1,328
edits
Phenix: Difference between revisions
no edit summary
(re-organization) |
No edit summary |
||
| Line 5: | Line 5: | ||
A short help, such as usage and options, is printed out by all PHENIX command line tools: just type phenix.TOOLNAME and hit Enter (or Return). | A short help, such as usage and options, is printed out by all PHENIX command line tools: just type phenix.TOOLNAME and hit Enter (or Return). | ||
The documentation below focuses on the non-GUI commandline tools and may not be complete, nor up-to-date. | |||
== Crystallographic data == | |||
* [http://www.phenix-online.org/documentation/xtriage.htm phenix.xtriage] - assessing data quality | * [http://www.phenix-online.org/documentation/xtriage.htm phenix.xtriage] - assessing data quality | ||
* [http://www.phenix-online.org/documentation/explore_metric_symmetry.htm phenix.explore_metric_symmetry] <font face="Courier">--unit_cell=145,44,67,90,110.5,90 --space_group=C2 --other_unit_cell=67,44,136,90,96,90 --other_space_group=p2</font> - investigate different settings | * [http://www.phenix-online.org/documentation/explore_metric_symmetry.htm phenix.explore_metric_symmetry] <font face="Courier">--unit_cell=145,44,67,90,110.5,90 --space_group=C2 --other_unit_cell=67,44,136,90,96,90 --other_space_group=p2</font> - investigate different settings | ||
| Line 16: | Line 18: | ||
* phenix.cif_as_mtz | * phenix.cif_as_mtz | ||
== Experimental phasing == | |||
* [http://www.phenix-online.org/documentation/autosol.htm phenix.autosol] - "wizard" using HYSS, SOLVE, Phaser, RESOLVE, xtriage and phenix.refine to solve a structure and generate experimental phases with the MAD, MIR, SIR, or SAD methods | * [http://www.phenix-online.org/documentation/autosol.htm phenix.autosol] - "wizard" using HYSS, SOLVE, Phaser, RESOLVE, xtriage and phenix.refine to solve a structure and generate experimental phases with the MAD, MIR, SIR, or SAD methods | ||
== Preparation for molecular replacement == | |||
* [http://www.phenix-online.org/documentation/sculptor.htm phenix.sculptor] - automate selection and editing of molecular replacement (MR) models | * [http://www.phenix-online.org/documentation/sculptor.htm phenix.sculptor] - automate selection and editing of molecular replacement (MR) models | ||
* [http://www.phenix-online.org/documentation/ensembler.htm phenix.ensembler] - multiple superposition tool to automate construction of ensembles for MR | * [http://www.phenix-online.org/documentation/ensembler.htm phenix.ensembler] - multiple superposition tool to automate construction of ensembles for MR | ||
== Molecular replacement == | |||
* [http://www.phenix-online.org/documentation/automr.htm phenix.automr] - "wizard" providing an interface to Phaser molecular replacement and feeding the results of molecular replacement directly into the AutoBuild Wizard for automated model rebuilding | * [http://www.phenix-online.org/documentation/automr.htm phenix.automr] - "wizard" providing an interface to Phaser molecular replacement and feeding the results of molecular replacement directly into the AutoBuild Wizard for automated model rebuilding | ||
== Ligands == | |||
* http://www.phenix-online.org/documentation/reel.htm phenix.reel - restraints editor especially for ligands | * http://www.phenix-online.org/documentation/reel.htm phenix.reel - restraints editor especially for ligands | ||
* [http://www.phenix-online.org/documentation/elbow.htm phenix.elbow] - electronic Ligand Builder and Optimisation Workbench | * [http://www.phenix-online.org/documentation/elbow.htm phenix.elbow] - electronic Ligand Builder and Optimisation Workbench | ||
== Model building and completion == | |||
* [http://www.phenix-online.org/documentation/autobuild.htm phenix.autobuild] - "wizard" for model rebuilding and completion. phenix.phase_and_build, phenix.build_one_model are fast ways to obtain results. | * [http://www.phenix-online.org/documentation/autobuild.htm phenix.autobuild] - "wizard" for model rebuilding and completion. phenix.phase_and_build, phenix.build_one_model are fast ways to obtain results. | ||
* [http://www.phenix-online.org/documentation/ligandfit.htm phenix.ligandfit] - "wizard" carrying out fitting of flexible ligands to electron density maps | * [http://www.phenix-online.org/documentation/ligandfit.htm phenix.ligandfit] - "wizard" carrying out fitting of flexible ligands to electron density maps | ||
* phenix.phase_and_build and phenix.build_one_model - fast autobuild | * phenix.phase_and_build and phenix.build_one_model - fast autobuild | ||
* [http://www.phenix-online.org/documentation/find_helices.htm phenix.find_helices] - rapid helix fitting to a map | * [http://www.phenix-online.org/documentation/find_helices.htm phenix.find_helices] - rapid helix fitting to a map | ||
| Line 51: | Line 41: | ||
* phenix.ligand_identification | * phenix.ligand_identification | ||
== Refinement with [http://www.phenix-online.org/documentation/refinement.htm phenix.refine] == | |||
== Example for use of phenix.refine == | === Example for use of phenix.refine === | ||
=== basic usage === | ==== basic usage ==== | ||
phenix.refine model.pdb data.mtz | phenix.refine model.pdb data.mtz | ||
Here "data.mtz" is your reflection data file. PHENIX automatically recognizes most of the known file formats, so it can be MTZ, CNS or ... | Here "data.mtz" is your reflection data file. PHENIX automatically recognizes most of the known file formats, so it can be MTZ, CNS or ... | ||
=== advanced usage === | ==== advanced usage ==== | ||
phenix.refine model.pdb data.mtz strategy=rigid_body+individual_sites+individual_adp \ | phenix.refine model.pdb data.mtz strategy=rigid_body+individual_sites+individual_adp \ | ||
simulated_annealing=true optimize_wxc=true optimize_wxu=true main.number_of_macro_cycles=5 \ | simulated_annealing=true optimize_wxc=true optimize_wxu=true main.number_of_macro_cycles=5 \ | ||
| Line 90: | Line 64: | ||
''Warning'': the file model.pdb in this example should '''not''' have any '''ANISOU''' records! If it has any, these would be refined as individual anisotropic which is most likely not desired. | ''Warning'': the file model.pdb in this example should '''not''' have any '''ANISOU''' records! If it has any, these would be refined as individual anisotropic which is most likely not desired. | ||
== Ligands == | === Ligands === | ||
If some ligand in model.pdb is unknown, phenix.refine will complain: | If some ligand in model.pdb is unknown, phenix.refine will complain: | ||
| Line 107: | Line 81: | ||
If no PDB file for a ligand is available, its SMILES string should be input to phenix.elbow, and phenix.ready_set should run to generate the LINK records (e.g. for a non-natural amino acid that is part of the polypeptide chain), using phenix.elbow's CIF file. | If no PDB file for a ligand is available, its SMILES string should be input to phenix.elbow, and phenix.ready_set should run to generate the LINK records (e.g. for a non-natural amino acid that is part of the polypeptide chain), using phenix.elbow's CIF file. | ||
== Constraints and restraints in real and reciprocal space == | === Constraints and restraints in real and reciprocal space === | ||
=== Hydrogens === | ==== Hydrogens ==== | ||
Use phenix.ready_set to add hydrogens to your PDB file, and (except at ultra-high resolution) the riding hydrogen model in phenix.refine (this is the default so you do not have to specify anything). | Use phenix.ready_set to add hydrogens to your PDB file, and (except at ultra-high resolution) the riding hydrogen model in phenix.refine (this is the default so you do not have to specify anything). | ||
| Line 116: | Line 90: | ||
See the [http://www.phenix-online.org/documentation/refinement.htm#anch32 phenix.refine documentation]. | See the [http://www.phenix-online.org/documentation/refinement.htm#anch32 phenix.refine documentation]. | ||
=== Occupancy === | ==== Occupancy ==== | ||
Adding "occupancy" to the "strategy" options will refine the occupancies of those parts of the model that have alternate conformations. | Adding "occupancy" to the "strategy" options will refine the occupancies of those parts of the model that have alternate conformations. | ||
