- backbone
- Fixed interactive behaviour when missing sequences
- mutateside
- Fixed bug. Mutated residue was deleted when using --rebuild
- 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.
- input
- Use of alternative pdb servers (--pdb_servers) for biounits/assemblies. Command-line parameter retained for back-compatibility.
- 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.
- 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.
- Added missing defaults for Notebook execution.
- Ionized/tautomeric residue names recognized.
- Fixed behaviour of structure headers output with missing entries.
- 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.
- Fixed banner format
- Fixed residue id on metals output
- Removed required usage N and C terms 4-letter residue names except of requested output
- Support for PDBQT files
- add_hydrogen
- Multiple charge sets accepted (currently ADP, CMIP)
-
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
- add_hydrogen
- Extended to Nucleic Acids
- added option to keep canonical residue names
- add_hydrogen
- Forced upper case for FF names
- Remove pinned numpy dependency
- Fixed tests
- Fixed behaviour with --non_interactive and missing command options
-
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
- 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
- sequences
- prints both canonical and structural sequences (protein or NA).
-
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)
- 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
- Added support for biopython 1.78
- 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
- --rename_terms
- Rename N and C terms as NXXX, CXXX
- 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
- --debug
- Psutils import failed even when --debug was not requested
- backbone
- Residue internal pointers corrupted when backbone was modified