Phenix: Difference between revisions
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(or similarly for .cshrc) and | (or similarly for .cshrc) and | ||
rosetta.build_phenix_interface | rosetta.build_phenix_interface | ||
needs to be run; the latter step takes hours. | needs to be run; the latter step takes hours when doing it for the first time. (According to the docs, this is only needed for rosetta_refine.) | ||
If this fails (for example, compiler error messages), then one must re-compile Phenix and/or Rosetta. Try to re-compile only Phenix first (and after that, try rosetta.build_phenix_interface again); Rosetta re-compilation may take hours. There are several issues associated with re-compilation: | If this fails (for example, compiler error messages), then one must re-compile Phenix and/or Rosetta. Try to re-compile only Phenix first (and after that, try rosetta.build_phenix_interface again); Rosetta re-compilation may take hours. There are several issues associated with re-compilation: |
Revision as of 09:23, 28 May 2017
PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is a software suite for the automated determination and refinement of macromolecular structures using X-ray crystallography and other methods. It integrates well with CCP4-formatted files for I/O, is highly automated, and very straightforward to use.
The suite (Phenix home page; documentation) has a GUI program (phenix) which can be used to run the programs, but they also work from the command line.
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). Note that you can get a complete list of jiffies with
phenix.list
There is also version-specific documentation, e.g. http://www.phenix-online.org/version_docs/dev-572 documents development version 572.
The documentation below focuses on the non-GUI commandline tools and may not be complete, nor up-to-date or even correct.
Installation problem on NFS for Mac OSX (posting of 23 Jan 2015)
The problem:
In an effort to save us from malware, OS X now adds a 'quarantine' attribute to downloaded files. This includes tar and compressed tar files. For most users the quarantine flag only really comes into play if the downloaded file is an application or installer package.
When Yosemite untars an archive with the quarantine attribute, it adds the quarantine attribute to every file it extracts from the archive.
This doesn't present a problem if you're extracting the archive to a local disk, or an AFP-mounted network volume. If you're extracting the archive to an NFS-mounted network volume, it can't store the quarantine flag as a resource fork on the file itself. Instead, it creates a ._<filename> file for each extracted file.
The Phenix installer doesn't like having an install tree full of unexpected ._ files. In some cases, such as where generate_henke_cpp.py tries to generate tables from all the files in a directory, it tries to read ._ files as normal files and dies.
The solution:
The solution is trivial once you know what the problem is. Remove the quarantine attribute from the tar file before extracting its contents. For example:
xattr -d com.apple.quarantine phenix-installer-1.9-1692-mac-intel-osx-x86_64.tar.gz
Of course, if the Phenix installer could be modified so that it doesn?t die when it finds unexpected ._ files, that would be lovely.
Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk
Crystallographic data
phenix.xtriage - assessing data quality
phenix.explore_metric_symmetry - investigate different settings
phenix.explore_metric_symmetry --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
The CCP4 equivalent is othercell.
phenix.reflection_statistics - compare datasets
There may be one or two data files.
phenix.xmanip - structure factor file manipulations
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:
[p][m]Fo+[q][D]Fc[kick][filled].
Examples: 2mFo-DFc, 3.2Fo-2.3Fc, Fc, anom, fo-fc_kick.
So, if you say
phenix.model_vs_data model.pdb data.mtz --map=fc
you will get an MTZ file with desired structure factors.
phenix.model_vs_data model.pdb data.mtz --comprehensive=true
will list (among other things) map CC for all atoms or per residue.
PDB deposition: phenix.model_vs_data model.pdb data.mtz will give B-factor statistics. Look for lines like this in the output:
ADP (min,max,mean): all (136 atoms): 4.4 97.6 25.3 side chains (48 atoms): 4.9 96.8 21.0 main chains (64 atoms): 4.4 97.6 28.3 macromolecule (112 atoms): 4.4 97.6 25.2 ligands (1 atoms): 6.6 6.6 6.6 solvent (23 atoms): 8.8 44.1 26.8 mean bonded (Bi-Bj) : 27.91 number_of_anisotropic : 0 number_of_non_positive_definite : 0
phenix.real_space_correlation - statistics
Like phenix.model_vs_data plus gives you more options and controls.
