Coot and Phenix

1. Coot and Phenix They just sound like birds.

2. Computational Crystallography Initiative (LBNL) • Paul Adams, Ralf Grosse-Kunstleve, Peter Zwart, • Nigel Moriarty, Nicholas Sauter, Pavel Afonine • Cambridge University • Randy Read, Airlie McCoy, Laurent Storoni, • Hamsapriye • Texas A&M University • Tom Ioerger, Jim Sacchettini, Kreshna Gopal, Tod Romo • Reetal Pai, Kevin Childs, Vinod Reddy 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/refinement.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.prefix=something something_001.(pdb/log/def/eff/geo/map) + output.serial=3 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_solvent=true Phenix.refine your.pdb my.mtz xray_data.labels=“F_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 strategy=individual_sites+individual_adp+tls • 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_solvent=true strategy=individual_sites+individual_adp+tls main.ncs=true tls_group_selections.params refinement.ncs.excessive_distance_limit=None output.prefix=mpfh simulated_annealing=true simulated_annealing.start_temperature=7000 main.number_of_macro_cycles=10 • 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 \ strategy=individual_sites+individual_adp+tls \ ordered_solvent=true \ main.ncs=true \ refinement.ncs.excessive_distance_limit=None \ tls_group_selections.params \ simulated_annealing=true \ simulated_annealing.start_temperature=7000 \ main.number_of_macro_cycles=10 \ output.prefix=mpfh 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_cycles=10 • ordered_solvent=true • simulated_annealing=true • simulated_annealing.start_temperature=7000 • main.ncs=true • ncs.find_automatically=False • optimize_wxc=true • xray_data.low_resolution=15.0 xray_data.high_resolution=2.0

12. Keeping track of things.phenix.params (not part of phenix) Use: phenix.params [foo.log / all] [dcoop Dinb80]->phenix.params dinb-4c_refine_002.log phenix.refine dinb-4c_refine_002.def simulated_annealing=true strategy=individual_sites+individual_adp+tls dinb-4c_refine_002.pdb R(work)=0.183 R(free)=0.253 Diff=0.070 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]->getrs 4 apc17.pdb R(work)=0.15760 R(free)=0.19878 Diff=0.04118 RESO = 2.10 rmsdBOND = 0.010 rmsdANGLES = 2.430 apc16f.pdb R(work)=0.15936 R(free)=0.18238 Diff=0.02302 RESO = 2.10 rmsdBOND = 0.010 rmsdANGLES = 2.426 apc16e.pdb R(work)=0.15813 R(free)=0.20773 Diff=0.04960 RESO = 2.10 rmsdBOND = 0.011 rmsdANGLES = 2.443 apc16d.pdb R(work)=0.15827 R(free)=0.20941 Diff=0.05114 RESO = 2.10 rmsdBOND = 0.011 rmsdANGLES = 2.455