Data Processing after WS-MR

1 Verify Results for Search Models

The first follow-up step for a search model resulting from WSMR is to repeat MR locally.

To download one of the search models; first click the "Load Top 100 Hits" button, click one of the yellow circles in the resulting plot, and then use the download link for the model.

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A typical input deck (MR01.in for this example) for phaser would look something like this (with the paths to your input MTZ and PDB files adjusted appropriately):

ROOT            MR01
MODE            MR_AUTO
HKLIn           reflections.mtz
LABIn           F=FP SIGF=SIGFP
ENSEmble        SearchModel PDB model.pdb IDENtity 0.3
COMPosition     PERCENTAGE 0.50
RESOlution      HIGH 3.1
SEARch          ENSEmble SearchModel NUM 1
SGALternative   SELECT ALL

This can be run with versions of phaser distributed with CCP4 or PHENIX (with phaser < MR01.in > MR01.out or phenix.phaser < MR01.in > MR01.out respectively). The statistics (LLG and Z-scores) from local runs may differ due to differences in phaser versions.

The SGALternative card is only necessary if you're checking alternative space-groups.

2 Expand Search

WSMR searches for a single copy of the search model - however there may be multiple copies of the model in the ASU. If so, the next step is the increase the NUM value for the SEARch card. When in doubt, it's better to set this too hight rather than too low - phaser will stop when unable to locate additional copies.

3 Autobuild

Once MR has been exhausted (no more copies of the search model can be placed), one possible next step is to use an autobuilder for an initial attempt to correct the sequence of the model.

Using the PHENIX autobuilder:

phenix.autobuild reflections.mtz MR_Results.pdb project.fasta nproc=4 > AutoBuild01.out

The input model (MR_Results.pdb) for the autobuilder is the final result modeles from the initial or expanded MR search.

The input MTZ file should be the original amplitudes (or intensities) used for searching, not the results from phaser. If phaser was run with the SGALternative card, make sure the spacegroup of this MTZ matches that of the search solutions.

The nproc=4 option should only be used if there are four (or more) available cores - when using the rebuild_in_place option, phenix.autobuild can't take advantage of more than 4 processors.