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There may be one or two data files. | There may be one or two data files. | ||
=== [http://www.phenix-online.org/documentation/xmanip.htm phenix.xmanip] - structure factor file manipulations === | === [http://www.phenix-online.org/documentation/reference/xmanip.htm phenix.xmanip] - structure factor file manipulations === | ||
=== [http://www.phenix-online.org/documentation/model_vs_data.htm phenix.model_vs_data] - statistics === | === [http://www.phenix-online.org/documentation/reference/model_vs_data.htm phenix.model_vs_data] - statistics === | ||
Just use "phenix.model_vs_data model.pdb data.hkl" where data.hkl is a reflection file in most of known formats. phenix.model_vs_data can output the map defined as: | Just use "phenix.model_vs_data model.pdb data.hkl" where data.hkl is a reflection file in most of known formats. phenix.model_vs_data can output the map defined as: | ||
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== Experimental phasing == | == Experimental phasing == | ||
=== [http://www.phenix-online.org/documentation/autosol.htm phenix.autosol] - experimental phasing "wizard" === | === [http://www.phenix-online.org/documentation/reference/autosol.htm phenix.autosol] - experimental phasing "wizard" === | ||
phenix.autosol uses HYSS, SOLVE, Phaser, RESOLVE, xtriage and phenix.refine to solve a structure and generate experimental phases with the MAD, MIR, SIR, or SAD methods | phenix.autosol uses 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/phaser_ep.htm phenix.phaser] - SAD phasing with Phaser === | === [http://www.phenix-online.org/documentation/reference/phaser_ep.htm phenix.phaser] - SAD phasing with Phaser === | ||
[http://www.phaser.cimr.cam.ac.uk/index.php/Phaser_Crystallographic_Software Phaser] can do SAD phasing - it is therefore called phaser_ep (ep stands for "experimental phasing"). The Phenix documentation is at [http://www.phenix-online.org/documentation/phaser_ep.htm]. The keywords are concisely (but somewhat lightly) documented at [http://www.phaser.cimr.cam.ac.uk/index.php/Keywords]. A script documenting the following features | [http://www.phaser.cimr.cam.ac.uk/index.php/Phaser_Crystallographic_Software Phaser] can do SAD phasing - it is therefore called phaser_ep (ep stands for "experimental phasing"). The Phenix documentation is at [http://www.phenix-online.org/documentation/reference/phaser_ep.htm]. The keywords are concisely (but somewhat lightly) documented at [http://www.phaser.cimr.cam.ac.uk/index.php/Keywords]. A script documenting the following features | ||
# using a PDB file (with origin-centered coordinates) as a heavy atom cluster template | # using a PDB file (with origin-centered coordinates) as a heavy atom cluster template | ||
# using two different substructure atomtypes (the cluster, and Fe) | # using two different substructure atomtypes (the cluster, and Fe) | ||
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== Molecular replacement == | == Molecular replacement == | ||
=== [http://www.phenix-online.org/documentation/automr.htm phenix.automr] - interface to Phaser and Resolve === | === [http://www.phenix-online.org/documentation/reference/automr.htm phenix.automr] - interface to Phaser and Resolve === | ||
This "wizard" provides an interface to Phaser molecular replacement and feeds the results of molecular replacement directly into the AutoBuild Wizard for automated model rebuilding | This "wizard" provides an interface to Phaser molecular replacement and feeds the results of molecular replacement directly into the AutoBuild Wizard for automated model rebuilding | ||
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</pre> | </pre> | ||
=== [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/reference/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/reference/ensembler.htm phenix.ensembler] - multiple superposition tool to automate construction of ensembles for MR === | ||
== Ligands == | == Ligands == | ||
=== [http://www.phenix-online.org/documentation/reel.htm phenix.reel] - restraints editor especially for ligands === | === [http://www.phenix-online.org/documentation/reference/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/reference/elbow.htm phenix.elbow] - electronic Ligand Builder and Optimisation Workbench === | ||
== Model building and completion == | == Model building and completion == | ||
=== [http://www.phenix-online.org/documentation/autobuild.htm phenix.autobuild] - "wizard" for model rebuilding and completion === | === [http://www.phenix-online.org/documentation/reference/autobuild.htm phenix.autobuild] - "wizard" for model rebuilding and completion === | ||
