I’ve got a few NURefine volumes from CryoSparc that I’d like to open in Coot. Ideally directly, without altering in any way, or having to assign a PDB model to this – as I’d like to quickly be able to compare many iterations of the map. However, File–>Open Map in Coot seems unresponsive - the map ‘opens’, and map histogram is not all zero, but I cannot see the map at all no matter how much zooming/altering of map parameters I do. Can someone please tell me what I am doing wrong?
The “interesting” part of the map is likely outside the map display radius given the current cursor position. You can change it in the map options, the default should be 55Å for cryo-EM maps, try a larger number at least to find the middle of the map. You could also reduce the contour threshold a lot and then just translate around and see if you see it.
IMO for this use case ChimeraX will be far more convenient. You can also look at maps in cryoSPARC on the Volumes tab of a job.
Thanks so much for your response. You were right - the map was just way out of my range. Eventually, utilizing the ‘Go to map molecule middle’ tool in the CryoEM tab was the best solution - even zooming/increasing radius gave no assistance.