phenix.fmodel - calculate structure factors from model
phenix.cif_as_mtz - convert cif to mtz format
phenix.find_tls_groups
- identifies suitable atom selections for TLS refinement
- similar to TLSMD, but uses cross-validation to yield one unique solution
phenix.data_viewer
- visualization of reciprocal-space reflection data (similar to 'hklview' in CCP4i)
- 3D OpenGL view of all data, or 2D view of planes (pseudo-precession photograph)
Experimental phasing
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.phaser - SAD phasing with Phaser
Phaser can do SAD phasing - it is therefore called phaser_ep (ep stands for "experimental phasing"). The Phenix documentation is at [1]. The keywords are concisely (but somewhat lightly) documented at [2]. A script documenting the following features
- using a PDB file (with origin-centered coordinates) as a heavy atom cluster template
- using two different substructure atomtypes (the cluster, and Fe)
- using a PDB file of a preliminary protein model, for finding sites
- using a MTZ file of a preliminary protein model, for finding sites
- using known sites (from e.g. SHELXD or HYSS)
- 3. and 5. are combined in this example
is shown below:
phenix.phaser <<eof CTITLe XXX W12 SAD MODE EP_AUTO # name for output files: ROOT XXXphaser COMPOSITION PROTEIN NRES 2000 NUMBER 1 WAVELENGTH 1.2029 RESOLUTION 70 4.5 # HAND BOTH # file with F+ F- SIGF+ SIGF- from XDS/XDSCONV using filetype CCP4_F: HKLIN XXXp.mtz CRYSTAL unknown DATASET unknown & LABIN Fpos = F(+) SIGFpos = SIGF(+) Fneg = F(-) SIGFneg = SIGF(-) # use a rough model of the protein to get phases: PARTIAL PDB rigid.1.pdb RMS 2. # alternatively a MTZ file can be used, but the PDB should be preferred # PARTIAL HKLIN rigid.1.mtz RMS 2. # if sites are known, use them: ATOM CRYSTAL unknown PDB knownsites.pdb # the next keywords are documented at http://www.phaser.cimr.cam.ac.uk/index.php/Keywords # here they are commented out since the file knownsites.pdb is from an earlier phaser job. # ATOM CHANGE BFACTOR WILSON ON # ATOM CHANGE SCATTERER XX # BFACTOR WILSON RESTRAINT OFF # the W12 cluster was found in Hicup (xray.bmc.uu.se/hicup/) and put at the origin # using moleman2's "xyz cen" command (I don't know if this is necessary!) CLUSTER PDB keg-cen.pdb # the scatterer XX is predefined and refers to the cluster! Where is this documented ?? # FP and FDP are just guesses; fortunately FDP is refined # however it is not documented what F0 of the cluster is! SCATTERING TYPE XX FP=-1 FDP=13 FIX OFF LLGCOMPLETE NCYC 50 LLGCOMPLETE COMPLETE ON LLGCOMPLETE SCATTERER XX LLGCOMPLETE SCATTERER Fe eof
Molecular replacement
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
phenix.phaser
Officially documented in the phaserwiki. It can be run from the commandline (and can serve as a replacement for the CCP4 phaser which is an older version!) and by the Phaser-MR GUI which supports the fine-tuning of parameters.
If you run this:
phenix.phaser params.eff
it will use the Phenix-style configuration file, but if you just run "phenix.phaser" with no arguments (or a shell redirect from a file), it will use the CCP4-style keyword input.
This is an example of params.eff.
Another example, this time for just doing rigid-body refinement (say, for transferring a model to a crystal with slightly different cell parameters):
#!/bin/csh -f rm rigid.1.pdb rigid.1.mtz phaser<<eof TITLE rigid body MODE MR_RNP ROOT rigid JOBS 1 HKLIN myprotein.mtz LABIN F=FP SIGF=SIGFP # use a preliminary refined model ENSEMBLE ensemble1 PDB mybestmodel.pdb IDENT 1.5 COMPOSITION BY COMPONENT COMPOSITION PROTEIN NRES 2000 NUMBER 1 SOLUTION ORIGIN ENSEMBLE ensemble1 eof
phenix.sculptor - automate selection and editing of molecular replacement (MR) models
phenix.ensembler - multiple superposition tool to automate construction of ensembles for MR
Ligands
phenix.reel - restraints editor especially for ligands
phenix.elbow - electronic Ligand Builder and Optimisation Workbench
Model building and completion
phenix.autobuild - "wizard" for model rebuilding and completion
phenix.phase_and_build, phenix.build_one_model are fast ways to obtain results.
phenix.ligandfit - "wizard" carrying out fitting of flexible ligands to electron density maps
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.assign_sequence - sequence assignment and linkage of neighboring segments
phenix.ligand_identification
Refinement with phenix.refine
Example for use of phenix.refine
basic usage
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 ...
advanced usage
phenix.refine model.pdb data.mtz strategy=rigid_body+individual_sites+individual_adp \ simulated_annealing=true optimize_xyz_weight=true optimize_adp_weight=true main.number_of_macro_cycles=5 \ ordered_solvent=True
This will do the following:
- Rigid body refinement first cycle only (MZ protocol = VERY high convergence radius);
- Refinement of individual xyz and b-factors every cycle with optimized weights (info: optimize_xyz_weight=true optimize_adp_weight=true makes the program take longer!);
- Simulated annealing at 2nd and one before the last cycles;
- find (and remove if necessary) water molecules
restricting the resolution
xray_data.high_resolution=2.5
will restrict the high resolution limit to 2.5 A.
Ligands
If some ligand in model.pdb is unknown, phenix.refine will complain:
Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 18 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary (see phenix.refine documentation). Also note that phenix.elbow is available to create restraint definitions for unknown ligands.
In that case, just running
phenix.elbow model.pdb --do-all --output=all_ligands
will produce all_ligands.cif, which may be fed to phenix.refine by
phenix.refine model.pdb data.mtz all_ligands.cif ...
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
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). 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 and not (element H or element D) to all selection strings. See the phenix.refine documentation.
