Note
Data used throughout this example can be found in <ROOT>/examples/morda_example
. If SIMBAD is part of your CCP4 installation,
then the example files can be downloaded as part of the GitHub repository.
Warning
You need to have a full copy of the MoRDa database installed locally. We also recommend that this search is not run on local machines, but clusters instead.
Check out this page explaining the simbad-morda script command line options.
In this example, the simbad-morda
script simply takes the crystallographic data file in MTZ format and the path to the local copy of the MoRDa database. It then runs the rotation function search with all models in the database against your crystallographic data.
morda_db="<PATH TO MORDA DB>"
nproc=4
simbad-morda \
-morda_db ${morda_db} \
-nproc ${nproc} \
input/1dtx.mtz
Upon running SIMBAD results will be output to the terminal
The MoRDa database Search outputs 2 tables. Below you can find information about each:
This shows the results from the AMORE Rotation Search carried out on the MoRDa database. The columns of the table are:
The structures are scored by CC_F_Z_score score where a higher score is better.
Molecular replacement is performed on the top 200 structures identified by the MoRDa database AMORE Rotation 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 dataset SIMBAD will try to validate the quality of the molecular replacement solution using by plotting the peaks from a phased anomalous fourier map. If run the following columns are added to the table: