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Mask-focused refinement

Starting with the version 4.05.2 of Auto3DEM, it is possible to follow It is controlled by the parameter po2r mask_map mask_filename which specify the filename of the binary mask around the feature of interest. The magic word none will indicate that no mask is given. Auto3dem will generate two reciprocal soft masks from this input and will apply to the reference map: the resulting maps will be given as input to PO2R. Currently the masking only work for the local and ticos_equiv modes in po2r (I'm thinking if it makes sense to extend to global mode)

Mask-guided refinement It is controlled by the parameter po2r mask_map mask_filename which specifies the filename of the binary mask around the feature of interest. The magic word none will indicate that no mask is given. Auto3dem will generate two reciprocal soft masks from this input and will apply them to the reference map: the resulting maps will be given as input to PO2R. Currently the masking only works for the local and ticos_equiv modes in po2r (does it make sense to extend to global mode?). I made a test on a capsid with tail, and I can definitely see some improvement. I envision some small adjustment, but the bulk of the method is there. The binary mask is defined as a mask that has zero in the regions to delete 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) I use the mask command in Chimera plus some pre/post-processing with bsoft. With the additions of the program a3dm_icosrotate and the procedure for mask-guide refinement, now the reconstruction of asymmetric features in icosahedral capsids should be more robust and flexible.

Generation of a binary mask

Always verify that the binary mask created is recognized in the 'auto3dem' world. Usually I 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).