PHENIX FAQS

If you use PHENIX please cite: Adams, P.D., Grosse-Kunstleve, R.W., Hung, L.-W., Ioerger, T.R., McCoy, A.J., Moriarty, N.W., Read, R.J., Sacchettini, J.C., Sauter, N.K., Terwilliger, T.C. (2002). PHENIX: building new software for automated crystallographic structure determination. Acta Cryst. D58, 1948-1954.

Where can I find sample data?

You can find sample data in the directories located in: $PHENIX/examples. Additionally there is sample MR data in $PHENIX/phaser/tutorial.

Can I easily run a Wizard with some sample data?

You can run sample data with a Wizard with a simple command. To run p9-sad sample data with the AutoSol wizard, you type:

phenix.run_example  p9-sad

This command copies the $PHENIX/examples/p9-sad directory to your working directory and executes the commands in the file run.csh.

What sample data are available to run automatically?

You can see which sample data are set up to run automatically by typing:

phenix.run_example  --help

This command lists all the directories in $PHENIX/examples/ that have a command file run.csh ready to use. For example:

phenix.run_example  --help 

PHENIX run_example script. Fri Jul  6 12:07:08 MDT 2007

Use: phenix.run_example example_name [--all] [--overwrite]
Data will be copied from PHENIX examples into subdirectories
of this working directory
If --all is set then all examples will be run (takes a long time!)
If --overwrite is set then the script will overwrite subdirectories

List of available examples:  1J4R-ligand a2u-globulin-mr gene-5-mad 
p9-build p9-sad

Are any of the sample datasets annotated?

The PHENIX tutorials listed on the main PHENIX web page will walk you through sample datasets, telling you what to look for in the output files. For example, the Tutorial 1: Solving a structure using SAD data tutorial uses the p9-sad dataset as example. It tells you how to run this example data in AutoSol and how to interpret the results.

Why does the AutoBuild Wizard say it is doing 2 rebuild cycles but I specified one?

The AutoBuild wizard adds a cycle just before the rebuild cycles in which nothing happens except refinement and grouping of models from any previous build cycles.

What is the difference between overall_best.pdb and cycle_best_1.pdb in the AutoBuild Wizard?

The AutoBuild Wizard saves the best model (and map coefficient file, etc) for each build cycle nn as cycle_best_nn.pdb. Also the Wizard copies the current overall best model to overall_best.pdb. In this way you can always pull the overall_best.pdb file and you will have the current best model. If you wait until the end of the run you will get a summary that lists the files corresponding to the best model. These will have the same contents as the overall_best files.

Can PHENIX do MRSAD?

Yes, PHENIX can run MRSAD (molecular replacement, combined with SAD phases) by determining the anomalous scatterer substructure from a model-phased anomalous difference Fourier. There two simple ways to do this; both are described in the AutoSol documentation.

How can I tell the AutoSol Wizard which columns to use from my mtz file?

The AutoSol Wizard will normally try to guess the appropriate columns of data from an input data file. If there are several choices, then you can tell the Wizard which one to use with the script command group_labels_list or the command_line keywords labels, peak.labels, infl.labels etc. For example if you have two input datafiles w1 and w2 for a 2-wavelength MAD dataset and you want to select the w1(+) and w1(-) data from the first file and w2(+) and w2(-1) from the second, you could put in a script file the following lines (see "How do I know what my choices of labels are for my data file" to know what to put in these lines):

input_file_list w1.mtz w2.mtz
group_labels_list 'w1(+) SIGw1(+) w1(-) SIGw1(-)' 'w2(+) SIGw2(+) w2(-) SIGw2(-)'

Note that all the labels for one set of anomalous data from one file are grouped together in each set of quotes. You could accomplish the same thing from the command line by specifying something like:

peak.data=w1.mtz infl.data=w2.mtz \
peak.labels='w1(+) SIGw1(+) w1(-) SIGw1(-)'  \
infl.labels='w2(+) SIGw2(+) w2(-) SIGw2(-)'

How do I know what my choices of labels are for my data file?

You can find out what your choices of labels are by running the command:

phenix.autosol show_labels=w1.mtz

This will provide a listing of the labels in w1.mtz and suggestions for their use in the PHENIX Wizards. For example the labels for w1.mtz yields:

List of all anomalous datasets in  w1.mtz
'w1(+) SIGw1(+) w1(-) SIGw1(-)'

List of all datasets in  w1.mtz
'w1(+) SIGw1(+) w1(-) SIGw1(-)'

List of all individual labels in  w1.mtz
'w1(+)'
'SIGw1(+)'
'w1(-)'
'SIGw1(-)'

Suggested uses:
labels='w1(+) SIGw1(+) w1(-) SIGw1(-)'
input_labels='w1(+) SIGw1(+) None None None None None None None'
input_refinement_labels='w1(+) SIGw1(+) None'
input_map_labels='w1(+) None None'

What can I do if a Wizard says this version does not seem big enough?

The Wizards try to automatically determine the size of solve or resolve, but if your data is very high resolution or a very large unit cell, you can get the message:

 ***************************************************
 Sorry, this version does not seem big enough...
 (Current value of isizeit is  30)
 Unfortunately your computer will only accept a size of  30
 with your current settings.
 You might try cutting back the resolution
 You might try "coarse_grid" to reduce memory
 You might try "unlimit" allow full use of memory
 ***************************************************

You cannot get rid of this problem by specifying the resolution with

resolution=4.0

because the Wizards use the resolution cutoff you specify in all calculations, but the high-res data is still carried along. The easiest solution to this problem is to edit your data file to have lower- resolution data. You can do it like this:

phenix.reflection_file_converter huge.sca --sca=big.sca --resolution=4.0

A second solution is to tell the Wizard to ignore the high-res data explicitly with:

resolution=4.0 \
resolve_command="'resolution 200 4.0'" \
solve_command="'resolution 200 4.0'" \
resolve_pattern_command="'resolution 200 4.0'"

Note the two sets of quotes; both are required for this command-line input. These commands are applied after all other inputs in resolve/solve/resolve_pattern and therefore all data outside these limits will be ignored.