Occupancy
Adding "occupancy" to the "strategy" options will refine the occupancies of those parts of the model that have alternate conformations.
Example:
occupancies { constrained_group { selection = "chain A and resseq 105 and altloc A" selection = "chain B and resseq 105 and altloc B" } }
Essentially, the above selection tells: "alternative conformation A of residue 105 in chain A is coupled with alternative conformation B of (NCS related) residue 105 in chain B". The sum of refined occupancies will be 1 in this case. It is essential that altlocs in both selections are different - this turn the non-bonded interaction off so the residues will get pushed apart.
NCS
more on this: see Phenix#NCS_usage
- Automatic detection of NCS groups:
phenix.refine data.hkl model.pdb main.ncs=True
- Manual specification of NCS groups:
phenix.refine data.hkl model.pdb ncs_groups.params main.ncs=True
where ncs_groups.params contains e.g.:
refinement.ncs.restraint_group { reference = chain A selection = chain B selection = chain C } refinement.ncs.restraint_group { reference = chain E selection = chain F }
It seems that since Phenix 1.10.1-2155 mains.ncs=True was replaced by ncs_search.enabled=True
- switching to torsion-angle NCS:
ncs.type=torsion
- switch off the restraints on NCS-related B-factors:
ncs.b_factor_weight=0
Secondary structure restraints
phenix.refine model.pdb data.mtz main.secondary_structure_restraints=true
You can find more information about secondary structure restraints in the PHENIX Newsletter (pages 12-17).
Low resolution refinement
Use an existing high resolution model (e.g. in a different spacegroup) for restraining the dihedrals:
phenix.refine data.hkl model.pdb main.reference_model_restraints=True reference_model.file=reference.pdb
The behaviour can be modified with the keywords reference_model.limit (default 15 degrees) and reference_model.sigma (default probably 1 degrees - the current documentation says 1 Angstrom which is probably not right).
In the case where your working model has four chains (A, B, C, D) and your reference model has only chain A, the selections would look like this:
refinement.reference_model.reference_group { reference = chain A selection = chain A } refinement.reference_model.reference_group { reference = chain A selection = chain B } refinement.reference_model.reference_group { reference = chain A selection = chain C } refinement.reference_model.reference_group { reference = chain A selection = chain D }
See the documentation.
DEN refinement (similar to what is in CNS)
DEN restraints can be activated in phenix.refine from the command-line with the current version and latest nightly builds, and they are the same deformable elastic network restraints available in CNS. PHENIX developers have been working closely with Axel Brunger and Gunnar Schroder to implement DEN in Phenix.
They have not yet officially announced the DEN restraints as they are still being tested and actively developed to get the implementation just right, and the parameterization is still very much in flux. It is hoped that by the next version it will become and a stable feature, and at that point DEN will be added as an option in the GUI.
These restraints have been shown to be particularly useful at low resolution, and there has been success in using at 4-5A and below. It is unclear how useful they would be at relatively high resolution (say 2.5A or higher), as there are other restraint methods that work well at that resolution range that are far less computationally intensive.
In almost all cases it is best to optimize the gamma and weight parameters, which is quite time intensive but is most likely to give the best results. Currently this can be parallelized, but only on cores that share memory. If you do optimize the gamma and weight parameters, you cannot simultaneously optimize B factor weights, which is another limitation that will be overcome in the future.
As soon as a stable version is announced in the context of a new release, documentation will be available.
To use DEN with the current release (1.7.3), you can use a parameterization such as this:
refinement { main { den_refinement = True number_of_macro_cycles = 1 nproc = 8 } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous } den { reference_file = reference.pdb optimize = True annealing_type = *torsion cartesian final_refinement_cycle = True } }
TLS
- run your model through TLSMD server to identify TLS domains (it will produce PHENIX friendly TLS groups selections);
http://skuld.bmsc.washington.edu/~tlsmd/
- use these selections for TLS refinement in PHENIX: see http://www.phenix-online.org/documentation/refinement.htm
for example:
phenix.refine model.pdb data.hkl strategy=individual_sites+individual_adp+tls tls_selections.def
with tls_selections.def something like:
refinement.refine { adp { tls = chain 'A' tls = chain 'B' } }
Alternatively, phenix.refine can identify TLS groups on-the-fly, using tls.find_automatically=True
- phenix.find_tls_groups now can find TLS groups automatically, and generate a tls_selections.def file.
At lower resolution than 1.5A if you run two consecutive refinements, first with TLS and the next one without TLS, then in the second run anisotropic ADPs will be converted to isotropic automatically. This is done by phenix.refine to prevent accidental refinement of individual anisotropic ADPs in such cases. The keyword and threshold are: switch_to_isotropic_high_res_limit=1.5. At better resolution, all atoms which have ANISOU records will be refined anisotropically in the second run, which may not be what the user wants.
Rigid body
example for file rigid_body.def defining 2 rigid bodies:
refinement.refine.sites { rigid_body = chain 'A' or chain 'B' rigid_body = chain 'L' or chain 'M' }
Fix His/Asn/Gln sidechain orientations
Use
phenix.refine data.hkl model.pdb main.nqh_flips=True
to automatically flip these sidechains to make them better fit the density and/or hydrogen bonding pattern.
