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PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is a new 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.
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 straightforward to use.


The suite has a GUI program (phenix) which can be used to run the programs, but they also work from the command line:
The suite ([http://www.phenix-online.org/ Phenix home page]; [http://www.phenix-online.org/documentation documentation]) has a GUI program (phenix) which can be used to run the programs, but they also work from the command line.
* [http://www.phenix-online.org/documentation/refinement.htm phenix.refine] - refinement program
* [http://www.phenix-online.org/documentation/xtriage.htm phenix.xtriage] - assessing data quality
* [http://www.phenix-online.org/documentation/find_helices.htm phenix.find_helices] - rapid helix fitting to a map
* [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, and so on
* [http://www.phenix-online.org/documentation/elbow.htm phenix.elbow] - electronic Ligand Builder and Optimisation Workbench
* [http://www.phenix-online.org/documentation/hydrogens.htm phenix.reduce] - tool for adding hydrogens to a PDB model
* ...


== Example ==
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


  phenix.refine model.pdb data.mtz strategy=rigid_body+individual_sites+individual_adp \
You can join the [http://www.phenix-online.org/mailman/listinfo/phenixbb PHENIX bulletin board] and/or view its archives.
    simulated_annealing=true optimize_wxc=true optimize_wxu=true main.number_of_macro_cycles=5
 
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 ==
 
=== [http://www.phenix-online.org/documentation/reference/xtriage.html phenix.xtriage] - assessing data quality ===
 
=== [http://www.phenix-online.org/documentation/reference/explore_metric_symmetry.html 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 [http://www.ccp4.ac.uk/html/othercell.html othercell].
 
=== [http://www.phenix-online.org/documentation/reference/reflection_statistics.html phenix.reflection_statistics] - compare datasets ===
There may be one or two data files.
 
=== [http://www.phenix-online.org/documentation/reference/xmanip.html phenix.xmanip] - structure factor file manipulations ===
 
=== [http://www.phenix-online.org/documentation/reference/model_vs_data.html 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.
 
=== [http://www.phenix-online.org/documentation/reference/fmodel.html 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 ==
 
=== [http://www.phenix-online.org/documentation/reference/autosol.html 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
 
=== [http://www.phenix-online.org/documentation/reference/phaser_ep.html 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/reference/phaser_ep.html]. 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 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:
<pre>
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
</pre>
 
== Molecular replacement ==
 
=== [http://www.phenix-online.org/documentation/reference/automr.html 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 [http://www.phaser.cimr.cam.ac.uk/index.php/Phaser_Crystallographic_Software 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 [[params.eff|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):
<pre>
#!/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
</pre>
 
=== [http://www.phenix-online.org/documentation/reference/sculptor.html phenix.sculptor] - automate selection and editing of molecular replacement (MR) models ===
 
=== [http://www.phenix-online.org/documentation/reference/ensembler.html phenix.ensembler] - multiple superposition tool to automate construction of ensembles for MR ===
 
== Ligands ==
 
=== [http://www.phenix-online.org/documentation/reference/reel.html phenix.reel] - restraints editor especially for ligands ===
 
=== [http://www.phenix-online.org/documentation/reference/elbow.html phenix.elbow] - electronic Ligand Builder and Optimisation Workbench ===
 
Using taxol as an example: this is also named Paclitaxel and one can easily obtain the [https://pubchem.ncbi.nlm.nih.gov/compound/paclitaxel#section=Canonical-SMILES SMILES string]. Then just watch [https://www.youtube.com/watch?v=8qVYTUVKlbQ this video on phenix.elbow].
 
But before you make restraints yourself, check whether it is already in the
dictionary - search on http://ligand-expo.rcsb.org . Taxol should be [http://ligand-expo.rcsb.org/reports/T/TA1/index.html TA1].
 
