| (no keyword)|| Name of PDB file|
| data=None|| Name of MTZ file|
| asu_file=None|<base>|| If given, this switches on file output and represents the base name for the output pdb files. Three types of files are written: |
- For each coset N, an asymmetric unit model in the target (higher) symmetry space group (containing only the matched peptides), to file <base>_coset<N>.pdb.
- For each coset N, a degenerate model in the input space group containing all atoms in the original structure but with potential symmetry applied, to file <base>_degen<N>.pdb.
- A structure factor file containing observations merged into the higher symmetry space group. File <base>_amplitude_<sg>.mtz (<sg> is the higher symmetry group), data label FOBS_MERGE_EQ.
- Only use this file if the original diffraction images are not available, otherwise re-integrate the data into the higher space group, using labelit.index pdb_file=<base>_coset0.pdb to constrain to the correct symmetry.
- If the input column label "R-free-flags" exists, then Rfree flags will be merged into the higher-symmetry space group, marking any reflection as rfree=1 if any one of its lower-symmetry equivalents was set to 1.
| asu_file_scratch=False|| If True, an additional file is written, <base>_scratch<N>.pdb, giving all input atoms, |
transformed in to the target (higher) symmetry space group setting. This is intended chiefly for transforming ligand atoms, which are not assigned to coset asu models by the program.
| d_min=-1.0|| Override for the outer resolution cutoff (Angstroms)|
| ignore_chain=None|| For a structure to qualify as having higher symmetry, each chain must be matched. Use ignore_chain=A to remove chain 'A' from the matching requirement, if it is known ahead of time to lack a higher-symmetry match. This is useful for oligopeptides. Program does not currently permit multiple chain id's (contact authors for fix).|
| max_delta=3.0|| Maximum Le Page delta (degrees) for determining the lattice symmetry |
| r_symop_tol=0.25 || Maximum allowable symmetry operator R factor on calculated intensities (eq 1)|
| peak_cutoff=0.8 || Minimum height of peak from fast translation search (eq 2)|
| score_tol=0.25 || Maximum allowable phase weighted score (eq 3)|
| rotation_tolerance=0.1|| Tolerance for rotation match of two alpha-carbon sets (fractional coords)|
| translation_tolerance=0.1|| Tolerance for translational match of two alpha-carbon sets (fractional)|
| verbose_match=False|| If True, amino acid sequences for the potentially symmetry-matched chains are printed.|