POLYVIEW-3D Tutorial

Part 1. Source of structural data

We start by reviewing the set of options that allows one to specify a PDB formatted file with the macromolecule of interest (e.g., protein or DNA/RNA) to be used as input for rendering.

Data source

Both the Protein Data Bank (PDB) deposited entries and the PDB formatted custom files can be submitted to the POLYVIEW server. Lines with ATOM cards are the only required data to be present in the file. For registered PDB entries, it is sufficient to enter a 4-letter code (e.g., 1a4y). NOTE: when both a PDB code and a custom PDB file are specified, the server will use only the PDB code as input, and will ignore the submitted file.

For protein structures registered in PDB, one can choose between the asymmetric unit and the biological unit if the latter is available from the (PISA) server. Below is example of difference between asymmetric and biological units, using the structure of a porin from Rh. blastica (PDB id 1bh3).

NOTE: Definition of biological unit is not a straight forward task and may not be always defined unambiguously. That is why different sources may sometimes provide alternative multimeric structures. The user can refer to Proteopedia to read more on this issue. Furthermore, if someone is not satisfied with definition of biological unit by PISA, one can create an alternative model, e.g., using the MakeMultimer utility, and subsequently submit it as a custom file to POLYVIEW-3D for visualization.

Asymmetric unit
(Default option)
Biological unit
Click on respective image to see options used for its rendering.

Last modified: Thu Feb 9 13:22:22 EST 2012

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