Refinement with CCP4
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Main Page - Using the CCP4 software - Refinement with CCP4
Refinement module
Model refinement involves the adjustment of the parameters of the atomic model (i.e. the positions and other properties of the atoms) in order to better explain the observed structure factors. This leads to a more accurate model.
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[edit] Using refinement tools in CCP4
Refinement tools in CCP4 are all located in the 'Refinement' module of CCP4i, accessed through the modules menu in the top left hand corner of the main CCP4i window.
[edit] Preparing for refinement
- Create/Edit TLS File
Create a TLSIN file for input to Refmac, or adjust a previously generated one. - Review Restraints
Run Refmac5 in review restraints mode to check that all geometric restraints are correct. - Monomer Library Sketcher
If your ligand geometry is not in Refmac's standard monomer library, then create a library description with Sketcher - Merge monomer libraries
If you have created more than one additional monomer library file (.cif file), then merge these into a single file for input to Refmac
[edit] Refinement in CCP4
CCP4 provides Refmac5 for model refinement:
- Refinement with Refmac5:
The REFMAC program can carry out rigid body, TLS, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. It minimises the coordinate parameters to satisfy a Maximum Likelihood residual.
[edit] Analysing the results of refinement
- Analyse TLS parameters
Analyse the XYZOUT and TLSOUT files after TLS refinement in Refmac.
[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:
