Validation with CCP4

From Media Wiki

Main Page - Using the CCP4 software - Validation with CCP4

CCP4 offers tools for the assessment of both experimental data and atomic models, and to assist with the deposition of data to the PDB.

Contents 1 Using validation tools in CCP4 2 Validation tools in CCP4 3 Assessment tools in CCP4 4 Third party software which can be used with CCP4

[edit] Using validation tools in CCP4

Validation tools in CCP4 are all located in the 'Validation and deposition' module of CCP4i, accessed through the modules menu in the top left hand corner of the main CCP4i window. Additional tools to assess atomic models are available in the 'Structure analysis' module.

[edit] Validation tools in CCP4

CCP4 provides the following tools for validation:

• Analyse experimental data with SFCHECK (Validate model and/or data task). SFCHECK will assess the quality of experimental data or an atomic model, or the agreement between both.

• Analyse atomic model against data with SFCHECK (Validate model and/or data task). SFCHECK will assess the quality of experimental data or an atomic model, or the agreement between both.

• Analyse atomic model with Rampage (Validate model and/or data task). Rampage is a modern tool for analysing protein geometry based on the latest data from the PDB, as analysed by the Richardsons.

• Analyse atomic model with Procheck (Validate model and/or data task). Procheck is a widely used tool for analysing protein geometry, however its Ramachandran plots are based on older data.

[edit] Assessment tools in CCP4

[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: MolProbity