Using a reference model
A good idea if refinement is done at low resolution but a high resolution model is available.
phenix.refine data.hkl model.pdb reference_model.enabled=True reference_model.file=reference.pdb
Use reference_model.sigma=0.5 to tighten the restraints (default 1.0 Angstrom), and use reference_model.limit=30 to enlarge the limit (default 15 degrees) up to which the reference torsion angle will be used.
Real-space refinement
good writeup at http://cci.lbl.gov/~afonine/rsr.pdf . In short, use
phenix.refine model.pdb data.hkl fix_rotamers=true
It would probably be a good idea to also use main.nqh_flips=True (but maybe this is already integrated into fix_rotamers=true ?)
Atom selection
e.g.
phenix.refine model.pdb data.mtz refine.sites.individual="not (chain A and resseq 123:156)"
or
phenix.refine model.pdb data.mtz strategy=individual_adp adp.individual.iso="chain A and resseq 10:20"
The latter will refine only the B-factors of A10:A20 . It should be noted that the overall B-factor can change by ± a constant. This is because the trace of overall anisotropic scale matrix is subtracted from it and added to all atoms and to Bsol.
Another example:
sel = "chain A and resseq 123 and resname LIG and name C1 and altloc A"
where "resseq 123" and "resname LIG" are probably redundant.
Yet another example:
sel = "altloc A or altloc ' ' or element H"
would select hydrogens of the only (or first, if there are several) alternate conformation of each residue.
Switching off specific interactions
- 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:
refinement.geometry_restraints.edits { zn_selection = chain X and resname ZN and resid 200 and name ZN his117_selection = chain X and resname HIS and resid 117 and name NE2 bond { action = *add atom_selection_1 = $zn_selection atom_selection_2 = $his117_selection distance_ideal = 2.1 sigma = 0.02 # use slack=None if you _want_ to restrain, use large slack if not slack = 1 } }
Using dummy atoms to avoid bulk solvent to be filled in
Fill the space where the ligand is supposed to be with dummy atoms (DA), e.g. water, that all have zero occupancy. And when you run phenix.refine with those dummy atoms make sure you use "refinement.mask.ignore_zero_occupancy_atoms=False" keyword. Also, make sure you exclude the DA from coordinate (refine.sites.individual="not xxx") and ADP refinement (either refine.adp.individual="not xxx" or refine.adp.individual.isotropic="not xxx"), too.
You can use phenix.grow_density to generate dummy atoms in spheres of defined radius placed in defined points.
An experimental feature currently being worked on
If there is a significant amount of model missing you can try the undocumented option "use_statistical_model_for_missing_atoms=true" - you need the latest version for this. For some details see pages #17-19 in http://cci.lbl.gov/~afonine/afonine.pdf
finding out the memory consumption
adding
--show-process-info
to the phenix.refine command line results in the log file containing memory usage throughout the run. Look for the max memory intake in the last record (towards the end of log file). This will give you an idea about how much memory you may need. It might well be that this also works for the other phenix tools.
Refinement with mmtbx.lockit
From RWGK's posting to phenixbb on Nov 14, 2010:
We have a tool for quick real-space refinement that's geared towards making the geometry ideal in the end. I'm not sure it is useful in your situation, but may be worth a try. It works like this:
mmtbx.lockit your.pdb your_refine_001_map_coeffs.mtz \ map.coeff_labels.f=2FOFCWT,PH2FOFCWT coordinate_refinement.run=True \ atom_selection='resname LIG'
It works in two stages. First it attempts to maximize the real-space weight allowing for a significant (but not totally unreasonable) distortion of the geometry. This is meant to move the ligand into the density. In the second stage it scales down the "best" real-space weight and runs a number of real-space refinements until the selected atoms do not move anymore. The expected result is nearly ideal geometry.
The procedure is usually very quick. If it turns out to be useful we could integrate it into phenix.refine, to be run after reciprocal-space refinement.
The mmtbx.lockit command is not as user-friendly as phenix.refine. It only works with mtz files, you have to manually specify the mtz labels, and the error messages may be unhelpful. Also be sure there is a valid CRYST1 card in your pdb file.
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. Can also calculate map CC for all atoms or per residue.
phenix.get_cc_mtz_mtz
phenix.fobs_minus_fobs_map - calculate difference density
Seems to have no specific documentation.
phenix.multi_crystal_average
phenix.grow_density - local density improvement
As originally described in Acta Cryst. (1997). D53, 540-543 (in development). There is a PDF file (or [3]) to explain some parameters of phenix.grow_density. It is very sketchy and may not be 100% up-to-date.
Defining several spheres where the DA (dummy atoms) are going to be placed is better than defining one large sphere, although it depends on the region size and shape. For example:
sphere { center = 21.698 7.730 33.974 radius = 5 } sphere { center = 23.483 10.877 35.583 radius = 5 }
phenix.mtz2map
with output=xplor produces an X-PLOR style map. Adding a PDB file will result in a masked map.
phenix.reciprocal_space_arrays
computes various arrays such as Fcalc, Fmask, Fmodel, Fbulk, and more.
