Hi,
In Class3D and Refine3D, you can declare in the GUI that the reference is not in the
correct grey scale. This instructs the program to perform the first iteration with
normalized correlation coefficients, which are insensitive to the grey scale,
instead of squared differences.
That being said, I myself don't use a map from atomic model for anything in RELION.
Not for autopicking, not as an initial model, not as a reference.
If a dataset is good enough to reach a reasonable resolution, picking and initial model generation
should be trivial.
Best regards,
Takanori Nakane
On 2020/09/18 22:22, Karl Herbine wrote:
> Thanks everyone for your thoughtful replies and suggestions. I will most likely continue with using 2D classes generated by LoG autopicking as a reference for a finer particle picking job.
>
> If it is generally not recommended to use a PDB reference for autopicking, what IS the PDB reference used for? I was originally going to use it as a replacement for an ab initio initial model but I guess it can also be used for 3D refinement and 3D class references, although there is still the grey-scale problem. Any thoughts on how to get the most (preferentially unbiased) use of the PDB structure?
>
> Best,
> Karl
>
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