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Tutorial 4: Iterative model-building, density modification and refinement starting from experimental phases
This tutorial will start with experimental SAD data and density-modified phases, and carry out the process of iterative model-building, density modification and refinement with AutoBuild. It is designed to be read all the way through, giving pointers for you along the way. Once you have read it all and run the example data and looked at the output files, you will be in a good position to run your own data through AutoBuild.
Setting up to run PHENIX
echo $PHENIXthen you should get back something like this:
/xtal//phenix-1.3If instead you get:
PHENIX: undefined variablethen you need to set up your PHENIX environment. See the PHENIX installation page for details of how to do this. If you are using the C-shell environment (csh) then all you will need to do is add one line to your .cshrc (or equivalent) file that looks like this:
source /xtal/phenix-1.3/phenix_env(except that the path in this statement will be where your PHENIX is installed). Then the next time you log in $PHENIX will be defined.
Running the demo p9-build data with AutoBuild
mkdir tutorials cd tutorialsNow type the phenix command:
phenix.run_example --helpto list the available examples. Choosing p9-build for this tutorial, you can now use the phenix command:
phenix.run_example p9-buildto build the p9-build structure with AutoBuild. This command will copy the directory $PHENIX/examples/p9-build to your current directory (tutorials) and call it tutorials/p9-build/ . Then it will run AutoBuild using the command file run.sh that is present in this tutorials/p9-build/ directory. This command file run.sh is simple. It says:
#!/bin/sh echo "Running AutoBuild on P9 data..." phenix.autobuild seq_file=p9.seq data=p9-solve.mtz \ input_map_file=p9-resolve.mtz resolution=2.4 \ ncs_copies=1The first line (#!/bin/sh) tells the system to interpret the remainder of the text in the file using the sh (or bash) -shell (sh). The command phenix.autobuild runs the command-line version of AutoBuild (see Automated Structure Solution using AutoBuild for all the details about AutoBuild including a full list of keywords). The arguments on the command line tell AutoBuild about the sequence file (seq_file=p9.seq), the data file (data=p9-solve.mtz), the map file with density-modified phases (input_map_file=p9-resolve.mtz), and the resolution resolution=2.4) and number of ncs copies to look for (ncs_copies=1). (Note that each of these is specified with an = sign, and that there are no spaces around the = sign.) Note the backslash "\" at the end of some of the lines in the phenix.autobuild command. This tells the C-shell (which interprets everything in this file) that the next line is a continuation of the current line. There must be no characters (not even a space) after the backslash for this to work. The structure factor amplitudes and experimental phase information are in the datafile p9-solve.mtz. This is an mtz file which is a binary file that contains summary information about the dataset as well as the reflection data. Although the phenix.run_example p9-build command has just run AutoBuild from a script (run.sh), you can run AutoBuild yourself from the command line with the same phenix.autobuild seq_file= ... command. You can also run AutoBuild from a GUI, or by putting commands in another type of script file. All these possibilities are described in Using the PHENIX Wizards.
Where are my files?
Once you have started AutoBuild or another Wizard, an output directory will be created in your current (working) directory. The first time you run AutoBuild in this directory, this output directory will be called AutoBuild_run_1_ (or AutoBuild_run_1_/, where the slash at the end just indicates that this is a directory). All of the output from run 1 of AutoBuild will be in this directory. If you run AutoBuild again, a new subdirectory called AutoBuild_run_2_ will be created. Inside the directory AutoBuild_run_1_ there will be one or more temporary directories such as TEMP0 created while the Wizard is running. The files in this temporary directory may be useful sometimes in figuring out what the Wizard is doing (or not doing!). By default these directories are emptied when the Wizard finishes (but you can keep their contents with the command clean_up=False if you want.)
What parameters did I use?
Once the AutoBuild wizard has started (when run from the command line), a parameters file called autobuild.eff will be created in your output directory (e.g., AutoBuild_run_1_/autobuild.eff). This parameters file has a header that says what command you used to run AutoBuild, and it contains all the starting values of all parameters for this run (including the defaults for all the parameters that you did not set). The autobuild.eff file is good for more than just looking at the values of parameters, though. If you copy this file to a new one (for example autobuild_lores.eff) and edit it to change the values of some of the parameters (resolution=3.0) then you can re-run AutoBuild with the new values of your parameters like this:
phenix.autobuild autobuild_lores.effThis command will do everything just the same as in your first run but use only the data to 3.0 A.