Why does the AutoBuild Wizard say Sorry, you need to define FP in labin but AutoMR was able to read my data file just fine?

When you run AutoMR and let it continue on to the AutoBuild Wizard automatically, the AutoBuild wizard guesses the input file contents separately from AutoMR. Usually it can guess correctly, but if it cannot then you can tell it what the labels for FP SIGFP FreeR_flag are like this:

autobuild_input_labels="myFP mySIGFP myFreeR_flag"

where you can say None for anything that you do not want to define. This has an effect that is identical to specifying input_labels directly when you run AutoBuild.

Why does the AutoBuild Wizard just stop after a few seconds?

When you run AutoBuild from the command line it writes the output to a file and says something like:

Sending output to  AutoBuild_run_3_/AutoBuild_run_3_1.log

Usually if something goes wrong with the inputs then it will give you an error message right on the screen. However a few types of errors are only written to the log file, so if AutoBuild just stops after a few seconds, have a look at this log file and it should have an error message at the end of the file.

What do I do if the PHENIX GUI hangs?

If the GUI hangs (windows do not respond or windows display partially) then you may want to try and kill it by clicking on the upper right corner , or right-clicking on the top bar of the GUI and closing it. If those fail, you can control-C in the window where you started up the GUI. In either case, you can restart the GUI by typing phenix again. You may find it necessary to start phenix up, then close it down nicely with Project/Exit, and restart it (this gets rid of some files that are deleted when the GUI closes normally). You may also occasionally find it necessary to kill any jobs that are still running by running top and noticing if there are python or resolve or solve jobs running that were part of your PHENIX job, then using k to kill those jobs while running top.

Why does the GUI Parameters window say Invalid input parameters...do you want to continue?

This happens if something in the window isn't correct. If no colored entry fields come up, have a look at the bottom where it says NAVIGATE SET VARIABLE AUTO MANUAL. The entry forms under these words should read: "Choose method to run" "Choose variable to set" and "Manual" (or "Automatic") unless you have intentionally set them. If that isn't it, look carefully at all the entries in the entire parameters window and make sure that they are of the type that is expected (file name, number, etc). If that doesn't work, just click YES and carry on.

Why is my TEMP0 directory empty after running a Wizard?

By default all the working files in the TEMP subdirectories are deleted at the end of a Wizard run. If you want to keep these files, then you can specify

clean_up=False

How do I stop a Wizard?

You can stop a Wizard in two ways. For a "soft" stop, press the "Pause" button if you are running from the GUI, or create a file with the name STOPWIZARD in the directory where the Wizard is running (i.e., create AutoBuild_run_4_/STOPWIZARD to stop run 4 of the AutoBuild Wizard). For a hard stop from the GUI, you can select "Strategy" on the top line of the GUI and then select "Stop Strategy" at the bottom of the choices. That kills the Wizard and all associated jobs. You can still go on from there; select the Parameters window (the lines at the upper left of the now-yellow GUI window) and choose what to do next.

What is an R-free flags mismatch?

When you run AutoBuild or phenix.refine you may get this error message or a similar one:

 ************************************************************
Failed to carry out AutoBuild_build_cycle:
Please resolve the R-free flags mismatch.
************************************************************

Phenix.refine keeps track of which reflections are used as the test set (i.e., not used in refinement but only in estimation of overall parameters). The test set identity is saved as a hex-digest and written to the output PDB file produced by phenix.refine as a REMARK record:

  REMARK r_free_flags.md5.hexdigest 41aea2bced48fbb0fde5c04c7b6fb64

Then when phenix.refine reads a PDB file and a set of data, it checks to make sure that the same test set is about to be used in refinement as it was in the previous refinement of this model. If it does not, you get the error message about an R-free flags mismatch. Sometimes the R-free flags mismatch error is telling you something important: you need to make sure that the same test set is used throughout refinement. In this case, you might need to change the data file you are using to match the one previously used with this PDB file. Alternatively you might need to start your refinement over with the desired data and test set. Other times the warning is not applicable. If you have two datasets with the same test set, but one dataset has one extra reflection that contains no data, only indices, then the two datasets will have different hex digests even though they are for all practical purposes equivalent. In this case you would want to ignore the hex-digest warning. If you get an R-free flags mismatch error, you can tell the AutoBuild Wizard to ignore the warning with :

skip_hexdigest=True

and you can tell phenix.refine to ignore it with:

refinement.input.r_free_flags.ignore_pdb_hexdigest=True

You can also simply delete the REMARK record from your PDB file if you wish to ignore the hex-digest warnings.

Can I use the AutoBuild wizard at low resolution?

The standard building with AutoBuild does not work very well at resolutions below about 3-3.2 A. In particular, the wizard tends to build strands into helical regions at low resolution. However you can specify "helices_strands_only=True" and the wizard will just build regions that are helical or beta-sheet, using a completely different algorithm. This is much quicker than standard building but much less complete as well.

Why doesn't COOT recognize my MTZ file from AutoBuild?

This happens if you use "auto-open MTZ" in COOT. COOT will say: FAILED TO FIND COLUMNS FWT AND PHWT IN THAT MTZ FILE FAILED TO FIND COLUMNS DELFWT AND PHDELFWT IN THAT MTZ FILE. The solution is to use "Open MTZ" and then to select the columns (usually FP PHIM FOMM, and yes, do use weights).