognition of CA-only structures.

  • Added automated sequence download for retrieved structure in PDB format

  • –sequence accepts remote download as pdb:{pdb_id}

  • Added remote downloads (structure and sequence) from plain URL’s (http(s) only).

• output

  • Added optional logging of building errors (as –build-warnings).

  • Improved phrasing for some log errors.

• run_time

  • Atom limit check made after download to avoid useless work.

  • Added –time_limit to avoid too lengthy runs. Useful on massive analysis.

• add_hydrogen

  • Full list of residues now requires –verbose.

Deprecated

• input

  • Use of alternative pdb servers (–pdb_servers) for biounits/assemblies. Command-line parameter retained for back-compatibility.

Bug Fixes

• input

  • Default download moved to https (instead of ftp) to avoid detected network restrictions.

• sequences.

  • Fixed errors in sequence recognition when non-protein and non-na chain.

  • Fixed FASTA headers when no gaps.

• models/chains/sequences. Fixed errors when differences in chain composition among models. All models are now analyzed as independent entities.

• Added error message when –rebuild is applied to N term residue. Fix pending.

v3.12.1 (2022.4)

Extended functions

• amide

  • Added –fix auto option to automatically find best fix combination

• chains

  • Added –rename. fixes empty chain labels

  • Added –renumber. allow to renumber/reorganize chains and residues

  • Added –rem_inscodes. removes insertion codes on renumbering

  • Added –rebuild. rebuild chains labels and residue ids from backbone connectivity

• inscodes

  • Added –renumber. Rebuild residue numbering to remove insertion codes

• models

  • Added –build_complex. Converts biounit’s selected models into actual complexes

• sequences

  • Added –output_fasta. Writes sequences found in an external FASTA file

• json

  • Extended information on json summary output

• input format

  • File format for remote download can be defined using extension as in pdb:2ki5.pdb

• output format

  • Added mmCif output (only atom records)

• input management

  • Added –nocache to avoid caching downloaded structures

  • Added –copy_input to recover a copy of the input structure

  • Added –coords_only to discard chain labels and residue ids from input. Used to revover faulty structure files

Bug Fixes

• Added missing defaults for Notebook execution

• Ionized/tautomeric residue names recognized

• Fixed behaviour of structure headers output with missing entries

v3.10.1 (2022.3)

Extended functions

• Structure details

  • Added hydrogen atoms count

• Input files

  • Support for PQR format

• backbone, sequences

  • Input Sequences are automatically assigned to the appropriate chain. No special requirements for FASTA headers

• add_hydrogen

  • Extended to support Nucleic Acids

• sequences

  • Structure sequence is always reported even in the absence of canonical one

• chains

  • Unlabelled chains can be fixed.

Bug Fixes

• Fixed banner format

• Fixed residue id on metals output

• Removed required usage N and C terms 4-letter residue names except of requested output

v3.9.11 (2021.4)

New Functions

• Support for PDBQT files

• add_hydrogen

  • Multiple charge sets accepted (currently ADP, CMIP)

v3.9.10 (2021.4)

New Functions

Extended functions

• Adding new option –keep_canonical_resnames to revert output to canonical residue names when modified by any operation.

• models

  • Select multiple models

  • Superimpose current models

  • Output models as multiple PDB files

Bug Fixes

• add_hydrogen

  • Extended to Nucleic Acids

  • added option to keep canonical residue names

Bug Fixes

• add_hydrogen

  • Forced upper case for FF names

v3.9.9 (2021.4)

Bug Fixes

• Remove pinned numpy dependency

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v3.9.7 (2021.4)

Bug Fixes

• Fixed tests

• Fixed behaviour with –non_interactive and missing command options

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v3.9.6 (2021.4)

Extended functions

• Jupyter Notebook support extended

  • Help(command) function

  • Settings accepted also as Python dictionaries-

• add_hydrogen

  • Added support for multiple atom type sets (currently ADP, CMIP)

  • Added support for pqr, pdbqt, cmip output formats following file extension

  • Added support for pqr input format

  • Terminal residue names available on 3 or 4 letter (N-, C-) codes

• command_list

  • Added support for inline command lists

• mutationside

  • Added support for RNA mutations

Bug Fixes

• Fix charge assignment for modified residues and terminals

• Fixed wrong assigment of RNA residues as protein

• Fixed tests

• Fixed behaviour with –non_interactive and missing command options

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V3.8.5 (2021.2)

New functions

• sequences

  • prints both canonical and structural sequences (protein or NA).

Extended functions

• mutateside

  • added support for mutation of DNA/RNA residues

  • –na_seq allows to set a desired final sequence in a single operation (for DNA duplexes)

• chains

  • allows to select chains according to molecular type (protein | dna | rna | na).

  • Improved guess of chain type.

• getss

  • can now mark CYS residues as part of SSBonds. Further commands like add_hydrogen reacts accordingly

• load

  • can now be used to convert downloaded cif to pdb format using –force_save

• Modeller based commands

  • adapted to support Modeller >= 10.1

• several commands

  • adapted to work with NA chains

• Extended support for verbosity

  • Default verbosity has been reduced to errors and warnigs

  • –nv –quiet removes all progress reports

  • -v adds extra progress report (original default)

Bugs fixed

• clashes, add_hydrogen did not work for modified or cap residues

• mutateside crashed when trying to delete already modified atoms

• added error message when chains will remove all chains in the structure

• added error message when mutateside has no available mutations

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v3.7.3 (2021.1)

Extended functionality

• Added support for biopython 1.78

Bugs fixed

• backbone

  • added error messages for incorrect or missing FASTA sequences

  • backbone reconstruction crashed when not all chains sequences were available even if missing chains where not needed

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v3.0.2

New functions

• –rename_terms

  • Rename N and C terms as NXXX, CXXX

Extended functions:

• mutateside & fixside –rebuild

  • Use Modeller for building the side chains, include conformational search

• backbone –extra_gap

  • Allows to use more residues from the built model to fill backbone breaks (experimental)

• add_hydrogen –add_charges

  • Adds point charges to atoms and produces a PDBQT output suitable for autodock

Bug fixes

• –debug

  • Psutils import failed even when –debug was not requested

• backbone

  • Residue internal pointers corrupted when backbone was modified