Begin forwarded message:
From: Jonathan Paul Remis <jpremis@berkeley.edu> Subject: opening cryoEM SPA maps using "volume" view mode Date: May 18, 2026 at 4:36:10 PM PDT To: chimerax-bugs@cgl.ucsf.edu
Hello wonderful people that build and maintain Chimera!
I have run into a bit of an odd observation which when compounded with some basic biochemistry has left me scratching my head. Essentially, when I open one of our SPA volumes in chimerax and choos "volume" in the volume viewer I am able to see a single bright spot in the volume. If I process our data with C2 symmetry we see two bright spots.
I had thought this was biologically relevant but I opened up a couple more structures from our lab and other labs and see this is pretty common. Please see the attached images and you can see ApoFerritin has 24 bright spots, and Aldolase has 4.
In the case of my sample - hemoglobin - the bright spot co-localizes with a iron element in the structure. I want to believe this has something to do with the density/scattering of the Fe but am at a loss for why we would not see 4 of them. Hemoglobin has 4 heme centers and 4 Fe atoms.
Thank you in advance for any suggestions or support you can provide.
Thanks, Remis


-- Jonathan Remis Scientific Engineer Müller Lab University of California, Berkeley
