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VolumeServer: Response Data Format

This document describes the CIF categories and fields generated by the server.

Query info

The reponse always contains a data block called SERVER with this format:

data_SERVER
#
_density_server_result.server_version     0.9.0 
_density_server_result.datetime_utc       '2017-03-09 20:35:45' 
_density_server_result.guid               f69581b4-6b48-4fa4-861f-c879b4323688 
_density_server_result.is_empty           no 
_density_server_result.has_error          no 
_density_server_result.error              . 
_density_server_result.query_source_id    xray/1cbs 
_density_server_result.query_type         box 
_density_server_result.query_box_type     cartesian 
_density_server_result.query_box_a[0]     14.555 
_density_server_result.query_box_a[1]     16.075001 
_density_server_result.query_box_a[2]     9.848 
_density_server_result.query_box_b[0]     29.302999 
_density_server_result.query_box_b[1]     35.737 
_density_server_result.query_box_b[2]     32.037001

Query data

If the query completed successfully with a non-empty result the response will contain one or more data blocks that correpond to the "channels" present in the data (e.g. for x-ray data there will be 2Fo-Fc and Fo-Fc) channels.

The format is this:

data_2FO-FC
#
_volume_data_3d_info.name                         2Fo-Fc

Axis order

Axis order determines the order of axes of origin, dimensions and sample_count fields. It also specifies the order of values in _volume_data_3d.values. 0 = X axis, 1 = Y axis, 2 = Z axis.

_volume_data_3d_info.axis_order[0]                0 
_volume_data_3d_info.axis_order[1]                1 
_volume_data_3d_info.axis_order[2]                2

Origin and dimensions

Specifies the fractional coordinates of the bounding box of the data present in the data block.

_volume_data_3d_info.origin[0]                    -0.5 
_volume_data_3d_info.origin[1]                    -0.5 
_volume_data_3d_info.origin[2]                    -0.5 
_volume_data_3d_info.dimensions[0]                1 
_volume_data_3d_info.dimensions[1]                1 
_volume_data_3d_info.dimensions[2]                1

Sample rate

Determines how many values of the original input data were collapsed in to 1 value.

_volume_data_3d_info.sample_rate                  8

Sample count

Determines how many values in _volume_data_3d.values are present along each axis (in axis_order).

_volume_data_3d_info.sample_count[0]              96 
_volume_data_3d_info.sample_count[1]              96 
_volume_data_3d_info.sample_count[2]              96

Spacegroup information

_volume_data_3d_info.spacegroup_number            1 
_volume_data_3d_info.spacegroup_cell_size[0]      798.72 
_volume_data_3d_info.spacegroup_cell_size[1]      798.72 
_volume_data_3d_info.spacegroup_cell_size[2]      798.72 
_volume_data_3d_info.spacegroup_cell_angles[0]    90 
_volume_data_3d_info.spacegroup_cell_angles[1]    90 
_volume_data_3d_info.spacegroup_cell_angles[2]    90

Values info

Contains mean, standard deviation, min, and max values for the entire (i.e. not just the slice present in response) original and the downsampled data. Both types of values are present so that relative iso-levels can be estimated when sampling changes between queries.

_volume_data_3d_info.mean_source                  0.026747 
_volume_data_3d_info.mean_sampled                 0.026748 
_volume_data_3d_info.sigma_source                 1.129252 
_volume_data_3d_info.sigma_sampled                0.344922 
_volume_data_3d_info.min_source                   -19.308199 
_volume_data_3d_info.min_sampled                  -2.692016 
_volume_data_3d_info.max_source                   26.264214 
_volume_data_3d_info.max_sampled                  3.533172

Values

The values are stored in the _volume_data_3d.values loop containg sample_count[0] * sample_count[1] * sample_count[2] values. axis_order[0] is the axis that changes the fastest, axis_order[2] is the axis that changes the slowest, same as in the CCP4 format).

loop_
_volume_data_3d.values
-0.075391 
-0.078252 
-0.078161 
...