Inputs:
- File with reflection data (Fobs or Iobs), R-free flags, and optionally HL coefficients. It can be in most of known formats and spread across multiple files;
- label(s) selecting which reflection data arrays should be used (in case there are multiple choices in input file, there is no need to provide labels otherwise);
- PDB file with input model.
Usage examples:
- phenix.reciprocal_space_arrays model.pdb data.hkl f_obs_label="IOBS"
- phenix.reciprocal_space_arrays model.pdb data.hkl r_free_flags_label="FREE"
Output: MTZ file with data arrays.
NCS usage
phenix.find_ncs - identification of NCS operators
from protein coordinates (chains), heavy atom coordinates, or a density map. Example:
phenix.find_ncs my_8_molecules.pdb
to get the NCS relationships in your structure into find_ncs.ncs_spec.
phenix.superpose_maps - transforms maps following a molecular superposition
Seems to have no specific documentation.
phenix.apply_ncs - applying NCS to a molecule to generate all NCS copies
Example:
phenix.apply_ncs find_ncs.ncs_spec chainA.pdb
and it will generate the copies based on find_ncs.ncs .
torsion NCS
Example:
mmtbx.find_torsion_angle_ncs_groups model.pdb
This command will output which NCS groups the torsion NCS routine finds by the automated method.
Model analysis and manipulation
phenix.pbdtools - PDB model manipulations and statistics
e.g.
phenix.pdbtools your_model.pdb model_statistics=True
will show you complete statistics about B-factors and 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.
Useful to prepare a model for Molecular Replacement:
phenix.pdbtools convert_to_isotropic=true keep="not (altloc B or element H or hetero)" occupancies.set=1 stop_for_unknowns=false model.pdb
phenix.pdb_interpretation - PDB bonds, distances, dihedrals, ...
phenix.pdb_interpretation model_1.pdb ligand.cif
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.
phenix.reduce - tool for adding hydrogens to a PDB model
phenix.pdb_atom_selection
phenix.pdb_atom_selection model.pdb "within(3, chain L and resseq 9 and name CA)" --write-pdb-file=cut.pdb
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.
phenix.superpose_pdbs - Superposition of models
phenix.superpose_ligands - Superposition of ligands
Example files at [4]
phenix.get_cc_mtz_pdb - shift model to find origin
Assuming map_coeffs1.mtz corresponds to model_1.pdb,
phenix.get_cc_mtz_pdb map_coeffs1.mtz model_2.pdb
will create offset.pdb which is a copy of model_2.pdb, adjusted for the origin of map_coeffs_1.mtz, and therefore superimposing on model_1.pdb with space-group symmetry plus allowed origin shifts. This will not change the hand, however.
secondary structure analysis
phenix.ksdssp model.pdb
will output HELIX and SHEET records which you can paste into the PDB header. You should verify the assignments yourself, however, as it occasionally runs adjacent helices together.
Validation
A summary can be obtained by
phenix.pdbtools model_stat=true model.pdb
comprehensive :
phenix.ramalyze model.pdb phenix.rotalyze model.pdb phenix.cbetadev model.pdb phenix.clashscore model.pdb phenix.pdb_interpretation model.pdb restraints.cif write_geo_file=True
Or for the really impatient:
mmtbx.validation_summary model.pdb
polygon
can be run from the GUI and runs calculations resulting in a 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
Prints out the worst contacts. The clash score should be below 20.
phenix.r_factor_statistics
prints out R, Rfree, R-Rfree histograms based on PDB structures. If run without parameters, prints out helpful text about its usage.
Other programs
phenix.tls - tool to convert between total and residual ADPs
It can recognize Refmac and phenix.refine formats of TLS records in PDB files.
phenix.tls model.pdb combine_tls=true
will combine TLS from PDB file header with 'residual' B from ATOM records.
phenix.tls model.pdb extract_tls=true
will split the total B-factor in ATOM records into TLS component and 'residual' part.
