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
On starting SIMBAD a separate window will appear summarising the progress of the SIMBAD MoRDA database search and any results found. The window will contain up to three tabs, the contents of which are explained below:
Output Tabs
This displays the text output by SIMBAD as it is running. Any problems or errors will be displayed here.
The MoRDa database Search Results tab contains 5 different sections. Below you can find information about each:
Sections
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:
Graphs showing the relationship between the final R-Free and various MR parameters are also presented alongside the Molecular Replacement Search results. These are:
If using MOLREP:
if using Phaser:
This section contains the refined placed model and mtz for the top 10 solutions in the MoRDa database search (as ranked by final_r_free)
Note
This section may contain less than 10 solutions if for example a solution was found and the molecular replacement search ended early
This section contains the molecular replacement and refinement logs for the top 10 solutions in the MoRDa database search (as ranked by final_r_free)
Note
This section may contain less than 10 solutions if for example a solution was found and the molecular replacement search ended early
The summary tab contains three different sections. Below you can find information about each:
This details the best model found by SIMBAD and reports the final_r_fact and final_r_free scores found
This section contains the refined placed model and mtz for best solution found by the MoRDa database search (as ranked by final_r_free)
This section contains the molecular replacement and refinement logs for best solution found by the MoRDa database search (as ranked by final_r_free)