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--- auto3dem:documentation:protocols:focused_refinement [2015/12/22 17:07]
gcardone created
+++ auto3dem:documentation:protocols:focused_refinement [2015/12/22 17:49] (current)
gcardone
@@ Line 1: / Line 1: @@
 ====== 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.
-Starting with the version 4.05.2 of Auto3DEM, it is possible to follow
+===== How to activate the focused refinement =====
-It is controlled by the parameter
-po2r mask_map  mask_filename
+For this purpose there is an additional parameter in the auto3dem configuration file
-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)
+  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.
-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:
+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:
   - the program can open it successfully;
   - the voxels in the masked out regions are set to zero;