Reading the log files for your AutoBuild run file
While the AutoBuild wizard is running, there are several places you can look to see what is going on. The most important one is the overall log file for the AutoBuild run. This log file is located in:
AutoBuild_run_1_/AutoBuild_run_1_1.logfor run 1 of AutoBuild. (The second 1 in this log file name will be incremented if you stop this run in the middle and restart it with a command like phenix.autobuild run=1). The AutoBuild_run_1_1.log file is a running summary of what the AutoBuild Wizard is doing. Here are a few of the key sections of the log files produced for the p9-build SAD dataset.
Summary of the command-line arguments
------------------------------------------------------------ Starting AutoBuild with the command: phenix.autobuild seq_file=p9.seq data=p9-solve.mtz \ input_map_file=p9-resolve.mtz resolution=2.4 ncs_copies=1This is just a repeat of how you ran AutoBuild; you can copy it and paste it into the command line to repeat this run.
Guessing the chain type
Guessing chain type from p9.seq Setting chain type to PROTEINIf you want to tell the Wizard what the chain type is, you can say, chain_type=PROTEIN.
Guessing column labels
Getting column labels from p9-solve.mtz for input data file SG: I 4 Cell: [113.94899749755859, 113.94899749755859, 32.4739990234375, 90.0, 90.0, 90.0] Input labels: ['FP', 'SIGFP', 'PHIB', 'FOM', 'HLA', 'HLB', 'HLC', 'HLD', 'None'] Getting column labels from p9-resolve.mtz for input map file SG: I 4 Cell: [113.94899749755859, 113.94899749755859, 32.4739990234375, 90.0, 90.0, 90.0] Map input labels: ['FP', 'PHIM', 'FOMM']These are indeed the appropriate columns to use for experimental phases and for map coefficients, respectively. Note the "None" in the input labels for p9-solve.mtz. The last input label in this list corresponds to FreeR_flag and there is no Free R data in the input data file. All the data that is expected for each input file in AutoBuild can be seen in the AutoBuild web page under "Specifying which columns of data to use from input data files".
Guessing cell contents
Number of residues in unique chains in seq file: 136 Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 4 (No. 79) CELL VOLUME :421654.549593 N_EQUIV:8 GUESS OF NCS COPIES: 1 SOLVENT FRACTION ESTIMATE: 0.65 Data file (for everything including refinement): p9-solve.mtz
The AutoBuild Wizard automatically runs phenix.xtriage on your input datafile to analyze it for twinning, outliers, translational symmetry, and other special conditions that you should be aware of. You can read more about xtriage in Data quality assessment with phenix.xtriage. The xtriage output is in the file p9-solve.mtz_xtriage.log. Part of the summary output from xtriage for this dataset looks like this:
The largest off-origin peak in the Patterson function is 6.40% of the height of the origin peak. No significant pseudotranslation is detected. The results of the L-test indicate that the intensity statistics behave as expected. No twinning is suspected.
Generation of FreeR flags
The AutoBuild Wizard will create a set of free R flags indicating which reflections are not to be used in refinement. By default 5% of reflections (up to a maximum of 2000) are reserved for this test set. If you supply a reflection file with free R flags already set, then they will be used. If you want to supply a file ref.mtzspecifically for refinement, you can do that with input_refinement_file=ref.mtz. Also if you want to supply a high-resolution datafile hires.mtz that has then you can do this with the keywords input_hires_file=hires.mtz. After generation of free R flags if necessary, and any merging of data files, the file to be used for refinement is called exptl_fobs_phases_freeR_flags.mtz.
