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). In the case when both PDB code
and custom PDB file name are specified simultaneously, the
server will use the first rather than the latter.
For registered PDB entries, one can choose between the
asymmetric unit and the
biological unit if the
latter is available from the Protein Quaternary Structure
(PQS)
server. In addition, one can indicate if ligands and/or
water molecules defined in the file should be included in
the image. The user can also specify the initial
orientation of a macromolecule and its relative position by
centering specific structural element, such as chain or
residue(s) of interest.
| Asymmetric unit (Default option) |
Biological unit |
|---|---|
|
|
| Click on respective image to see options used for its rendering. | |