Hi @saif,
If you use the Chimera command getcrd sel when you have selected a coordinate using the Volume Tracer tool, then you should divide the returned coordinate values by the pixel size of the volume, rather than the raw movies. Note that if you have done any downsampling during extraction or otherwise, the pixel size will not be this value. To find the pixel size of the volume (if it is open in Chimera), click on “Features > Coordinates” in the Volume Viewer. This will show the pixel size under the “Voxel Size” entry.
Regarding the out of memory error – this may happen when the box size is especially large, but shouldn’t be related to the fulcrum chosen. If the memory error persists after re-running the job with no other concurrent processes using up GPU memory, could you create a new post and include the full traceback that was raised, and indicate as well the box size of the refinement?
Best,
Michael