Performing a lattice search with SIMBAD

Note

Data used throughout this example can be found in <ROOT>/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 simbad-lattice script command line options.

SIMBAD Output

Upon running SIMBAD results will be output to the terminal:

../../_images/command_line_lattice.png

Lattice Parameter Search Results

The Lattice Parameter Search outputs 2 tables. Below you can find information about each:

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