Model-building with RESOLVE
The AutoBuild Wizard by default uses RESOLVE to build an atomic model of your structure. In each cycle of model-building, the AutoBuild Wizard breaks up the building process into separate steps that can be run in parallel and then combines the results. In the first model-building cycle, the AutoBuild Wizard builds 4 separate models by running 4 subprocesses, each of which runs the AutoBuild Wizard to just build a single model and refine it and return:
Build cycle 1 of 17 method:build Build cycle 1 of 17 method:build Running 3 parallel build jobs Standard build in parallel This is the first try at building this model Setting background=False as nproc=1 Try: 1 building 1 model Try: 2 building 1 model Try: 3 building 1 model Running up to 1 jobs in parallel... with total of 3 jobs Splitting work into 3 jobs and running 1 at a time with sh in /net/idle/scratch1/terwill/run_072908a/p9-build/AutoBuild_run_1_/TEMP0 Starting job 1... Starting job 2...Starting job 3... Collecting models.... Solution for try : 1 cycle_best_1.pdb Solution 1 from build cycle 1 R= 0.24 Saving /net/idle/scratch1/terwill/run_072908a/p9-build/AutoBuild_run_1_/TEMP0/ AutoBuild_run_1_/cycle_best_1.pdb as MODEL_1.pdb in AutoBuild_run_1_/TEMP0 Solution for try : 2 cycle_best_1.pdb Solution 1 from build cycle 1 R= 0.24 Saving /net/idle/scratch1/terwill/run_072908a/p9-build/AutoBuild_run_1_/TEMP0/ AutoBuild_run_2_/cycle_best_1.pdb as MODEL_2.pdb in AutoBuild_run_1_/TEMP0 Solution for try : 3 cycle_best_1.pdb Solution 1 from build cycle 1 R= 0.24 Saving /net/idle/scratch1/terwill/run_072908a/p9-build/AutoBuild_run_1_/TEMP0/ AutoBuild_run_3_/cycle_best_1.pdb as MODEL_3.pdb in AutoBuild_run_1_/TEMP0 Done with 3 parallel build jobs... Running standard build to merge and extend these models now.If you want to look at the log files for these individual model-building steps, you can look in the directory listed above:
/net/cci-filer1/vol1/tmp/terwill/phenix_examples/p9-build/AutoBuild_run_1_/TEMP0This will contain subdirectories with the model-building runs:
AutoBuild_run_1_/TEMP0/AutoBuild_run_1_/AutoBuild_run_1_1.log AutoBuild_run_1_/TEMP0/AutoBuild_run_2_/AutoBuild_run_2_1.log AutoBuild_run_1_/TEMP0/AutoBuild_run_3_/AutoBuild_run_3_1.logIn this case model 1 is the best. It is then used to start a merging process in which the best parts of each model are kept to create a composite model. This model is then refined, extended (by building off all the ends of chains) and saved:
Model completion cycle 1 Models to combine and extend: ['MODEL_1.pdb', 'MODEL_2.pdb', 'MODEL_3.pdb'] Model 1: Residues built=126 placed=118 Chains=2 Model-map CC=0.82 This is new best model with score = 240 Refining model: Build_combine_extend_1.pdb Model: AutoBuild_run_1_/TEMP0/refine_1.pdb R/Rfree=0.23/0.28 ... New best overall: AutoBuild_run_1_/overall_best.pdb Model obtained on cycle 1 R (work): 0.229221223063 R (free): 0.278562331997 Residues built: 126 Residues placed: 118 Model-map CC: 0.82 Chains: 2In the second overall cycle of model building, the AutoBuild Wizard carries out several density modification steps to obtain an improved map:
Using coordinates of model from previous cycle in buildingThis is the key aspect of iterative model-building, density modification and refinement. The model from each cycle is used to improve the density (even in places where the model was not built) in the map for the next cycle. This is done by using density calculated from the model as part of a real-space target for statistical density modification. The first stage of density modification uses the identification of local patterns of density unique to macromolecules (such as characteristic distances between atoms), and the presence of helices and strands in the map to improve map quality. The pattern and fragment information comes from an analysis of the map from the previous cycle and is combined into a pseudo-map combine.map. This real-space information is then merged with the experimental phase information in exptl_fobs_phases_freeR_flags.mtz:
Density modifying with patterns/fragments and model Adding pattern/fragment phase information from combine.map to exptl_fobs_phases_freeR_flags.mtz to create image.mtzThe composite phase information is then used in density modification. In this step the model density is used as part of the real-space target for statistical density modification. An omit map is also created that does not include the model-based information.
