changes can also be obtained by running the Analyze
pre-refinement results script.
3.5 Consensus
Refinement
After the pre-refinement is complete, the full refinement using the
extracted particles can take place. This refinement finally corrects
for the local distortions of the 2D crystals. As in the pre-refinement,
the FOCUS script Prepare refinement will generate the mparameters file and generate the proper file structure for the frealign2dx refinement. At this stage, the extracted particles will inherit the
pre-refined alignment parameters from their “parent” 2D crystals
(Subheading 3.4). This is done internally by the Python script
SPR_FrealignParameterInheritance. The extracted particles
Fig. 3 Single particle refinement from 2D crystals. Left: The initial reconstruction uses parameters from 2D
crystallographic data processing. Center: The map is then improved by doing a “pre-refinement” with frealign2dx using crystal averages. Right: Using particles (local patches) extracted from the 2D crystals starting with
parameters obtained in the pre-refinement, the map is refined to high resolution with frealign-2dx. Both the
height and the color of the cylinders (here shown for the asymmetric unit only) indicate the proportion of
particles or crystal averages in the corresponding orientation, relative to each dataset (red: high particle
density, blue: low particle density; a.u.). Maps shown are not sharpened. Scale bar: 50 A ˚
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