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Phenix: Difference between revisions
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== Maps == | == Maps == | ||
=== phenix.maps - a command line tool to compute various maps === | |||
Seems to have no specific documentation. Can do B-factor sharpening for improving low-resolution maps. | |||
=== phenix.real_space_correlation - compute correlation between two maps === | |||
Can work with ensembles of structures. Seems to have no specific documentation. | |||
=== [http://www.phenix-online.org/documentation/get_cc_mtz_mtz.htm phenix.get_cc_mtz_mtz] === | |||
=== phenix.fobs_minus_fobs_map - calculate difference density === | |||
Seems to have no specific documentation. | |||
=== [http://www.phenix-online.org/documentation/multi_crystal_average.htm phenix.multi_crystal_average] === | |||
=== phenix.grow_density - local density improvement === | |||
As originally described in Acta Cryst. (1997). D53, 540-543 (in development). Seems to have no specific documentation. | |||
== NCS usage == | == NCS usage == | ||
=== [http://www.phenix-online.org/documentation/find_ncs.htm phenix.find_ncs] - identification of NCS operators === | |||
from protein coordinates (chains), heavy atom coordinates, or a density map | |||
=== phenix.superpose_maps - transforms maps following a molecular superposition === | |||
Seems to have no specific documentation. | |||
=== [http://www.phenix-online.org/documentation/apply_ncs.htm phenix.apply_ncs] - applying NCS to a molecule to generate all NCS copies === | |||
== Model analysis and manipulation == | == Model analysis and manipulation == | ||
=== [http://www.phenix-online.org/documentation/pdbtools.htm phenix.pbdtools] - PDB model manipulations and statistics === | |||
e.g. | |||
phenix.pbdtools your_model.pdb --show-adp-statistics | |||
will show you complete statistics about B-factors; | |||
phenix.pbdtools your_model.pdb --show-geometry-statistics | |||
will show you complete statistics about stereochemistry, | |||
phenix.pbdtools your_model.pdb set_b_iso=25.3 selection="chain A and resname ALA and name CA" | |||
will set all B=25 for all CA atoms in all ALA residues of chain A. | |||
=== [http://www.phenix-online.org/documentation/hydrogens.htm phenix.reduce] - tool for adding hydrogens to a PDB model === | |||
=== [http://www.phenix-online.org/documentation/superpose_pdbs.htm phenix.superpose_pdbs] - Superposition of models === | |||
== Validation == | == Validation == | ||
=== [http://www.phenix-online.org/documentation/validation.htm#anch14 phenix.polygon] === | |||
starts the GUI and runs calculations resulting in a [http://dx.doi.org/10.1107/S0907444908044296 POLYGON] drawing of important characteristics of your PDB file in relation to the data | |||
=== phenix.validate_model and phenix.validate === | |||
are also GUI-only | |||
=== phenix.ramalyze, phenix.rotalyze, and phenix.cbetadev === | |||
=== phenix.clashscore === | |||
== See also == | == See also == | ||