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
v3.9.7 (2021.4)¶
Bug Fixes¶
- Fixed tests
- Fixed behaviour with –non_interactive and missing command options
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
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
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
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