Density modifying image.mtz including model information from refine.pdb_1 to make resolve_work.mtz. Then building model Creating omit map from image.mtz and previous modelsA new model is then built, using the best model available so far (in this case from cycle 1), combined with pieces of a model built in four ways. The first is to "fit_loops", in which case all gaps in the model (places where the sequence file says there are residues but for which there is no model yet, and for which the residues on either side of the gap are present in the model) are systematically rebuilt. The method used is to try to build from either end of the gap and if the two chains connect with the correct number of residues then the gap is considered filled. The second method is to "connect" ends of chains. This is the same as the gap-filling procedure except that it is used in cases where the model has not been assigned to sequence so that the ends to be connected are not known in advance and the number of residues in the gap is also not known. The third method is to "build_outside", in which case the current model is used to mask out the density in the region of the model, and a model is built into the remaining density. The fourth method is simply to build a new model from scratch.
Standard build in parallel starting with refine.pdb_1 and ['overall_best.pdb'] Setting background=False as nproc=1 Try: 1 fit_loops=True Try: 2 connect=True Try: 3 build_outside=TrueThen the current best model and the models built from each of these tries are combined together to make a composite model. As in cycle 1 it is then refined, extended, and saved (if it is an improvement):
Solution for try : 1 cycle_best_1.pdb Solution 1 from build cycle 1 R= 999.9 Saving /net/idle/scratch1/terwill/run_072908a/p9-build/ AutoBuild_run_1_/TEMP0/AutoBuild_run_4_/cycle_best_1.pdb as MODEL_1.pdb in AutoBuild_run_1_/TEMP0 Solution for try : 2 cycle_best_1.pdb Solution 1 from build cycle 1 R= 999.9 Saving /net/idle/scratch1/terwill/run_072908a/p9-build/ AutoBuild_run_1_/TEMP0/AutoBuild_run_5_/cycle_best_1.pdb as MODEL_2.pdb in AutoBuild_run_1_/TEMP0 Solution for try : 3 cycle_best_1.pdb Solution 1 from build cycle 1 R= 0.23 Saving /net/idle/scratch1/terwill/run_072908a/p9-build/ AutoBuild_run_1_/TEMP0/AutoBuild_run_6_/cycle_best_1.pdb as MODEL_3.pdb in AutoBuild_run_1_/TEMP0 Done with 3 parallel build jobs... Running standard build to merge and extend these models now.In this case the building outside-model gave a good model but the gap-filling and connecting did not fill any gaps or loops. (they gave an R of 999. meaning nothing was refined). Model completion with these models and the current best model from cycle 1 gave:
Model completion cycle 1 Models to combine and extend: ['overall_best.pdb', 'starting_model.pdb', 'MODEL_1.pdb', 'MODEL_2.pdb', 'MODEL_3.pdb'] Model 1: Residues built=123 placed=107 Chains=2 Model-map CC=0.80 This is new best model with score = 226 Refining model: Build_combine_extend_1.pdb Model: AutoBuild_run_1_/TEMP0/refine_1.pdb R/Rfree=0.23/0.27This process of model-building iterated with generation of real-space targets for density modification based on local patterns, fragments of structure, and the model is repeated until the R-factor does not decrease for several cycles. In this example, the best model using this procedure is obtained on cycle 2 with an R/Rfree of 0.22/0.27:
New best overall: AutoBuild_run_1_/overall_best.pdb Model obtained on cycle 2 R (work): 0.224655082668 R (free): 0.266763231999 Residues built: 120 Residues placed: 112 Model-map CC: 0.79 Chains: 1
Model-rebuilding with RESOLVE
Once the model-building procedure has converged, the AutoBuild Wizard carries out cycles of rebuilding using a slightly different protocol. The main differences in this set of cycles are that the local patterns and fragments approaches are no longer used (the maps by this time look so much like a macromolecule that these procedures do not add anything), and that the starting point for density modification is a model-based map, not the experimental map. In this example, the rebuilding steps improve the model just a little, and the process ends after 2 cycles of rebuilding:
