Dear all,
I’m trying to do a local refinement and for this, I have used Chimera to segment my map, selected regions and saved them as mrc file. When trying to import this map into CS, I get the following error:
Does anyone have any hints as to what is happening? Is there an issue with me segmenting the map? I have previously imported saved maps when using the chimera volume eraser for local refinement which was absolutely fine. We are running CS v 2.15.0.
Thank you for any help you may be able to provide!
Cheers,
Claudia
Hej again,
my bad, I simply forgot to run the resample command in Chimera to have the segmented map saved on the same grid. Easy fix 
Cheers,
Claudia
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Hi @ClaudiaKielkopf,
Nice catch! I believe the error was thrown because cryoSPARC expects all imported volumes to be cubic (same shape along the x, y, and z axes), which explains why resampling onto the initial grid that the input volume was defined on would result in the output volume having the correct shape.
Best,
Michael
Hej Michael,
yeah, exactly, it makes total sense. Re-reading both the tutorial for local refinement (https://cryosparc.com/blog/local-refinement-snRNP-case-study) and the blog entry (https://cryosparc.com/blog/local-refinement) on this topic though, they do differ slightly in the instructions on how to create the mask. The tutorial actually doesn’t mention the resample command but then in there, they select the fulcrum.
Anyone with more experience can commend as to why that is?
Thank you,
Claudia
Hey Claudia,
Apologies for the delayed reply! In my experience, when just using the thresholding operations and the volume eraser tool (and not using the segmentation tool), vop resample is not necessary, as the map is already sampled on the same grid as originally. The tutorial only uses these operations, so it doesn’t mention the resample command. But, in the blog post, the segmentation tool and the “fit in map” tool are also mentioned as options to help create a mask. I believe both of these (well, certainly the segmentation tool) require the vop resample command in order to ensure that the volume retains the original grid upon export. (Fit in map actually rotates/translates the map, so resampling is probably needed).
Best,
Michael
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