Inverted densities
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Frealign is running nicely in Appion, with one exception. The densities of the resulting volumes and class averages are flipped. A quick fix is to flip it back after each iteration. However I am concerned that this is a symptom for something being messed up within the code and that Frealign might not run correctly. At this point we can't tell if this is an Appion issue, or if that is something Frealign does. That's why I want to ask, if you have an idea and/or if that happened to you before?
We actually want to release Appion as soon as possible (with Frealign included) but are hesitant as we need this bug to be fixed beforehand.
Currently we are using Frealign version 8.08.
I am not sure I fully
I am not sure I fully understand your question. Frealign does not work with class averages. But there is a contrast flip between input particle images and output 3D density: On input, Frealign expects dark protein density on light background and on output it will produce light protein density on dark background. The reason is the CTF correction. Remember that the CTF goes negative at low resolution. Therefore the flip in the contrast after CTF correction.