version 0.9.5
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
| Name | Description |
|---|---|
| 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
| Name | Description |
|---|---|
| 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 or fractional coordinates (determined by the &space query parameter). |
| u,v,w | Top right corner of the query region in Cartesian or fractional coordinates (determined by the &space query parameter). |
| 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=1Parameters
| Name | Description |
|---|---|
| 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 v20.10.0