- chainidPDB (version 1.1.0, previously named “change_chainid”)
- Added the ability to specify in finer detail which PDB components have their chain identifiers modified.
Option '--model=' ('-a') was added to restrict modification to individual MODELs.
Option '--from=' ('-f') now accepts either a simple list of chain identifiers or a triplet list of existing chain identifier, residue #, atom #.
This triplet list allows flexible target specifications to be made that are either very restrictive
(e.g., either a specific atom in a specific residue in a specific chain in a specific model)
or more general (e.g., all records with residue 'N' regardless of chain identifier, etc.)
- Residue numbers for output chains are now automatically changed to be unique;
new option '--noresiduechange' ('-x') may be used to prevent residue numbers from being changed.
- Output records are now automatically fixed to new chain order;
new option '--nopositionchange' ('-p') may be used to prevent record position from being changed.
- New option '--map=' ('-m') may be used to generate a text file listing atom changes.
- "REMARK 250" lines are now added to the output PDB header specifying execution details.
- The character tilde ('~') may be used as a short-hand for your home directory for all specified files.
- combinePDB (version 1.1.1, previously named “combine”)
- Fixed the output of some error lines from stdout to stderr.
- Fixed the fourth connected atom index for output CONECT records.
- Residue numbers for output chains are now automatically changed to be unique;
new option '--noresiduechange' ('-x') may be used to prevent residue numbers from being changed.
- Output records are now automatically fixed to new chain order;
new option '--nopositionchange' ('-p') may be used to prevent record position from being changed.
- The character tilde ('~') may be used as a short-hand for your home directory for all specified files.
- deviation (version 1.0.1)
- The character tilde ('~') may be used as a short-hand for your home directory for all specified files.
- dist (version 1.0.2)
- The character tilde ('~') may be used as a short-hand for your home directory for all specified files.
- stripPDB (version 1.0.2)
- stripPDB is a new program.
stripPDB removes specified atoms from an input PDB file and writes a new output PDB file.
The atoms to be removed may be specified with simple preset options, a simple list of chain identifiers, or a triplet list (as defined above for 'change_chainid').
- twwistPDB (version 1.3.0, previously named “twwist”)
- Fixes made for more accurate positioning.
- Fixes made for more efficient execution.
- "REMARK 250" lines are now added to the output PDB header specifying execution details.
- The character tilde ('~') may be used as a short-hand for your home directory for all specified files.
- wwavePDB (version 1.0.4, previously named “wwaves”)
- Fixes made for more efficient execution.
- Added the ability to restrict set reference atoms by atom type with the command line option/value pairs: “--restrict=only_ref_atom” ('-r g'), “--restrict=only_ref_hetatm” ('-r h'), and “--restrict=ref_any_type” ('-r i').
- The character tilde ('~') may be used as a short-hand for your home directory for all specified files.
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