How to show AlphaFold error estimates with ChimeraX 

if you are multimer the file should be "scores_rank_001_alphafold2_multimer_v3_model_4_seed_000.json"

The error plot was added April 2022 and is in the ChimeraX daily builds. It is not in ChimeraX 1.3 which is from November 2021.

AlphaFold uses OpenMM for energy minimization with the Amber force field. If the predicted structure has bad clashes minimization will often fail as you have observed. In the ChimeraX daily build the AlphaFold panel has an Options button "Energy minimize predicted structures". Turn that off and rerun your prediction. I thought I made ChimeraX give you the unminimized structure if minimization fails but I'll have to check. If I haven't done that I'll try to update the code so at least you get the unminimized structure. With bad clashes there is no simple way to minimize. You might be able to fix the problems by hand moving residues and then minimizing.

I looked at the ChimeraX AlphaFold Google Colab code and it does not handle OpenMM minimization failures. So I've made a request to improve it so it provides the unminimized structure instead of just failing. www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6945

@@ucsfchimerax8387 Thank you so much for the fast and very complete answer. The version of Chimera X I currently own on my computer has no "Options" button on the AlphaFold panel, but I will install the most recent daily build. The request you made is fantastic and if I could make a suggestion, I think it would be great if Chimera X could provide the 5 unminimized structures, not only when the minimization step fails, but also when the Google Colab server runtime is terminated in that particular step. It is frustrating knowing you were so close of getting the final product, to just end up with nothing when the unminimized models are right there.

Nevertheless, and in order to confirm that this error is dependent on the predicted structure, I tried to predict the structure of a 70 amino acid protein whose model has been calculated several times through AlphaFold in classes by many students, and the error still pops up: ValueError Traceback (most recent call last) in () 692 seq_list = seq_list[1:] 693 --> 694 run_prediction(seq_list, energy_minimize = not dont_minimize) 5 frames /usr/local/lib/python3.7/dist-packages/alphafold/relax/amber_minimize.py in _run_one_iteration(pdb_string, max_iterations, tolerance, stiffness, restraint_set, max_attempts, use_gpu, exclude_residues) 417 logging.info(e) 418 if not minimized: --> 419 raise ValueError(f"Minimization failed after {max_attempts} attempts.") 420 ret["opt_time"] = time.time() - start 421 ret["min_attempts"] = attempts ValueError: Minimization failed after 100 attempts.

@@tomasfernandes7944 Yes a fixed version would give you all 5 unminimized structures. The ChimeraX AlphaFold Colab script only tries to minimize the best scoring structure of the 5 and by the time it tries that minimization it already has 5 unminimized structures computed.