Phase improvement with CCP4
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Density improvement module
Phase improvement exploits out chemical knowledge about what a good electron density map should look like to improve initial phase estimates, in order to obtain a better electron density map.
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[edit] Using phase improvement tools in CCP4
Phase improvement (density modification) tools in CCP4 are all located in the 'Density improvement' module of CCP4i, accessed through the modules menu in the top left hand corner of the main CCP4i window.
[edit] Automated phase improvement tools in CCP4
CCP4 provides the following tools for automated phase improvement:
- Automated phase improvement with Pirate:
Pirate performs phase improvement by statistical density modification. This is a more time consuming calculation than traditional methods, but may yield better results in some cases.
[edit] Non-automated phase improvement tools in CCP4
CCP4 provides the following tools for non-automated phase improvement:
- Phase improvement with DM:
DM is a fast and robust phase improvement program which implements traditional density modification by solvent flattening and histogram matching. An initial set of phases and an estimate of the solvent content are required.
- Phase improvement by NCS averaging with DM:
DM may also be used for non-crystallographic symmetry averaging, to provide greater improvement to the map. For the normal case of a single rigid averaging domain, the averaging mask is calculated automatically, however the NCS operators must be known in advance.
[edit] Third party software which can be used with CCP4
The following third-party packages may also be used from within the CCP4i graphical user interface, if they have been installed at your site: