Python-based
Hierarchical
ENvironment
for
Integrated
Xtallography
The routine show_map_info will show a summary of the data in a map file (ccp4/mrc/map).
A map file contains a box of data on a grid. This box of data may be the original box of data or it might be a smaller box cut out of the original box of data.
The map file also contains meta-data including a 'unit cell' and gridding for a unit cell. The unit cell usually corresponds to the full original box of data. The 'unit cell grid' is the grid corresponding to the unit cell. The unit cell has dimensions defined by 'unit cell parameters'.
The map that is present is represented on part or all of the unit cell grid. It starts at the grid point called the 'origin' and goes to one grid point in each direction before the grid point called 'last'. The map that is present has 'all' grid points in each direction. The map that is present has a 'map unit cell' and 'map grid' that correspond to the dimensions 'all'.
Example: a full map with a unit cell grid of (10, 10, 10) goes from (0, 0, 0) to (9, 9, 9) and has dimensions of (10, 10, 10).
Example: a partial map with a unit cell grid of (10,10,10) and an origin of (0, 0, 2) and a map grid or 'all' of (6, 6, 6), would go from (0, 0, 2) to (5, 5, 7).
A map file has a 'pixel size' in each direction (usually they are all the same). The pixel size is the dimension along x, y, or z divided by the number of grid points along that direction.
A map file has a 'map unit cell' which corresponds to the dimensions of the box of data that is present in the map. This will be the same as the unit cell of the full map if the entire map is present.
A map file can have an 'external_origin' defined. The external origin is an offset that is intended to be applied to a model file to superimpose the model on the map. If a map has an external origin defined, show_map_info will print out this value.
Phenix does not generally support the external_origin values. You can however shift a model file (PDB/mmCIF) based on a value of the external_origin with the tool phenix.shift_model_to_match_map
phenix.shift_model_to_match_map map_file.mrc model_file.pdb
Maps can be periodic (wrapping = True) or non-periodic (wrapping = False). If you cut out a box from a periodic map, the new map is non-periodic.
If a map is periodic, then values at coordinates (x,y,z) outside the map are defined and can be obtained simply by translating (x,y,z) by integral numbers of the unit cell translations a,b,c (N * a, M * b, O * c) where N,M and O are integers. If a map is not periodic, values outside the supplied map are not defined.
In most Phenix methods, it is assumed that cryo-EM maps are non-periodic and X-ray (crystal) maps are periodic. You can specify in many cases whether your map is periodic or not, however, using the 'wrapping' keyword.
When you run show_map_info it will tell you whether the map supports wrapping.
You can use show_map_info to summarize a map file like this:
phenix.show_map_info my_map_file.mrc
You can get the value of the map at a particular grid point with:
phenix.show_map_info my_map_file.mrc grid_point_to_show=6,2,5
The MRC (ccp4/mrc/map) file format is defined at MRC/CCP4 file format for images and volumes