.. _ccp4i2_script_lattice_search: Performing a lattice search with SIMBAD --------------------------------------- .. note:: Data used throughout this example can be found in ``/examples/lattice_example``. If SIMBAD is part of your CCP4 installation, then the example files can be downloaded as part of the `GitHub repository `_. 0. Command line options ^^^^^^^^^^^^^^^^^^^^^^^ Check out this page explaining the :ref:`simbad-lattice ` script command line options. 1. Running the SIMBAD lattice search ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The lattice parameters for a crystallised protein are often unique and therefore provide a quick and easy route to identify previously solved structures. The SIMBAD lattice search compares the lattice parameters of an input MTZ file to all the structures in the PDB. In this example, the ``simbad-lattice`` script simply takes the crystallographic data file in MTZ format, and runs the lattice search followed by Molecular Replacement on your local machine. SIMBAD can be found under the Molecular Replacement menu in the CCP4i GUI: .. figure:: ../images/ccp4i2_simbad.png :width: 50% :align: center Opening SIMBAD will bring you to the following menu: .. figure:: ../images/ccp4i2_simbad_run.png :width: 50% :align: center Additionally the following advanced options can be selected: .. figure:: ../images/ccp4i2_simbad_run_2.png :width: 50% :align: center To run the lattice search, all that is needed is an MTZ file: .. figure:: ../images/ccp4i2_simbad_lattice.png :width: 50% :align: center SIMBAD Output ------------- 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: .. contents:: Output Tabs :depth: 1 :local: Summary ^^^^^^^ The summary tab contains a summary of the best solution found by SIMBAD. .. figure:: ../images/ccp4i2_lattice_summary.png :width: 50% :align: center ------------------------------------------------------------------ Lattice Parameter Search Results ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The Lattice Parameter Search Results are not shown by default. If selected however, 2 tables are displayed: .. contents:: Tables :depth: 1 :local: .. figure:: ../images/ccp4i2_lattice_results.png :width: 50% :align: center ------------------------------------------------------------------ Molecular Replacement Search Results ==================================== 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: * **molrep_score:** MOLREP score for the Molecular Replacement solution * **molrep_tfscore:** MOLREP translation function score for the Molecular Replacement solution Alternatively SIMBAD can run Molecular replacement using PHASER. If run the following columns are added to the table: * **phaser_llg:** PHASER Log-likelihood gain for the Molecular Replacement solution * **phaser_tfz:** PHASER Translation Function Z-score for the Molecular Replacement solution * **phaser_rfz:** PHASER Rotational Function Z-score for the Molecular Replacement solution Following Molecular replacement, refinement is run using REFMAC. This add the following columns are added to the table: * **final_r_fact:** R-fact score for REFMAC refinement of the Molecular Replacement solution * **final_r_free:** R-free score for REFMAC refinement of the Molecular Replacement solution .. 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: * **dano_peak_height:** The highest anomalous peaks found * **dano_z_score:** DANO peak Z-score Lattice Parameter Search Results ================================ This shows the results from the Lattice Parameter Search. The columns of the table are: * **PDB_code:** The 4 letter code representing the protein in the protein data bank * **alt:** Alternative Niggli cell, denoted by a * * **a:** Lattice parameter a * **b:** Lattice parameter b * **c:** Lattice parameter c * **alpha:** Lattice parameter alpha * **beta:** Lattice parameter beta * **gamma:** Lattice parameter gamma * **length_penalty:** The sum of the differences between lattice parameters a, b and c for the model and the target * **angle_penalty:** The sum of the differences between lattice parameters alpha, beta and gamma for the model and the target * **total_penalty:** The sum of the length penalty and the angle penalty * **Probability_score:** The probability that a structure giving a total penalty score will provide a solution The structures are scored by total_penalty score where a lower 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.