ValidatorDB:Plugin

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ValidatorDB extension allows for download and display validation reports from the Protein Data Bank. This process is useful for analyses of structural discrepancies found in ligands and non-standard residues within the PDB archive. The plugin archive for PyMOL and UCSF Chimera software is available for download here.

Installation

PyMOL

Installation of the ValidatorDB extension in the PyMOL environment is fairly simple. First, select in the PyMOL menu Plugin -> Plugin Manager. Click Install New Plugin tab and select the *.zip directory with the programmatic extension. After the PyMOL restart, ValidatorDB extension can be found in the Plugin tab. The entire process is highlighted at the following figures:

Chimera

Installation of the ValidatorDB extension in the UCSF Chimera environment can be summarized in the following steps:

  • Click 'Favorites tab' and select Add to Favorites/Toolbar (Fig. 1)
  • Click 'Add button' and select parent directory with the unzipped extension archive (Fig. 2)

The ValiatorDB extension is available from the Tool icons menu by clicking on its icon and in the menu Tools->Structure Analysis-> ValidatorDB