=== NCS === | ==== NCS ==== | ||
Automatic detection of NCS groups: | Automatic detection of NCS groups: | ||
| Line 139: | Line 113: | ||
} | } | ||
=== Secondary structure restraints === | ==== Secondary structure restraints ==== | ||
phenix.refine model.pdb data.mtz main.secondary_structure_restraints=true | phenix.refine model.pdb data.mtz main.secondary_structure_restraints=true | ||
| Line 145: | Line 119: | ||
You can find more information about secondary structure restraints in the [http://www.phenix-online.org/newsletter/CCN_2010_07.pdf PHENIX Newsletter] (pages 12-17). | You can find more information about secondary structure restraints in the [http://www.phenix-online.org/newsletter/CCN_2010_07.pdf PHENIX Newsletter] (pages 12-17). | ||
=== Low resolution refinement === | ==== Low resolution refinement ==== | ||
Use an existing high resolution model (e.g. in a different spacegroup) for restraining the dihedrals: | Use an existing high resolution model (e.g. in a different spacegroup) for restraining the dihedrals: | ||
| Line 152: | Line 126: | ||
See the [http://www.phenix-online.org/documentation/refinement.htm#anch26 full documentation]. | See the [http://www.phenix-online.org/documentation/refinement.htm#anch26 full documentation]. | ||
=== TLS === | ==== TLS ==== | ||
* run your model through TLSMD server to identify TLS domains (it will produce PHENIX friendly TLS groups selections); | * run your model through TLSMD server to identify TLS domains (it will produce PHENIX friendly TLS groups selections); | ||
| Line 170: | Line 144: | ||
} | } | ||
=== Rigid body === | ==== Rigid body ==== | ||
example for file rigid_body.def defining 2 rigid bodies: | example for file rigid_body.def defining 2 rigid bodies: | ||
| Line 178: | Line 152: | ||
} | } | ||
=== [http://www.phenix-online.org/documentation/refinement.htm#anch28 Fix His/Asn/Gln sidechain orientations] === | ==== [http://www.phenix-online.org/documentation/refinement.htm#anch28 Fix His/Asn/Gln sidechain orientations] ==== | ||
Use | Use | ||
| Line 184: | Line 158: | ||
to automatically flip these sidechains to make them better fit the density and/or hydrogen bonding pattern. | to automatically flip these sidechains to make them better fit the density and/or hydrogen bonding pattern. | ||
== Atom selection == | === Atom selection === | ||
e.g. | e.g. | ||
phenix.refine model.pdb data.mtz refine.sites.individual="not (chain A and resseq 123:156)" | phenix.refine model.pdb data.mtz refine.sites.individual="not (chain A and resseq 123:156)" | ||
== Switching off specific interactions == | === Switching off specific interactions === | ||
To switch off the interaction between a specific atom and its environment, e.g. to obtain unbiased (by restraints) estimates of distances, see http://www.phenix-online.org/documentation/refinement.htm#anch80 - you just add restraints of the form: | To switch off the interaction between a specific atom and its environment, e.g. to obtain unbiased (by restraints) estimates of distances, see http://www.phenix-online.org/documentation/refinement.htm#anch80 - you just add restraints of the form: | ||
| Line 206: | Line 180: | ||
} | } | ||
} | } | ||
== 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 == | |||
* [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 copiea | |||
== Model analysis and manipulation == | |||
* [http://www.phenix-online.org/documentation/pdbtools.htm phenix.pbdtools] - PDB model manipulations and statistics; e.g. <font face="Courier">phenix.pbdtools your_model.pdb --show-adp-statistics</font> will show you complete statistics about B-factors; <font face="Courier">phenix.pbdtools your_model.pdb --show-geometry-statistics</font> will show you complete statistics about stereochemistry, <font face="Courier">phenix.pbdtools your_model.pdb set_b_iso=25.3 selection="chain A and resname ALA and name CA" </font>- this 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 == | |||
* [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 == | ||