I am experiencing a shift in my map after local refinement. It is present on the first iteration of the local refinement. It is around the width of a helix, which makes it inconvenient for model building with multiple maps. Is there some sort of realignment which happens during this refinement process and is anyone else experiencing this problem?
What are the parameters you are using? Specifically, what are the fulcrum positions and the local shift extent?
@ali.h Thanks a lot for the reply.
The fulcrum position is slightly off centre but no more than 5 pixels in any direction.
The shift extent is 3 pixels and the rotational search is 4 degrees and 0.2 degree resolution.
The movement appears to be a simple translation rather than any sort of transformation.
Could you repeat the job with the fulcrum positions blank and let us know if you still see the movement? I haven’t seen something like this before, so I’m not quite sure what may have caused it but we are looking into it.
A correction: the local refinement job outputs a shifted version of the volume such that the fulcrum is now at the center of the box. To re-align the output of the local refinement to the original volume, you can shift it back in Chimera by the difference between the fulcrum point and the center of the volume, which is at (box size)/2 + 1.