Mask-focused refinement

Starting with the version 4.05.2 of Auto3DEM, it is possible to refine the orientation and the origin of the particles while focusing on a sub-volume of interest. This is advantageous, for example, when trying to determine the structure of an asymmetric feature in a icosahedral model. The approach implemented is to define a sub-volume by means of a binary mask, so that the reference map will only contain the region of interest. The volume excluded can then be interpreted as 'background' information, which needs to be subtracted from the experimental projections before comparing them with projections from the reference map.

For this purpose there is an additional parameter in the auto3dem configuration file

po2r mask_map  mask_filename

where to specify the filename of the binary mask around the feature of interest. The magic word 'none' will indicate that no mask is given. Auto3dem generates two reciprocal soft masks from this input and applies both of them to the reference map: the resulting maps are given as input to PO2R, which uses them accordingly. Currently the masking only work with local and ticos_equiv modes.

The binary mask is defined as a mask that has zero in the regions to ignore and any positive number in the region of interest. In order to get a mask with these range of values in pif format (mode 20, short int) one possible procedure is to load the map in Chimera, generate a surface around the region of interest and then use the mask command. The conversion to .pif format can be done either with mrc2pif or within the software package bsoft.

It is recommended, before using the binary map, to verify that it is compatible with Auto3DEM. One way to achieve this is to open it in Robem and verify that:

1. the program can open it successfully;
2. the voxels in the masked out regions are set to zero;
3. the voxels inside the region-of-interest are positive (any positive number is accepted).