VolumeServer

What is VolumeServer

Provides near-instantaneous access to volumetric data including density maps (for instance, from X-ray crystallography or cryo-electron microscopy experiments), spatial distribution data, output from electrostatic calculations. It works by utilizing adaptive downsampling (similar to how Google Earth works).

It uses the text based CIF and BinaryCIF formats to deliver the data to the client.

For quick info about the benefits of using the server, check out the examples.

Installing and Running

Requires nodejs 8+.

From GitHub

git clone https://github.com/molstar/molstar
npm install

Afterwards, build the project source:

npm run build:lib

and run the server by

node lib/commonjs/servers/volume/server

From NPM

npm install --production molstar
./volume-server

(or node node_modules\.bin\volume-server in Windows).

The NPM package contains all the tools mentioned here as “binaries”:

• volume-server
• volume-server-pack
• volume-server-query

Production use

In production it is required to use a service that will keep the server running, such as forever.js.

Memory issues

Sometimes nodejs might run into problems with memory. This is usually resolved by adding the --max-old-space-size=8192 parameter.

Preparing the Data

For the server to work, CCP4/MAP (models 0, 1, 2 are supported) input data need to be converted into a custom block format. To achieve this, use the pack application (node lib/commonjs/servers/volume/pack or volume-server-pack binary from the NPM package).

Local Mode

The program lib/commonjs/servers/volume/query (volume-server-query in NPM package) can be used to query the data without running a http server.

Navigating the Source Code

The source code is split into 2 mains parts: pack and server:

• The pack part provides the means of converting CCP4 files into the internal block format.
• The server includes
  • query: the main part of the server that handles a query. execute.ts is the “entry point”.
  • algebra: linear, “coordinate”, and “box” algebra provides the means for calculations necessary to concent a user query into a menaningful response.
  • API wrapper that handles the requests.

Consuming the Data

The data can be consumed in any (modern) browser using the ciftools library (or any other piece of code that can read text or binary CIF).

The Data Format document gives a detailed description of the server response format.

As a reference/example of the server usage is available in Mol* mol-plugin module.

Hosting the server

Example

node lib/commonjs/servers/volume/server --idMap x-ray '/opt/data/xray/${id}.mdb'

Usage

Argument=	Description
--cfg	JSON config file path. If a property is not specified, cmd line param/OS variable/default value are used.
--printCfg	Print current config for validation and exit.
--cfgTemplate	Prints default JSON config template to be modified and exit.
--apiPrefix	Specify the prefix of the API, i.e. <host>/<apiPrefix>/<API queries>
--defaultPort	Specify the port the server is running on
--shutdownTimeoutMinutes	Server will shut down after this amount of minutes, 0 for off.
--shutdownTimeoutVarianceMinutes	Modifies the shutdown timer by +/- timeoutVarianceMinutes (to avoid multiple instances shutting at the same time)
--idMap	Map ids for a type to a file path. Example: x-ray '../../data/mdb/xray/${id}-ccp4.mdb' - Inside ${}, use id with optional chained calls to toLowerCase(), toUpperCase(), substr(n, m), substring(n[, m]), or slice(n[, m]), e.g. ${id.substring(1, 3).toLowerCase()}/${id}.mdb. Calls are applied in order; substr takes a start and length, while substring and slice take a start and optional exclusive end index. - Can be specified multiple times. - The TYPE variable (e.g. x-ray) is arbitrary and depends on how you plan to use the server. By default, Mol* Viewer uses x-ray and em, but any particular use case may vary. - If using URL, it can be http://, https://, gs:// or file:// protocol.
--maxRequestBlockCount	Maximum number of blocks that could be read in 1 query. This is somewhat tied to the maxOutputSizeInVoxelCountByPrecisionLevel in that the &lt;maximum number of voxel&gt; = maxRequestBlockCount * &lt;block size&gt;^3. The default block size is 96 which corresponds to 28,311,552 voxels with 32 max blocks.
--maxFractionalBoxVolume	The maximum fractional volume of the query box (to prevent queries that are too big).
--maxOutputSizeInVoxelCountByPrecisionLevel	What is the (approximate) maximum desired size in voxel count by precision level - Rule of thumb: &lt;response gzipped size&gt; in [&lt;voxel count&gt; / 8, &lt;voxel count&gt; / 4]. The maximum number of voxels is tied to maxRequestBlockCount.

node lib/commonjs/servers/volume/server [-h] [-v]
        [--cfg CFG]
        [--printCfg]
        [--cfgTemplate]
        [--apiPrefix PREFIX]
        [--defaultPort PORT]
        [--shutdownTimeoutMinutes TIME]
        [--shutdownTimeoutVarianceMinutes VARIANCE]
        [--idMap TYPE PATH]
        [--maxRequestBlockCount COUNT]
        [--maxFractionalBoxVolume VOLUME]
        [--maxOutputSizeInVoxelCountByPrecisionLevel LEVEL [LEVEL ...]]