Overview

DensityServer is a service for accessing subsets of volumetric density data. It automatically downsamples the data depending on the volume of the requested region to reduce the bandwidth requirements and provide near-instant access to even the largest data sets. It uses the text based CIF and binary BinaryCIF formats to deliver the data to the client. mmCIF format is the archival format for the Protein Data Bank and there are numerous parsers and software in the structural biology domain that can readily consume this data format, whereas BinaryCIF is the corresponding compressed format which provides a compact and efficient way of storing and transmitting data.

How it works

Any structure in the PDB and EMDB archives can be queried with a simple GET request to a URL, with each endpoint in the URL corresponding to a specific query. Parameters can be passed to the query as parameters in the URL. For a list of available queries and corresponding parameters, as well as example URLs, please refer to the documentation section.

Advantages

The DensityServer can provide a slice of electron density map at full resolution (e.g. around ligand) or a map at reduced resolution of the complete structure (down-sampled map). To further reduce the size of transferred data, it supports the BinaryCIF format. This enables a dramatic reduction in data transfer size by providing on-demand access to relevant data, thus eliminating the need to send complete data sets.

Released versions

The following versions are released and available :

  • version 0.9.4

Contributors

PDBe NCBR