Note
Data used throughout this example can be found in <ROOT>/examples/contaminant_example
. If SIMBAD is part of your CCP4 installation,
then the example files can be downloaded as part of the GitHub repository.
Check out this page explaining the simbad-contaminant script command line options.
In this example, the simbad-contaminant
script simply takes the crystallographic data file in MTZ format, and runs the contaminant search on your local machine.
SIMBAD can be found under the Molecular Replacement menu in the CCP4i GUI:
Opening SIMBAD will bring you to the following menu:
Additionally the following advanced options can be selected:
To run the lattice search, all that is needed is an MTZ file:
On starting SIMBAD a results page will appear summarising the progress of the SIMBAD lattice search and any results found. The window will contain two sections, the contents of which are explained below:
Output Tabs
The Contaminant Search Results are not shown by default. If selected however, 2 tables are displayed:
Molecular replacement is performed on the top 20 structures identified by the Lattice Parameter Search. This section displays the results of that molecular replacement.
By default SIMBAD runs Molecular replacement using MOLREP. If run the following columns are added to the table:
Alternatively SIMBAD can run Molecular replacement using PHASER. If run the following columns are added to the table:
Following Molecular replacement, refinement is run using REFMAC. This add the following columns are added to the table:
Note
Typically a result with a final_r_fact and a final_r_free below 0.45 is indicative of a solution.
Additionally if there is anomalous signal in your data set SIMBAD will try to validate the quality of the molecular replacement solution using by plotting the peaks from an anomalous fourier map. If run the following columns are added to the table:
This shows the results from the AMORE Rotation Search carried out on the contaminant database. The columns of the table are:
The structures are scored by CC_F_Z_score score where a higher score is better.
At the bottom of the results page is a button labelled ‘Manual coot’, selecting this will allow you to view the best result SIMBAD has found.