ijk_step_for_voxel_limit (
        ijk_min,
        ijk_max,
        ijk_step,
        limit_voxel_count,
        mvoxel_limit,
        )

Return ijk step size so that voxels displayed is at or below the limit. The given ijk step size may be increased or decreased by powers of 2.

distance ( xyz1,  xyz2 )

open_volume_file (
        path,
        format=None,
        name=None,
        representation=None,
        open_models=None,
        model_id=None,
        show_data=None,
        show_dialog=None,
        )

Open and display a map.

show_one_plane (
        data_region,
        show_plane,
        min_voxels,
        )

Decide whether a data region is large enough that only a single z plane should be shown.

maximum_data_diagonal_length ( data )

full_region ( size,  ijk_step=None )

show_when_opened (
        data_region,
        show_on_open,
        max_voxels,
        )

Decide whether a data region is small enough to show when opened.

volume_from_grid_data (
        grid_data,
        representation=None,
        open_model=None,
        model_id=None,
        show_data=None,
        show_dialog=None,
        )

Open and display a map using Volume Viewer.

is_empty_region ( ijk_region )

resize_region_for_zone (
        data_region,
        points,
        radius,
        initial_resize=None,
        )

Adjust volume region to include a zone. If current volume region is much bigger than that needed for the zone, then shrink it. The purpose of this resizing is to keep the region small so that recontouring is fast, but not resize on every new zone radius. Resizing on every new zone radius requires recontouring and redisplaying the volume histogram which slows down zone radius updates.

clamp_region ( region,  size )

map_from_periodic_map (
        grid,
        ijk_min,
        ijk_max,
        )

subarray_size (
        ijk_min,
        ijk_max,
        step,
        )

map_covering_atoms (
        atoms,
        pad,
        volume,
        )

Use a periodic unit cell map to create a new map that covers a PDB model plus some padding. Written for Terry Lang.

region_volume ( ijk_min,  ijk_max )

limit_voxels (
        voxel_count,
        ijk_step,
        limit_voxel_count,
        mvoxel_limit,
        )

Return ijk step size so that voxels displayed is at or below the limit. The given ijk step size may be increased or decreased by powers of 2.

saturate_rgba ( rgba )

extend_region (
        ijk_min,
        ijk_max,
        factor,
        )

transformed_points ( points,  xform )

show_planes (
        dr,
        axis,
        plane,
        depth,
        extend_axes=None,
        show=None,
        save_in_region_queue=None,
        )

region_contains_region ( r1,  r2 )

Volume

Volume_Manager

Region_List

Remember visited subregions.

Rendering_Options

Outline_Box