DIMPLE (CCP4: Supported Program)

NAME

DIMPLE - automated difference map calculation

SYNOPSIS

dimple [-D] hklin foo_in.mtz xyzin foo_in.pdb hklout foo_out.mtz xyzout foo_out.pdb
[Key-worded input]

DESCRIPTION

DIMPLE is a simple pipeline to calculate a difference map for us in ascertaining the presence of a bound ligands to a target protein. It takes in a merged MTZ file containing intensities and a PDB coordinate file containing the already solved protein structure. It outputs an MTZ file containing the calculated electron density map and difference map along with the positioned structure.

DEPENDENCIES

Before DIMPLE can be used, the following dependencies should be installed on the local system.

INPUT AND OUTPUT FILES

HKLIN

Input structure factor file for target structure. Must contain intensities! (e.g. IMEAN and SIGIMEAN). DIMPLE will assume the column labels are IMEAN and SIGIMEAN. If running from the command line and these are not the labels then you need to specifiy their names using the LABIN keyword.

XYZIN

Input coordinate file for the protein structure.

HKLOUT

MTZ file from Refmac5 refinement containing difference map.

XYZOUT

PDB coordinate file from Refmac5 refinement.

KEYWORDED INPUT

Use of the "-D" option in the command line sets the default value for IMEAN and SIGIMEAN to IMEAN and SIGIMEAN. If the MTZ column labels differ from these labels you must enter them using the LABIN keyword.

Main keywords:

LABIn,

LABIN <program label>=<file label>...

Optional. This keyword tells the program which columns in the MTZ file should be used as intensities and sigmas. Available program labels are IMEAN and SIGIMEAN.

END

End keyworded input.

EXAMPLE KEYWORD INPUT FILES

Simple example with minimal input using default values: 

LABIN IMEAN=IMEAN SIGIMEAN=SIGIMEAN 
END

AUTHORS

Ronan Keegan, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, UK
Graeme Winter, Diamond Light Source, Rutherford Appleton Laboratory, UK
George Pelios, Reasearch Complex at Harwell, STFC Rutherford Appleton Laboratory, UK

ACKNOWLEDGEMENTS

Alun Ashton, Mark Basham, Olof Svensson, Jerome Kieffer, Dave Brown.

DIMPLE Program References

Any publication arising from use of DIMPLE should include the following reference:

M. D. Winn et al. (2011) Acta. Cryst. D67, 235-242 - "Overview of the CCP4 suite and current developments"

In addition, authors of specific programs should be referenced where applicable:
PHASER
McCoy, A.J., Grosse-Kunstleve, R.W., Storoni, L.C. & Read, R.J. (2005). "Likelihood-enhanced fast translation functions" Acta Cryst D61, 458-464
REFMAC
G.N. Murshudov, A.A.Vagin and E.J.Dodson, (1997) "Refinement of Macromolecular Structures by the Maximum-Likelihood Method" Acta Cryst. D53, 240-255