.. _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. .. literalinclude:: /../examples/lattice_example/run.sh :language: bash :lines: 10-11 Alternatively the ``simbad-lattice`` search can be run without Molecular Replacement by providing the unit cell and the space group for a data set, as shown below: .. code-block:: bash simbad-lattice -uc 73.5820,38.7330,23.1890,90.0000,90.0000,90.0000 -sg P212121 SIMBAD Output ------------- Upon running SIMBAD results will be output to the terminal: .. figure:: ../images/command_line_lattice.png :width: 50% :align: center Lattice Parameter Search Results ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The Lattice Parameter Search outputs 2 tables. Below you can find information about each: .. contents:: Tables :depth: 1 :local: ------------------------------------------------------------------ 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. 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 a phased 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