1 / 13

Coot and Phenix

Coot and Phenix . They just sound like birds. 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.

yessica
Download Presentation

Coot and Phenix

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  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

More Related