List of programs
This is the output of phenix.list (version 1630):
durandal.cluster_pdbs: Entropy-accelerated exact clustering of protein decoys durandal.rank_pdbs: Entropy-accelerated exact clustering of protein decoys fable.cout: Convert Fortran sources to C++ fable.show_calls: Show Fortran call graph iotbx.cif.validate: Validation of CIF files against core CIF dictionary iotbx.cns.transfer_crystal_symmetry: Read unit cell and space group from many file formats, add to CNS input file iotbx.crystal_symmetry_from_any: Read unit cell and space group from many file formats iotbx.dtrek.to_cns: Convert d*trek reflection file to CNS format iotbx.lattice_symmetry: Determination of lattice symmetry given unit cell iotbx.pdb.add_conformations: Add alternate conformation to a PDB file (for entire model or atom selection) iotbx.pdb.join_fragment_files: Join multiple PDB files constituting one model iotbx.pdb.link_as_geometry_restraints_edits: Convert PDB LINK records to phenix.refine parameter file format iotbx.pdb.print_sequence: Extract FASTA sequence string from PDB file iotbx.pdb_as_fasta: Extract FASTA sequence string from PDB file iotbx.pdb_labels_comparison: Compare two pdb files, ignoring coordinates iotbx.pdb_labels_diff: Diff between two pdb files, ignoring coordinates iotbx.phil: Check syntax of parameter file iotbx.r_free_flags_accumulation: Determine fraction of R-free flags as function of Miller indices sorted by resolution iotbx.shelx.as_cif: Convert SHELX .ins or .res file to CIF format iotbx.show_distances: Show interatomic distances given input in PDB format labelit.image: Illustrate the raw data with marked up Bragg spots labelit.pdf: Illustrate the raw data with marked up Bragg spots mmtbx.lockit: Experimental command for real-space refinement, mainly ligands mmtbx.mon_lib_cif_triage: Check syntax of monomer library CIF files phaser.MRage: Molecular replacement pipeline phaser.MRage.solutions: Calculates model and map from MRage results phaser.domain_analysis: Determine domain boundaries from homologues phaser.ensembler: Superpose PDB files to create ensemble for MR phaser.sculptor: Improve molecular replacment models using sequence alignment and structural infomation phaser.unit: Run phaser unittests phenix: Run Phenix graphical user interface phenix.about: Summarize contributors, packages, and info for phenix phenix.acknowledgments: Summarize third-party components of Phenix phenix.adjust_robetta_resid: Apply sequence offset to a fragments file phenix.apply_ncs: Apply NCS (.ncs_spec file) to a chain to create molecule phenix.assign_sequence: Assign sequence to a chain using a map and seq file phenix.autobuild: Iterative model-building density modification and refinement phenix.automr: Automated MR and model-building phenix.autosol: Automated structure solution by MR/MAD/SAD phenix.average_map_coeffs: Average a set of map coefficients from several files phenix.b_factor_statistics: Display summary of atomic displacement parameters for a model (or atom selection) phenix.build_one_model: Build one model using a map and data file phenix.build_rna_helices: Build RNA helices into a map phenix.cablam_training: C-alpha-based protein secondary structure exploration phenix.cablam_validate: C-alpha-based protein secondary structure exploration phenix.cbetadev: Validate protein sidechain C-beta geometry phenix.cc_star: Calculate cc_star values for correlation of data vs resolution phenix.cif_as_mtz: Convert CIF to MTZ phenix.cif_as_pdb: Convert CIF to PDB format phenix.clashscore: Evaluate model based on all-atom contacts phenix.cns_as_mtz: Convert CNS to MTZ phenix.combine_models: Take best parts of two models phenix.commands: List command line Phenix methods phenix.compare_datasets: Similar to phenix.data_viewer, as side-by-side view phenix.composite_omit_map: Generate composite omit map, with our without refinement and simulated annealing phenix.csv_as_mtz: Convert csv reflection files to MTZ phenix.cut_out_density: Create MTZ coeffs with density cut out from a map phenix.data_viewer: View pseudo-precession planes through a dataset phenix.default_gui_settings: Print out base PHENIX GUI configuration (mostly useful for site admins) phenix.den_refine: Carry out DEN refinement of a model phenix.density_outside_model: Remove density near a model from a map phenix.doc: Phenix documentation phenix.dynamics: Shake up structure with simple molecular dynamics phenix.elbow: Ligand builder (CIF from PDB, SMILES etc) phenix.emma: Compare heavy-atom solutions phenix.ensemble_refinement: run ensemble refinement phenix.ensembler: Superpose PDB files to create ensemble for MR phenix.erraser: Run ERRASER phenix.explore_metric_symmetry: Compare unit cells phenix.fest: Experimental Delta F and FA estimation phenix.find_all_ligands: Find ligands from a list in a map phenix.find_alt_orig_sym_mate: Superimpose structures allowing origin shifts (see also map_to_object) phenix.find_helices_strands: Build helices and strands into a map phenix.find_ncs: Find NCS in a model, map or heavy-atom sites phenix.find_ncs_from_density: Find NCS from a map (use phenix.find_ncs) phenix.find_tls_groups: Automatic identification of appropriate TLS groups in model phenix.fit_loops: Fit missing loops in a model phenix.fmodel: Calculate structure factors from model phenix.form_factor_query: f' and f" table lookup given element and wavelength phenix.get_cc_mtz_mtz: Offset maps using allowed origin shifts and get correlation phenix.get_cc_mtz_pdb: Offset PDB to match map using allowed origin shifts and get residue correlation phenix.get_latest_version: Download