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Retrieving PDB Complexes Online

LigandScout provides the possibility to directly import PDB data from web sources specified in the Preferences/PDB & Proxy Settings . Just type a valid PDB code into the PDB 4-letter code field in the control panel of the Structure-Based Modeling Perspective. If the data is available in either the Local Repository or Shared Repository ( Local and Shared Repository ) then it is loaded immediately and the button will be labeled Renew 'PDB code' . If the PDB complex was not found in the repositories the button will be labeled Download 'PDB code' . Anyway, by clicking the button the PDB complex is loaded from the web source, automatically interpreted, stored in the Local Repository, and displayed in LigandScout.
PDB panel
Figure 3.3. PDB panel

LigandScout connects to the PDB servers listed in Preferences/PDB & Proxy Settings according to their appearance. The listing of the servers from top to bottom is the order in which the servers are contacted until a valid PDB structure is found and downloaded correctly or all listed servers were contacted. After a successful download LigandScout activates the PDB interpretation algorithm, shows the complex in the Macromolecule View , and stores a copy in the Local Repository automatically for faster access if this code should be entered again sometime later. Please see Local and Shared Repository for detailed information.
If you experience problems connecting to the PDB server(s), please see the PDB & Proxy Settings in the Preferences/Program & Network Settings for more information.

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Page designed & authored by G. Wolber

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