Model building with CCP4
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Main Page - Using the CCP4 software - Model building with CCP4
CCP4 offers both automated and graphical model building tools.
When starting from experimental phasing, no model is available. In this case, automated model building tools will be used to obtain an initial model. This model will usually require additional work before it is good enough to deposit at the PDB. This is acheived through cycles of grahpical rebuilding and refinement.
When starting from a molecular replacement model, it is most common to move directly to grahpical rebuilding and refinement. However in cases where the molecular replacement model gives a poor fit to the unknown structure, automated model building may still be useful.
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[edit] Using model building tools in CCP4
Model building tools in CCP4 are all located in the 'Model Building' module of CCP4i, accessed through the modules menu in the top left hand corner of the main CCP4i window.
[edit] Automated model building tools in CCP4
CCP4 provides the following tools for automated model building:
- Automated model building with Buccaneer:
Buccaneer is an automated protein model building program. It features robust handling of limited data resolution, and is competitive in terms of speed. It is particularly useful at resolutions of worse than 2.5A, although it can also be used at high resolution.
- Automated model building with ARP/wARP: (external program: see below)
ARP/wARP is a mature and widely used automated model building package, which can automatically build models to a high degree of completeness and refinement. It is particularly useful at higher resolutions.
[edit] Graphical model building tools in CCP4
CCP4 provides the following tools for automated model building:
- Graphical model building with Coot:
Coot is a powerful tool for graphical model building, incorporating a wide range of powerful tools for automated, semi-automated and manual building and refinement of atomic models. In addition to proteins and nucleatides it can build ligands and fit water molecules.
[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:
- The ARP/wARP software provides a sophisticated and capable tool for automated model building and completion. It is particularly effective at higher resolutions, and with good data can take the model building process close to completion.