Dear Chimera team,
We are currently aligning our in‑house cryo‑EM structure validation with community standards and encountered an issue with reproducing Q‑scores:
The wwPDB references the original Chimera/MapQ implementation, but as Chimera is being phased out in favor of ChimeraX, we can no longer reproduce the original Q‑scores in ChimeraX.
We have already evaluated available alternatives:
ChimeraX Q‑score plugin: We observe systematic differences between Q‑scores from ChimeraX and values in wwPDB/EMDB reports. The plugin author (Tristan Croll) indicated that differences likely stem from sampling not matching the original implementation and possibly slightly different averaging. The tool has also not been actively maintained for some time.
Python implementations (e.g., jamaliki/qscore and an internal prototype): These likewise yield different Q‑scores on the same model–map pairs, likely for similar reasons.
Given this, we would appreciate your guidance on two points:
- Are there plans to migrate the original Chimera/MapQ Q‑score implementation into ChimeraX?
- If not (or not soon), would it be possible to obtain free or reduced‑cost access to Chimera solely for the purpose of Q‑score calculations? We are otherwise fully using ChimeraX in our workflow.
Thank you very much for your feedback.
Best regards,
Oliver Schanz