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Clipper utilities

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This module provides a set of interfaces for utilities based on Kevin Cowtan's Clipper libraries. It should be noted that the documentation for many of these interfaces is incomplete or missing - please contact CCP4 or Kevin Cowtan if you have questions or problems.

See also: Kevin Cowtan's home page: http://www.ysbl.york.ac.uk/~cowtan

The clipper utilities module contains the following tasks:
Make reference
Phase improvement (pirate)
Calculate FoM from HL
Calculate E's
Calculate map
Calculate patterson
Combine phases
Phase comparison
Map to structure factors
Model to structure factors
Sigma-A weights

The layout of each task window, i.e. the number of folders present, and whether these folders are open or closed by default, depends on the choices made in the Protocol folder of the task (see Introduction). Although certain folders are closed by default, there are specific reasons why you should or may want to look at them. These reasons are described in the Task Window Layout sections below.

Make reference

This task should be used to generate suitable reference structures can be constructed from the PDB. See phase improvement module for further details.

See program documentation: cpirate

Phase improvement (pirate)

This task is used to run the pirate program to perform statistical phase improvement. See phase improvement module for further details.

See program documentation: cpirate

Calculate FoM from HL

Convert to/from Hendrickson-Lattman coefficients.

See program documentation: chltofom

Calculate E's

No documentation available, see notes below

Calculate map

No documentation available, see notes below

Calculate patterson

No documentation available, see notes below

Combine phases

No documentation available, see notes below

Phase comparison

No documentation available, see notes below

Map to structure factors

No documentation available, see notes below

Model to structure factors

No documentation available, see notes below

Sigma-A weights

No documentation available, see notes below

Notes on the Clipper "jiffy" applications

The jiffy programs above perform a specific crystallographic task. Please note that the csigmaa is not a replacement for the sigmaa program.

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