New best overall: AutoBuild_run_1_/overall_best.pdb Model obtained on cycle 2 R (work): 0.224655082668 R (free): 0.266763231999 Residues built: 120 Residues placed: 112 Model-map CC: 0.79 Chains: 1
The AutoBuild_summary.dat summary file
A quick summary of the results of your AutoBuild run is in the AutoBuild_summary.dat file in your output directory. This file lists the key files that were produced in your run of AutoBuild (all these are in the output directory) and some of the key statistics for the run. Here is the summary for this p9-build model-building run:
Summary of model-building for run 1 Sun Jun 29 12:02:56 2008 Files are in the directory: /net/idle/scratch1/terwill/run_072908a/p9-build/AutoBuild_run_1_/ Starting mtz file: /net/idle/scratch1/terwill/run_072908a/p9-build/p9-solve.mtz Sequence file: /net/idle/scratch1/terwill/run_072908a/p9-build/p9.seq Best solution on cycle: 4 R/Rfree=0.22/0.27 Summary of output files for Solution 3 from rebuild cycle 4 --- Model (PDB file) --- pdb_file: AutoBuild_run_1_/cycle_best_4.pdb --- Refinement log file --- log_refine: AutoBuild_run_1_/cycle_best_4.log_refine --- Model-building log file --- log: AutoBuild_run_1_/cycle_best_4.log --- Model-map correlation log file --- log_eval: AutoBuild_run_1_/cycle_best_4.log_eval --- 2FoFc and FoFc map coefficients from refinement 2FOFCWT PH2FOFCWT FOFCWT PHFOFCWT --- refine_map_coeffs: AutoBuild_run_1_/cycle_best_refine_map_coeffs_4.mtz --- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag --- hklout_ref: AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz --- Density-modification log file --- log_denmod: AutoBuild_run_1_/cycle_best_4.log_denmod --- Density-modified map coefficients FP PHIM FOM --- hklout_denmod: AutoBuild_run_1_/cycle_best_4.mtz You might consider making one very good model now with: phenix.autobuild \ data=AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz \ model=AutoBuild_run_1_/cycle_best_4.pdb \ rebuild_in_place=True \ seq_file=/net/idle/scratch1/terwill/run_072908a/p9-build/p9.seq SOLUTION CYCLE R RFREE BUILT PLACED 1 1 0.23 0.28 126 118 2 2 0.22 0.27 120 112 3 4 0.22 0.27 123 111 4 5 0.22 0.26 121 113Note that the file AutoBuild_run_1_/cycle_best_4.log_eval in this example has a complete analysis of the the fit of the model in AutoBuild_run_1_/cycle_best_4.pdb to the best map in AutoBuild_run_1_/cycle_best_4.log_denmod. This is useful in identifying places where additional rebuilding needs to be done.
Creating an improved model after AutoBuild
You might consider making one very good model now with: phenix.autobuild \ data=AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz \ model=AutoBuild_run_1_/cycle_best_4.pdb \ rebuild_in_place=True \ seq_file=/net/cci-filer1/vol1/tmp/terwill/phenix_examples/p9-build/p9.seqThis is a command-line command to take the final model from this AutoBuild run, rebuild it 4 times using the "rebuild_in_place" algorithm, combine the resulting models to make a composite model, refine it, and write out the final model. This method is very effective at improving models from AutoBuild (or from any other source). You can see more details of this in Tutorial 6: Automatically rebuilding a structure solved by Molecular Replacement
How do I know if iterative model-building, density modification and refinement worked?
What to do next
Once you have run AutoBuild and have obtained a good model, you will want to inspect and touch up the model carefully, rebuilding any parts of the model that do not agree well with the final map. You should also have a close look at all the solvent molecules in your model, making sure that they all have reasonable relationships to the macromolecule and to each other, and that they are not simply filling up density where a ligand or the macromolecule really goes. The next thing to do is to add in any ligands (metals, cofactors) if there is density for them. You can use the LigandFit Wizard (see Automated Ligand Fitting using LigandFit ) to help you fit ligands into your map automatically. If you do not obtain a good model, then it's not quite time to give up yet. There are a number of standard things to try that may improve the model building. Here are a few that you should try:
For details about the AutoBuild Wizard, see Automated Model building and Rebuilding using AutoBuild. For help on running Wizards, see Using the PHENIX Wizards.