Installing SBGrid Software
Using the SBGrid Environment
Support for Site Administrators
Hardware Support Notes
Getting Help
Support for Developers
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.
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.
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.
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.
This version of the page was edited by key at 2021-05-05 15:07:58. View the most recent version.