I extracted my particles by scale them down to a factor of 0.5. I built a initial model with these particles, which looks fine. For the 3d refinement i extracted the particles again with no downscaling.
When i start the refinement, i always get this error:
Warning the reference pixelsize is 2.127 A but the smallest pixelsize in the data is 1.0635
I always end up at a resolution of 4.6 A and can not get any further.
Do you have any suggestions how i can overcome this issue?
It complains that the pixel size of the reference map is not the same as that of the particles. How about generating an ab initio reference map using the unbinned particles? Or perhaps you can upsample your reference map using the volume tools?
Which type of refinement did you run, and did you connect only the unbinned particles, or both the unbinned and binned?
The reference being on a different pixel size is a warning but is actually fully supported in most job types - the reference is automatically scaled.