Phenix: Difference between revisions

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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/]
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edits