This can then be used in elbow as a chemical component. This option provides more information than the SMILES string.
 
phenix.elbow --chemical_component TA1
 
== Model building and completion ==
=== [http://www.phenix-online.org/documentation/reference/autobuild.html 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/reference/ligandfit.html phenix.ligandfit] - "wizard" carrying out fitting of flexible ligands to electron density maps ===
=== [http://www.phenix-online.org/documentation/reference/find_helices_strands.html phenix.find_helices_strands] - rapid helix/strand fitting to a map ===
=== phenix.fit_loops - fill short gaps using a loop library, and longer gaps (up to 15 residues) iteratively ===
=== [http://www.phenix-online.org/documentation/reference/assign_sequence.html phenix.assign_sequence] - sequence assignment and linkage of neighboring segments ===
=== phenix.ligand_identification ===
 
== Refinement with [http://www.phenix-online.org/documentation/reference/refinement.html 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 ...
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:
This will do the following:


# Rigid body refinement first cycle only (MZ protocol = VERY high convergence radius);
# Rigid body refinement first cycle only (MZ protocol = VERY high convergence radius);
# Refinement of individual xyz and b-factors every cycle with optimized weights;
# 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;
# 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 ===


== 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:
  Sorry: Fatal problems interpreting PDB file:
  Sorry: Fatal problems interpreting PDB file:
Line 34: Line 264:
   definitions for unknown ligands.
   definitions for unknown ligands.
In that case, just running
In that case, just running
  phenix.elbow model.pdb --do-all --output=all_ligands
  phenix.ready_set model.pdb  
will produce all_ligands.cif, which may be fed to phenix.refine by
will produce model.updated.pdb and model.ligands.cif, which may be fed to phenix.refine by
  phenix.refine model.pdb data.mtz all_ligands.cif ...
  phenix.refine model.updated.pdb data.mtz model.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 ====


== Occupancy refinement ==
Use phenix.ready_set to add hydrogens to your PDB file, and use (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 <font face="Courier"> and not (element H or element D)</font> to all selection strings.
See the [http://www.phenix-online.org/documentation/reference/refinement.html#anch32 phenix.refine documentation].
 
==== 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 ==
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.
 
==== Special positions ====
 
Single atoms on (or close enough to) a special position (i.e. on one or more 2-,3-,4- or 6-fold rotation axis/axes) are automatically restrained to stay on that special position. For anything else (like a ligand crossing a symmetry element) the trick is: reducing occupancy to 1/n for a n-fold rotation axis, and excluding atoms from non-bonded repulsions with their symmetry mates - see [[Phenix#Switching_off_specific_interactions]] .
 
==== Bond across symmetry axis ====
There is a small hint at
[https://www.phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles]
 
For bonds to symmetry copies, specify the symmetry operation in xyz notation, for example:
symmetry_operation = -x-1/2,y-1/2,-z+1/2
 
The whole .eff file might look like:
refinement.geometry_restraints.edits {
    bond {
      action = *add delete change
      atom_selection_1 = chain A and resid 1199 and name O4
      atom_selection_2 = chain A and resid 1196 and name C1
      symmetry_operation = X-1/2,-Y+1/2,-Z
      distance_ideal = 1.439
      sigma = 0.020
    }
}
(this is from a posting of Oleg Sobolev to PHENIXBB on  Wed, 27 May 2020 15:55:27 -0700)


Automatic detection of NCS groups:
==== NCS ====


phenix.refine data.hkl model.pdb main.ncs=True
more on this: see [[Phenix#NCS_usage]]


Manual specification of NCS groups:
* Automatic detection of NCS groups:
  phenix.refine data.hkl model.pdb ncs_groups.params main.ncs=True
phenix.refine data.hkl model.pdb ncs=True ncs_search.enabled=True
* Manual specification of NCS groups:
  phenix.refine data.hkl model.pdb ncs_groups.params  
where ncs_groups.params contains e.g.:
where ncs_groups.params contains e.g.:
  refinement.ncs.restraint_group {
  refinement.ncs.restraint_group {
Line 61: Line 341:
  }
  }


