Molecular replacement with MolRep

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Main Page - Using the CCP4 software - Molecular replacement with CCP4 - Automated molecular replacement with MolRep

MolRep is program for automated molecular replacement in the case where a homologous structure has already been identified. The program will attempt to find the number of molecules expected in the asymmetric unit as entered by the user. A PDB file for the best solution is output.

Contents

[edit] Running MolRep

The MolRep user interface
The MolRep user interface

From the Molecular Replacement module select MolRep - auto MR. The default mode for running MolRep is to do molecular replacement performing rotation and translation function.

Select the input experimental data file in the box labelled "MTZ in".

Select the input model in the box labelled "Model in".

In the folder "Search Parameters", enter the expected number of monomers in the asymmetric unit in the box labelled "Search for ... monomers in the asymmetric unit."

Select 'Run now' to start MolRep.

[edit] Program output

The program outputs a list of cross rotation function solutions in spherical polar angles and in Euler angles (CCP4 convention). It then outputs a list of translation function solutions, giving the translation in fractional coordinates together with the particular rotation function solution used in each case.

Solutions are given a score which is the product of the Correlation Coefficient of intensities and the maximal value of the Packing Function. The latter is computed from the overlap of electron densities (PF = 1 means no overlap) and downweights solutions with overlapping molecules.

The program outputs a CONTRAST, which is the ratio of the top score to the mean score:

  • >2.5 - definitely solution
  • <2.5 and > 1.8 - solution
  • <1.8 and > 1.5 - maybe solution
  • <1.5 and > 1.3 - maybe not solution, but program accepts it
  • <1.3 - probably not solution

If there is expected to be more than one molecule in the asymmetric unit then the program will continue with additional Translation Functions, using rotations from the original Rotation Function calculation.

Provided the program finds at least one molecule with a reasonable Contrast value, it outputs a PDB file containing the positioned molecule(s).

[edit] Advanced options

Input line for the sequence file (FILE_S) of the target protein
Input line for the sequence file (FILE_S) of the target protein

It can be useful to supply the sequence file for the target protein. Select "Use sequence" and input the name of the sequence file in the folder that appears. Molrep will align the input model against this sequence, and adjust the model accordingly. This assumes that the model is a complete PDB file. If you have previously prepared the model, e.g. using Chainsaw, then you should not use this option.

[edit] Related pages

[edit] Program documentation

The latest version of the documentation is available here. This provides information on program keywords which may be used from the command line. The program homepage is here.

This page describes MolRep version 9.2 (CCP4 version 6.1.0).

--Kevin Cowtan 05:52, 24 April 2008 (CDT)

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