most recent installer replacing current installation phenix.get_ligand_pdb: Create PDB file for a 3-letter ligand in the PDB phenix.grow_density: Density modification to enhance chain ends phenix.guess_molecular_centers: Guess molecular centers from local RMS density phenix.help: Load Phenix documentation (same as phenix.doc) phenix.hyss: Identify heavy-atom sites from anomalous dataset phenix.import_and_add_free: Import a data file and add Free R set phenix.kinemage: Generates a multi-criterion validation kinemage file, for viewing in KiNG phenix.king: Run KiNG molecular graphics phenix.ksdssp: Identify secondary structure in a model phenix.ligand_identification: Identify ligands from a map phenix.ligand_pipeline: Automated molecular replacement, refinement, and ligand fitting for high-throughput crystallography phenix.ligandfit: Fit ligands into a map phenix.list: Use instead: phenix.commands phenix.map_box: Simple cut out map around a PDB file phenix.map_to_model_histogram: Compute averaged radial density distribution phenix.map_to_object: Superimpose using SG symmetry only (see also find_alt_orig_sym_mate) phenix.map_to_structure_factors: Calculate structure factors and HL coefficients from ccp4 map file and save in MTZ phenix.map_value_at_point: Get map value at given coordinates phenix.maps: Create maps from PDB and MTZ files phenix.maximum_entropy_map: Compute maximum entropy map from map coefficients phenix.merging_statistics: Calculate statistics on unmerged data phenix.metal_coordination: Generate metal coordination bond and angle restraints phenix.model_model_distances: Distance between two PDB files: per atom, residue, chain, model and overall phenix.model_vs_data: Evaluate model using experimental data phenix.model_vs_sequence: Detect residue mismatches in a PDB file phenix.molprobity: Run molprobity phenix.morph_model: Morph a model to match a map phenix.mr_model_preparation: Download and edit PDB files for MR phenix.mr_rescoring: Model scoring for mr_rosetta phenix.mr_rosetta: MR and model improvement with phaser/autobuild/Rosetta phenix.mr_rosetta_rebuild: Rebuild model with Rosetta phenix.mtz.dump: Dump MTZ file contents phenix.mtz2map: Convert MTZ file to map (superseded by phenix.maps) phenix.mtz_as_cif: Convert mtz to CIF format phenix.multi_crystal_average: Multi-crystal averaging phenix.muscle: sequence alignment tool phenix.ncs_and_number_of_ha: Guess solvent content and number of heavy-atom sites phenix.ncs_average: NCS average (no density modification) and write map file phenix.old_gui: Run old version of Phenix GUI phenix.pdb.hierarchy: Quick summary of PDB file content phenix.pdb_as_cif: Convert PDB format to CIF phenix.pdb_atom_selection: Extract selected atoms from PDB file (useful for experimenting with atom selections) phenix.pdb_editor: Edit PDB files graphically phenix.pdb_interpretation: Read PDB file and build restraints for refinement (useful for trouble-shooting) phenix.pdbtools: Manipulate PDB files phenix.perigee: Interaction finder phenix.phase_and_build: Rapid density modification and model-building phenix.phaser: Run PHASER phenix.print_sequence: Print sequence from PDB file phenix.probe: Run PROBE, for analysis of all-atom contacts phenix.pulchra: PULCHRA conversion from CA to full chain phenix.pymol: Pymol phenix.python: Run phenix-cognizant version of python phenix.r_factor_statistics: Distribution of Rfree, Rwork and Rfree-Rwork for PDB models at similar resolution phenix.ramalyze: Validate protein backbone Ramachandran dihedral angles phenix.ready_set: Set up files for refinement, including addition of hydrogens, generation of ligand restraints, and metal coordination restraints phenix.real_space_refine: Extensive real-space refinement phenix.reciprocal_space_arrays: Create MTZ file with Fmodel,Fcalc,Fbulk,Fmask,FOM,HL, resolution and more phenix.reduce: Run REDUCE, software for addition or trimming of hydrogens phenix.reel: Graphical ligand restraints editor phenix.refine: Carry out refinement of a model phenix.reflection_file_converter: Basic conversion between reflection file formats (command-line) phenix.reflection_statistics: Evaluation and comparison of reflection data (e.g. anomalous difference correlations) phenix.reindex: Reindex an MTZ file phenix.remove_aniso: Remove anisotropy from columns of an MTZ dataset phenix.remove_free_from_map: Set all map coeffs of free reflections to zero phenix.resolve: Run resolve phenix.resolve_pattern: run resolve_pattern phenix.rna_validate: Validate RNA sugar puckers, backbone bond and angle geometry, and backbone suite conformations phenix.rotalyze: Validate protein sidechain rotamers phenix.run_example: Run an example from the phenix_examples directory phenix.sculptor: Improve molecular replacment models using sequence alignment and structural infomation phenix.secondary_structure_restraints: generate pseudo H-bond restraints for alpha helices, beta sheets, and nucleic acid base pairs phenix.show_build_path: Show path to Phenix build directory phenix.show_dist_paths: Show paths to all components of Phenix phenix.simple_ncs_from_pdb: NCS from a PDB file (use instead phenix.find_ncs) phenix.solve: Run SOLVE phenix.start_coot: Coot molecular graphics phenix.superpose_ligands: Superimpose two ligands phenix.superpose_maps: Superimpose PDB files and transform map to match phenix.superpose_pdbs: Superimpose PDB files using aligned sequences phenix.trim_pdb: Remove hydrogen atoms from a PDB file phenix.version: Print version of Phenix phenix.where_mon_lib_list_cif: Show location of monomer library used by Phenix phenix.xmanip: