Analyze Tutorial

Example: HIV-1 Protease Inhibitor, XK-263

Using Autoanalyze to read in and visualize the results of a docking experiment.

Analyze :

Please Note: AutoDock3.05 (or later versions) must be have been used in order to look at docked ligand conformations with this section of adt .

Read Docking Log

Choosing the docking log

Choosing which docked conformations to visualize: None, Input Ligand Only, Input and the best docked conformation of the best cluster, Input and the best docked conformation of each cluster or All of the available ligand conformations. (the number of available docked conformation is set by the output level keyword 'outlev' specified in the dpf)

Analyze :

Delete Docking Log

Choosing which docking log to delete from a list of dockings which had been read into the molecular viewer.

Analyze :

Select Docking Log

Choosing which one of the dockings present in the molecular viewer is to be the current docking log.

Analyze :

Choose a Docked Conformation

Selecting a docked conformation from the current docking

Analyze :

Show Macromolecule

Adding the macromolecule of the current docking

Analyze :

Show Histogram

Summarizes results of current docking

Analyze :

Read directory of dlgs

Choosing the directory. This command lets the user read in a group of docking log files without having to manually select each one. Each file with the extension '.dlg' in the selected directory is read.

Analyze :

Show Chart

Choosing the docking logs to be included in chart

This creates a chart with one button per input ligand and one per best docked conformation in each docking log. The set of docking logs represented in the following Results Chart docked three peptides against one protein '1hefCorr.pdbqs' and one ligand '1hihLCorr.out.pdbq' against two proteins. This output format is designed for sets of dockings of this kind.