Hi,
Did you specify (more-or-less) the same size
to "diameter background circle (px)" in Extract and
"Mask diameter" in Class3D/Refine3D?
Note that the former is in pixel of the motion corrected
images, while the latter is in angstrom.
Best regards,
Takanori Nakane
On 2020/09/02 20:29, Xian, Yuejiao wrote:
> Hello, all,
>
> I am using relion3.1 for my dataset. After extracting the particles in Relion with " Normalize particles?" set to "Yes", I would still get the
> following warning saying the image is not normalized in the downstream processes. I have the following questions:
>
> 1. How to check if the images are normalized properly?
> 2. I wonder if it has something to with having very few particles in each micrograph? I am processing a large particle, there is usually one particle
> per micrograph. If this will lead to issue with the normalizing the particle, what would be the right way to normalize the particles?
> 3. Following this warning, I would get the error of " zero sum of weight" in 2D and 3D classification, I wonder if it has something to do with the
> normalization?
>
> Please advise. Thank you.
>
> The error message:
> ----------------------------------------------------------------
> *
>
> fn_img= [log in to unmask] bg_avg= 0.567277 bg_stddev= 1.06925
> bg_radius= 179.104
>
> WARNING: It appears that these images have not been normalised to an average background value of 0 and a stddev value of 1.
>
> Note that the average and stddev values for the background are calculated:
>
> (1) for single particles: outside a circle with the particle diameter
>
> (2) for helical segments: outside a cylinder (tube) with the helical tube diameter
>
> You can use the relion_preprocess program to normalise your images
>
> If you are sure you have normalised the images correctly (also see the RELION Wiki), you can switch off this warning message using the
> --dont_check_norm command line option
>
> *----------------------------------------------------------------
>
> Best,
> Yuejiao Xian
> Ph.D candidate,
> University of Texas at El Paso
>
>
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