Author(s)

• phase_and_build: Tom Terwilliger

Purpose

phase_and_build is a new and rapid method for improving the quality of your map and building a model. The approach is to carry out an iterative process of building a model as rapidly as possible and using this model in density modification to improve the map. This approach is related to the older phenix.autobuild approach. The difference is that in phenix.autobuild much effort was spent on building the best possible model at each stage before carrying out density modification, while in phenix.phase_and_build speed of model-building is optimized. The result is that phenix.phase_and_build is 10 times faster than phenix.autobuild, yet it produces nearly as good a model in the end. The phenix.phase_and_build approach will also find NCS from your starting map and apply it during density modification.

Usage

How phase_and_build works:

phase_and_build first identifies a free set of reflections if they are not supplied. A map without the test set reflections is created for real-space refinement. A set of data for density modification is created which contains anisotropy-corrected data (if supplied).

• Next phase_and_build estimates the solvent fraction (if not supplied) from the sequence file and cell parameters and the maximum and most likely number of NCS copies.
• A starting map is obtained by density modification of the input data (unless a map coefficients file is supplied).
• NCS is identified from the starting map (if the maximum number of NCS copies is greater than 1). If a heavy-atom file is supplied, NCS will first be identified from the heavy-atom sites, and the map will be used if the expected number of sites is not obtained.
• Next one or more cycles of phase improvement are carried out. In each cycle a model is built using phenix.build_one_model, the model is refined in real-space and/or in reciprocal space, and then the model is included in density modification to create a new map.
• Finally, a full model-building cycle is carried out using the most recent map. One or more models are built with phenix.build_one_model and are refined, then are combined, again with phenix.build_one_model. The resulting model is refined and sequence assignment and fitting of short loops is carried out with phenix.assign_sequence. Then longer loops are fit with phenix.fit_loops and the final model is refined and written out.

Output files from phase_and_build

phase_and_build.pdb: A PDB file with the resulting model phase_and_build_map_coeffs.mtz: An MTZ file with optimized phases phase_and_build_refine_data.mtz: An MTZ file with data and test set used in refinement

Parameters files in phase_and_build

When you run phenix.phase_and_build it will write out a phase_and_build_params.eff parameter file that can be used to re-run phenix.phase_and_build (just as for essentially all PHENIX methods). In addition, phenix.phase_and_build will write out the parameters files for the intermediate methods used as part of phenix.phase_and_build to the temporary directory used in building. You can run these with:

phenix.find_ncs temp_dir/find_ncs_params.eff # runs NCS identification
phenix.autobuild temp_dir/AutoBuild_run_1_/autobuild.eff   # runs first cycle of density modification
phenix.build_one_model temp_dir/build_one_model_params.eff # runs most recent model-building
phenix.assign_sequence temp_dir/assign_sequence_params.eff # runs sequence assignment and filling short gaps
phenix.fit_loops temp_dir/fit_loops_params.eff # runs loop fitting

This gives you control of all the steps in map improvement and model-building in addition to letting you run them all together with phenix.phase_and_build

Examples

Standard run of phase_and_build:

Running phase_and_build is easy. From the command-line you can type:

phenix.phase_and_build exptl_fobs_phases_freeR_flags.mtz sequence.dat

If you want to supply a file with anisotropy-corrected data to use in density modification you can do so:

phenix.phase_and_build data=exptl_fobs_phases_freeR_flags.mtz \
seq_file=sequence.dat \
aniso_corrected_data=solve_1.mtz

where solve_1.mtz is anisotropy-corrected (the amplitudes are not measured amplitudes, but rather are corrected with an anisotropic B-factor), and exptl_fobs_phases_freeR_flags.mtz contains experimental amplitudes. These two files normally will contain the same phase information. (Usually these files will come from phenix.autosol.)

You can also add a starting model or a starting map to phenix.phase_and_build. This means that you can run it once, get a new model and map, then run it again to further improve your model and map.

Possible Problems

Specific limitations and problems:

phenix.phase_and_build does not have the full flexibility of phenix.autobuild, so you may want to get a nearly-complete model with phenix.phase_and_build and then use phenix.autobuild to increase the completeness and quality.

Literature

Additional information