Experimental tool for manipulation of reflection data phenix.xtriage: Analyze data files for quality and unusual conditions phenix_regression.phenix_doc.test_phenix_html: Test generation of documentation phenix_regression.run_tests_mp: Run solve-resolve tests in parallel phenix_regression.test_all_parallel: Test wizards phenix_regression.test_apps: Relatively short tests of selected major phenix applications phenix_regression.test_rosetta_refine: Test rosetta refine phenix_regression.testwizard: Run wizard tests phenix_regression.wizards.list: list all wizard regression tests phenix_regression.wizards.test_all: Run all wizard tests phenix_regression.wizards.test_all_parallel: Run all wizard tests in parallel phenix_regression.wizards.test_command_line: General wizard tests phenix_regression.wizards.test_command_line_build: Wizard model-building tests phenix_regression.wizards.test_command_line_ligands: Wizard ligand-building tests phenix_regression.wizards.test_command_line_loops: Wizard loop-fitting tests phenix_regression.wizards.test_command_line_misc: misc wizard tests phenix_regression.wizards.test_command_line_ncs: Wizard NCS tests phenix_regression.wizards.test_command_line_non_standard: Wizard non-standard SG tests phenix_regression.wizards.test_command_line_omit: Wizard omit tests phenix_regression.wizards.test_command_line_resolve_memory: resolve in memory phenix_regression.wizards.test_command_line_rosetta: mr_rosetta tests phenix_regression.wizards.test_command_line_rosetta_iter: multi-cycle mr_rosetta tests phenix_regression.wizards.test_command_line_rosetta_quick: quick mr_rosetta tests phenix_regression.wizards.test_command_line_trace: tests of trace_chain phenix_regression.wizards.test_commands_in_doc: Test Wizard commands in documentation phenix_regression.wizards.test_help: Test Wizard help commands phenix_regression.wizards.test_input_files: Test data files in Wizards phenix_regression.wizards.test_labels: Test various label formats in Wizards phenix_regression.wizards.test_map_to_object: Test map_to_object phenix_regression.wizards.test_maps_only: Test making maps in wizards phenix_regression.wizards.test_misc_methods: Test misc Wizard methods phenix_regression.wizards.test_missing_data: Test Wizards with missing data phenix_regression.wizards.test_mult: Test multiple-model autobuild phenix_regression.wizards.test_multi: Test multi-crystal averaging phenix_regression.wizards.test_ncs: Test NCS identification phenix_regression.wizards.test_ncs_in_phenix_refine: Test using NCS in phenix.refine phenix_regression.wizards.test_omit: Test omit maps phenix_regression.wizards.test_omit_lig: Test omit maps with ligand phenix_regression.wizards.test_residue_codes: Test residue names phenix_regression.wizards.test_resno: Test rebuild_in_place residue numbers phenix_regression.wizards.test_resolve: Run comprehensive solve/resolve tests phenix_regression.wizards.test_short_seq: Test Wizards with short sequence
Tips and Tricks
A handy tip: to check the syntax of a Phenix parameter file (for any program, not just phenix.refine), you can run this command (replacing params.eff with the file of interest):
libtbx.phil params.eff
If it works, it will just print out the parameters - if not, the error message should give some indication where the error occurred.
Installation from source, and of Rosetta interface
Phenix can be installed from a binary installer. Despite this designation, it has the source files for re-compilation. However, re-compilation is normally not required, and requires to specify the --source option to the ./install command.
phenix.rosetta_refine (and phenix.mr_rosetta) requires a working Rosetta installation. The easiest way is to download one of the weekly binary+source Rosetta bundles (to be found following this link). The tar-file only has to be unpacked; binaries and libraries are pre-compiled. Your .bashrc has to be modified to have e.g.
export PHENIX_ROSETTA_PATH=/usr/local/src/rosetta_src_2017.08.59291_bundle
(or similarly for .cshrc) and
rosetta.build_phenix_interface
needs to be run; the latter step takes hours when doing it for the first time. (According to the docs, this is only needed for rosetta_refine.)
If this fails (for example, compiler error messages), then one must re-compile Phenix and/or Rosetta. Try to re-compile only Phenix first (and after that, try rosetta.build_phenix_interface again); Rosetta re-compilation may take hours. There are several issues associated with re-compilation:
- if the Phenix binary installer is not used: the Phenix source installer requires (on Fedora and RHEL) the openssl-devel and libXt-devel to be installed on the system
- to re-compile Rosetta: go to the main/source directory and issue:
./scons.py -j8 mode=release bin
(The -j8 should be used if your machine has 8 or more cores.)
See also
http://phenix-online.org/presentations/neutron_japan_2009/phenix_japan_part1.pdf
http://cci.lbl.gov/~afonine/for_ak/validation.pdf
- 42 pages of general introduction to structure refinement: [5]
- 45 pages of phenix.refine overview (including extended details about its use from the command line): [6]
- 42 pages of "Some Facts About Maps": [7]
- 50 pages of "Crystallographic Structure Validation": [8]
- 31 pages of introduction to PHENIX: [9]
server producing custom RNA/DNA base pairing restraints
References
- electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation. Nigel W. Moriarty, Ralf W. Grosse-Kunstleve and Paul D. Adams, ActaCryst. (2009). D65, 1074-1080
- phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD. (2010) J Appl Crystallogr. 43, 669-676. [10]