Coot and Phenix

1
Coot and Phenix

• They just sound like birds.

2
The PHENIX project

• Crystallographic software for
• automated macromolecular structure determination

• Los Alamos National Lab (LANL)
• Tom Terwilliger, Li-Wei Hung, Thiru Radhakannan

• Duke University
• Jane Richardson, David Richardson, Ian Davis

3
PHENIX Wizards

• AutoSol Wizard Structure solution
• AutoBuild Wizard Iterative density modification,
  model-building and refinement model rebuilding
  in place simple OMIT SA-OMIT Iterative-build
  OMIT OMIT around atoms in a PDB file
• LigandFit Wizard Ligand fitting
• AutoMR Wizard Phaser molecular
• replacement followed by automatic
• rebuilding

4
phenix.xtriageData assessment program

• Basic sanity checks performed by xtriage are
• Wilson plot sanity
• Probabilistic Matthews analysis
• Data strength analysis
• Ice ring analysis
• Twinning analysis
• Reference analysis (determines possible
  re-indexing. optional)
• De-twinning and data massaging (optional)
• Anomalous signal estimation.
• Use phenix.xtriage my_xtal.sca
• My script datacheck.sh file.sca res
• Creates file.triage and reports key stats.

5
What can phenix.refine do?

• The best explanation is at the top of the manual.
• http//www.phenix-online.org/documentation/refinem
  ent.htm
• Or follow the links on
• http//ginsberg.med.virginia.edu
• The manual is dense, but fairly well written.

6
Running phenix.refine

• Most simple case
• phenix.refine your.pdb my.mtz
• Output files will be your_refine_001.(pdb/log/def
  /eff/geo)
• Its good to add an alert to tell you when it is
  done
• phenix.refine your.pdb my.mtz barf
• Change the output file names
• phenix.refine your.pdb my.mtz
  output.prefixsomething
• something_001.(pdb/log/def/eff/geo/map)
• output.serial3 something_003
• Overwrite files (Necessary if you have aborted a
  run)
• phenix.refine your.pdb my.mtz --overwrite
• Change a default value
• phenix.refine your.pdb my.mtz ordered_solventtrue
  
• Phenix.refine your.pdb my.mtz xray_data.labelsF
  _pk,MyPhi

7
The Strategies

• - individual_sites
• (refinement of individual atomic coordinates)
• - individual_adp
• (refinement of individual atomic B-factors)
• - group_adp
• (group B-factors refinement)
• - group_anomalous
• (refinement of f' and f" values)
• - tls
• (TLS refinement refinement of ADP through TLS
  parameters)
• - rigid_body
• (rigid body refinement)
• - none
• (bulk solvent and anisotropic scaling only)
• Combine with strategyindividual_sitesindividual_
  adptls
• Can use different strategies for different parts
  of the model.

8
Long command lines

• Order is not important, and strings will be
  matched to closest parameter.
• phenix.refine dinb-4c_refine_001FH.pdb
  dinb80-pkb.mtz ../NI.cif ordered_solventtrue
  strategyindividual_sitesindividual_adptls
  main.ncstrue tls_group_selections.params
  refinement.ncs.excessive_distance_limitNone
  output.prefixmpfh simulated_annealingtrue
  simulated_annealing.start_temperature7000
  main.number_of_macro_cycles10
• Can edit a .def or .eff file and run as
• phenix.refine data.hkl model.pdb custom.params
• Can put in a command file with line
  continuations.

9
Line continuations

• phenix.refine \
• dinb-4c_refine_001FH.pdb dinb80-pkb.mtz
  ../NI.cif \
• strategyindividual_sitesindividual_adptls \
• ordered_solventtrue \
• main.ncstrue \
• refinement.ncs.excessive_distance_limitNone \
  tls_group_selections.params \
  simulated_annealingtrue \ simulated_annealing
  .start_temperature7000 \
• main.number_of_macro_cycles10 \
• output.prefixmpfh
• NOTHING (not even spaces) can follow the \

10
A look at the .eff and .def files

• Each run create a .eff file that controls that
  run and a .def file that can be used for the next
  run.
• Stars in a list specify which option is used.
• strategy individual_sites rigid_body
  individual_adp group_adp tls occupancies
  group_anomalous
• To continue with current strategy
• phenix.refine file_002.def
• phenix.refine --diff-params file.eff
• Will list all of the non-default values
• phenix.refine --show-defaults(all,level)

11
Key options

• main.number_of_macro_cycles10
• ordered_solventtrue
• simulated_annealingtrue
• simulated_annealing.start_temperature7000
• main.ncstrue
• ncs.find_automaticallyFalse
• optimize_wxctrue
• xray_data.low_resolution15.0 xray_data.high_resol
  ution2.0

12
Keeping track of things.phenix.params (not part
of phenix)

• Use phenix.params foo.log / all
• dcoop Dinb80-gtphenix.params dinb-4c_refine_002.l
  og
• phenix.refine dinb-4c_refine_002.def
  simulated_annealingtrue strategyindividual_sites
  individual_adptls
• dinb-4c_refine_002.pdb R(work)0.183
  R(free)0.253 Diff0.070
• RESO 2.51 rmsdBOND 0.007
  rmsdANGLES 1.058
• Phenix.params all will collect all of the input
  lines for the directory and put them in a file
  called params. Stats on the resulting pdb is
  shown.

13
getrs

• Use getrs of pdbs / . for all

dcoop CCp4-gtgetrs 4 apc17.pdb
R(work)0.15760 R(free)0.19878 Diff0.04118
RESO 2.10 rmsdBOND 0.010
rmsdANGLES 2.430 apc16f.pdb
R(work)0.15936 R(free)0.18238 Diff0.02302
RESO 2.10 rmsdBOND 0.010
rmsdANGLES 2.426 apc16e.pdb
R(work)0.15813 R(free)0.20773 Diff0.04960
RESO 2.10 rmsdBOND 0.011
rmsdANGLES 2.443 apc16d.pdb
R(work)0.15827 R(free)0.20941 Diff0.05114
RESO 2.10 rmsdBOND 0.011
rmsdANGLES 2.455