phenix.phase_and_build, phenix.build_one_model are fast ways to obtain results. | 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/reference/ligandfit.htm phenix.ligandfit] - "wizard" carrying out fitting of flexible ligands to electron density maps === | ||
=== [http://www.phenix-online.org/documentation/find_helices.htm phenix.find_helices] - rapid helix fitting to a map === | === [http://www.phenix-online.org/documentation/reference/find_helices.htm phenix.find_helices] - rapid helix fitting to a map === | ||
=== phenix.fit_loops - fill short gaps using a loop library, and longer gaps (up to 15 residues) iteratively === | === phenix.fit_loops - fill short gaps using a loop library, and longer gaps (up to 15 residues) iteratively === | ||
=== [http://www.phenix-online.org/documentation/assign_sequence.htm phenix.assign_sequence] - sequence assignment and linkage of neighboring segments === | === [http://www.phenix-online.org/documentation/reference/assign_sequence.htm phenix.assign_sequence] - sequence assignment and linkage of neighboring segments === | ||
=== phenix.ligand_identification === | === phenix.ligand_identification === | ||
== Refinement with [http://www.phenix-online.org/documentation/refinement.htm phenix.refine] == | == Refinement with [http://www.phenix-online.org/documentation/reference/refinement.htm phenix.refine] == | ||
=== Example for use of phenix.refine === | === Example for use of phenix.refine === | ||
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phenix.ready_set internally uses phenix.elbow for ligands and phenix.reduce for the protein. phenix.pdbtools can also add hydrogens (FIXME: what are the differences?). | phenix.ready_set internally uses phenix.elbow for ligands and phenix.reduce for the protein. phenix.pdbtools can also add hydrogens (FIXME: what are the differences?). | ||
Hydrogens should not be used in NCS and TLS groups - it might be a good idea to add <font face="Courier"> and not (element H or element D)</font> to all selection strings. | Hydrogens should not be used in NCS and TLS groups - it might be a good idea to add <font face="Courier"> and not (element H or element D)</font> to all selection strings. | ||
See the [http://www.phenix-online.org/documentation/refinement.htm#anch32 phenix.refine documentation]. | See the [http://www.phenix-online.org/documentation/reference/refinement.htm#anch32 phenix.refine documentation]. | ||
==== Occupancy ==== | ==== Occupancy ==== | ||
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} | } | ||
See the [http://www.phenix-online.org/documentation/refinement.htm#anch26 documentation]. | See the [http://www.phenix-online.org/documentation/reference/refinement.htm#anch26 documentation]. | ||
==== DEN refinement (similar to what is in CNS) ==== | ==== DEN refinement (similar to what is in CNS) ==== | ||
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* 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); | ||
http://skuld.bmsc.washington.edu/~tlsmd/ | http://skuld.bmsc.washington.edu/~tlsmd/ | ||
* use these selections for TLS refinement in PHENIX: see http://www.phenix-online.org/documentation/refinement.htm | * use these selections for TLS refinement in PHENIX: see http://www.phenix-online.org/documentation/reference/refinement.htm | ||
for example: | for example: | ||
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} | } | ||
==== [http://www.phenix-online.org/documentation/refinement.htm#anch28 Fix His/Asn/Gln sidechain orientations] ==== | ==== [http://www.phenix-online.org/documentation/reference/refinement.htm#anch28 Fix His/Asn/Gln sidechain orientations] ==== | ||
Use | Use | ||
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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. | ||
==== [http://www.phenix-online.org/documentation/refinement.htm#anch30 Using a reference model] ==== | ==== [http://www.phenix-online.org/documentation/reference/refinement.htm#anch30 Using a reference model] ==== | ||
A good idea if refinement is done at low resolution but a high resolution model is available. | A good idea if refinement is done at low resolution but a high resolution model is available. | ||
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* In specific (rare !) situations one wants to exclude specific interactions. The pdb_interpretation.custom_nonbonded_symmetry_exclusion=<selection> command line keyword was designed for this purpose. | * In specific (rare !) situations one wants to exclude specific interactions. The pdb_interpretation.custom_nonbonded_symmetry_exclusion=<selection> command line keyword was designed for this purpose. | ||
* 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/reference/refinement.htm#anch80 - you just add restraints of the form: | ||
refinement.geometry_restraints.edits { | refinement.geometry_restraints.edits { | ||
