DensityServer
version 0.9.2

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. The server support is integrated into the LiteMol Viewer.

Data Header / Check Availability /<source>/<id>
Returns a JSON response specifying if data is available and the maximum region that can be queried.

Examples

/x-ray/1cbs
/em/emd-8116

Parameters

NameDescription
source Specifies the data source (determined by the experiment method). Currently, x-ray and em sources are supported.
id Id of the entry. For x-ray, use PDB ID (i.e. 1cbs) and for em use EMDB id (i.e. emd-8116).

Box /<source>/<id>/box/<a,b,c>/<u,v,w>?<optional parameters>
Returns density data inside the specified box for the given entry. For X-ray data, returns 2Fo-Fc and Fo-Fc volumes in a single response.

Examples

/em/emd-8003/box/-2,7,10/4,10,15.5?excoding=cif&space=cartesian
/x-ray/1cbs/box/0.1,0.1,0.1/0.23,0.31,0.18?space=fractional

Parameters

NameDescription
source Specifies the data source (determined by the experiment method). Currently, x-ray and em sources are supported.
id Id of the entry. For x-ray, use PDB ID (i.e. 1cbs) and for em use EMDB id (i.e. emd-8116).
a,b,c Bottom left corner of the query region in Cartesian coordinates.
u,v,w Top right corner of the query region in Cartesian coordinates.
encoding Determines if text based CIF or binary BinaryCIF encoding is used. An optional argument, default is BinaryCIF encoding.
space Determines the coordinate space the query is in. Can be cartesian or fractional. An optional argument, default values is cartesian.
detail Determines the maximum number of voxels the query can return. Possible values are in the range from 0 (0.52M voxels) to 6 (25.17M voxels). Default value is 0. Note: different detail levels might lead to the same result.

Cell /<source>/<id>/cell?<optional parameters>
Returns (downsampled) volume data for the entire "data cell". For X-ray data, returns unit cell of 2Fo-Fc and Fo-Fc volumes, for EM data returns everything.

Example

/em/emd-8116/cell?detail=1

Parameters

NameDescription
source Specifies the data source (determined by the experiment method). Currently, x-ray and em sources are supported.
id Id of the entry. For x-ray, use PDB ID (i.e. 1cbs) and for em use EMDB id (i.e. emd-8116).
encoding Determines if text based CIF or binary BinaryCIF encoding is used. An optional argument, default is BinaryCIF encoding.
detail Determines the maximum number of voxels the query can return. Possible values are in the range from 0 (0.52M voxels) to 6 (25.17M voxels). Default value is 0. Note: different detail levels might lead to the same result.
© 2016 – now, David Sehnal | Node v7.8.0