== TLS ==
 
* 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 [http://www.phenix-online.org/newsletter/CCN_2010_07.pdf 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 <font face="Courier">reference_model.limit</font> (default 15 degrees) and <font face="Courier">reference_model.sigma</font> (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 [http://www.phenix-online.org/documentation/reference/refinement.html#anch26 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);
* 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
* or use <code>phenix.find_tls_groups</code> to find TLS groups, and to generate a tls_selections.def file.
* use these selections for TLS refinement in PHENIX: see http://www.phenix-online.org/documentation/reference/refinement.html


for example:
for example:
Line 78: Line 450:
   }
   }
  }
  }
Alternatively, phenix.refine can identify TLS groups on-the-fly, using <pre>tls.find_automatically=True</pre>
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'
}
==== [http://www.phenix-online.org/documentation/reference/refinement.html#anch28 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.
==== [http://www.phenix-online.org/documentation/reference/refinement.html#anch30 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 ?)
=== [http://www.phenix-online.org/documentation/reference/atom_selections.html 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. Example (either simply add this on the commandline, after setting the selection appropriately, or if using GUI, find this parameter in "All parameters", and type in atom selection):
custom_nonbonded_symmetry_exclusions="chain A and resseq 123 and sidechain"
* 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.html#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#phenix.grow_density_-_local_density_improvement|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.
== 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.
=== [http://www.phenix-online.org/documentation/reference/get_cc_mtz_mtz.html 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/reference/multi_crystal_average.html 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 [http://cci.lbl.gov/~afonine/tmp/grow_density.pdf PDF] file (or [http://phenix-online.org/pipermail/phenixbb/attachments/20110811/a73f1428/attachment.htm]) 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.
=== [http://www.phenix-online.org/documentation/reference/reciprocal_space_arrays.html 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 ==
=== [http://www.phenix-online.org/documentation/reference/find_ncs.html 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.
=== [http://www.phenix-online.org/documentation/reference/apply_ncs.html 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 ==
=== [http://www.phenix-online.org/documentation/reference/pdbtools.html 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.
=== [http://www.phenix-online.org/documentation/reference/hydrogens.html 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.
=== [http://www.phenix-online.org/documentation/reference/superpose_pdbs.html phenix.superpose_pdbs] - Superposition of models ===
===  phenix.superpose_ligands - Superposition of ligands ===
Example files at [http://cci.lbl.gov/~afonine/superpose_ligands/]
===  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 [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 ===
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):
<pre>
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
</pre>
== Tips and Tricks ==
1) 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.
2) To check the proper functioning of a Phenix program, e.g. phenix.auto_sharpen, with Phenix's regression tests, type this on the command line:
    phenix_regression.list auto_sharpen
This will then list the command(s) that you can run on your computer to test
phenix.auto_sharpen.  On Tom Terwilliger's computer the output looks like:
libtbx.python "/net/anaconda/raid1/terwill/misc/PHENIX/modules/phenix_regression/segment_and_split_map/tst_auto_sharpen.py"
Copy and paste the line with the regression test you are interested in, and make sure that it runs and
ends with "OK". (For phenix.refine, there are >300 regression tests!)
== 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.
[http://www.phenix-online.org/documentation/reference/rosetta_refine.html phenix.rosetta_refine] (and [http://www.phenix-online.org/documentation/reference/mr_rosetta.html 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 [https://www.rosettacommons.org/software/license-and-download 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 nproc=2
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, libXt-devel, libtiff, libtiff-devel and bzip2-devel RPM to be installed on the system
* to re-compile Rosetta: go to the main/source directory and issue:
phenix.python scons.py bin mode=release extras=python  -j 2


== See also ==
== See also ==
Line 84: Line 948:


[http://www.phenix-online.org/pipermail/phenixbb/ Phenix mailing list]
[http://www.phenix-online.org/pipermail/phenixbb/ Phenix mailing list]
[http://www.phenix-online.org/newsletter/ PHENIX Newsletter]
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: [http://www.phenix-online.org/presentations/latest/pavel_refinement_general.pdf]
* 45 pages of phenix.refine overview (including extended details about its use from the command line): [http://www.phenix-online.org/presentations/latest/pavel_phenix_refine.pdf]
* 42 pages of "Some Facts About Maps": [http://www.phenix-online.org/presentations/latest/pavel_maps.pdf]
* 50 pages of "Crystallographic Structure Validation": [http://www.phenix-online.org/presentations/latest/pavel_validation.pdf]
* 31 pages of introduction to PHENIX: [http://www.phenix-online.org/presentations/latest/pavel_phenix_intro.pdf]
[http://rna.ucsc.edu/pdbrestraints/ 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. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2906258/pdf/j-43-00669.pdf]
Kay
Bureaucrats
1,330

edits

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