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Can work with ensembles of structures. Seems to have no specific documentation. Can also calculate map CC for all atoms or per residue. | Can work with ensembles of structures. Seems to have no specific documentation. Can also calculate map CC for all atoms or per residue. | ||
=== [http://www.phenix-online.org/documentation/get_cc_mtz_mtz.htm phenix.get_cc_mtz_mtz] === | === [http://www.phenix-online.org/documentation/reference/get_cc_mtz_mtz.htm phenix.get_cc_mtz_mtz] === | ||
=== phenix.fobs_minus_fobs_map - calculate difference density === | === phenix.fobs_minus_fobs_map - calculate difference density === | ||
Seems to have no specific documentation. | Seems to have no specific documentation. | ||
=== [http://www.phenix-online.org/documentation/multi_crystal_average.htm phenix.multi_crystal_average] === | === [http://www.phenix-online.org/documentation/reference/multi_crystal_average.htm phenix.multi_crystal_average] === | ||
=== phenix.grow_density - local density improvement === | === phenix.grow_density - local density improvement === | ||
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with output=xplor produces an X-PLOR style map. Adding a PDB file will result in a masked map. | with output=xplor produces an X-PLOR style map. Adding a PDB file will result in a masked map. | ||
=== [http://www.phenix-online.org/documentation/reciprocal_space_arrays.htm phenix.reciprocal_space_arrays] === | === [http://www.phenix-online.org/documentation/reference/reciprocal_space_arrays.htm phenix.reciprocal_space_arrays] === | ||
computes various arrays such as Fcalc, Fmask, Fmodel, Fbulk, and more. | computes various arrays such as Fcalc, Fmask, Fmodel, Fbulk, and more. | ||
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== NCS usage == | == NCS usage == | ||
=== [http://www.phenix-online.org/documentation/find_ncs.htm phenix.find_ncs] - identification of NCS operators === | === [http://www.phenix-online.org/documentation/reference/find_ncs.htm phenix.find_ncs] - identification of NCS operators === | ||
from protein coordinates (chains), heavy atom coordinates, or a density map. Example: | from protein coordinates (chains), heavy atom coordinates, or a density map. Example: | ||
phenix.find_ncs my_8_molecules.pdb | phenix.find_ncs my_8_molecules.pdb | ||
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Seems to have no specific documentation. | 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 === | === [http://www.phenix-online.org/documentation/reference/apply_ncs.htm phenix.apply_ncs] - applying NCS to a molecule to generate all NCS copies === | ||
Example: | Example: | ||
phenix.apply_ncs find_ncs.ncs_spec chainA.pdb | phenix.apply_ncs find_ncs.ncs_spec chainA.pdb | ||
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== Model analysis and manipulation == | == Model analysis and manipulation == | ||
=== [http://www.phenix-online.org/documentation/pdbtools.htm phenix.pbdtools] - PDB model manipulations and statistics === | === [http://www.phenix-online.org/documentation/reference/pdbtools.htm phenix.pbdtools] - PDB model manipulations and statistics === | ||
e.g. | e.g. | ||
phenix.pdbtools your_model.pdb model_statistics=True | phenix.pdbtools your_model.pdb model_statistics=True | ||
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will result in a output file model_1.pdb.geo which contains ALL geometry information (bonds, angles, torsions, planarity, non-bonded ...) for each and every atom in your model. | will result in a output file model_1.pdb.geo which contains ALL geometry information (bonds, angles, torsions, planarity, non-bonded ...) for each and every atom in your model. | ||
=== [http://www.phenix-online.org/documentation/hydrogens.htm phenix.reduce] - tool for adding hydrogens to a PDB model === | === [http://www.phenix-online.org/documentation/reference/hydrogens.htm phenix.reduce] - tool for adding hydrogens to a PDB model === | ||
=== phenix.pdb_atom_selection === | === phenix.pdb_atom_selection === | ||
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In this example, selects all atoms within 3 A from CA atom in chain A of residue number 9, and writes them into cut.pdb file. | In this example, selects all atoms within 3 A from CA atom in chain A of residue number 9, and writes them into cut.pdb file. | ||
=== [http://www.phenix-online.org/documentation/superpose_pdbs.htm phenix.superpose_pdbs] - Superposition of models === | === [http://www.phenix-online.org/documentation/reference/superpose_pdbs.htm phenix.superpose_pdbs] - Superposition of models === | ||
=== phenix.superpose_ligands - Superposition of ligands === | === phenix.superpose_ligands - Superposition of ligands === | ||
Example files at [http://cci.lbl.gov/~afonine/superpose_ligands/] | Example files at [http://cci.lbl.gov/~afonine/superpose_ligands/] | ||