Hi, from “just an update,” I suspect there was an original message that I haven’t seen (not in spam either). From what I read below: - “very low values” for B need to be defined; - refined B around zero likely means you refined against a sharpened map and can’t be “fixed” unless you use the original (unsharpened) map; - changing the context of a file with a refined model generally invalidates the statistics and is not advisable; - ADP, or B factors, have a well-defined physical meaning, and that is what the corresponding column in your model file is reserved for. Setting it to something else sounds nonsensical to me, unless you want to use it to color your model by whatever values you place there and then throw the model away; - since in cryo-EM there is nothing like Rfree in MX, you need to manage overfitting (which is much less of a problem in cryo-EM than in MX) by watching CCmask and overall geometry metrics. Sometimes decreasing CCmask can mean “lowering Rfree,” essentially, which is not a bad thing of that happens at the cost of geometry improvement. I can provide more diagnostics if you send the model and map. Good luck! Pavel On 3/4/26 07:35, [email protected] wrote:
OK, just an update:
My cheating did not work. Even after I changed the chain name to get everything as chain A, and set up the ADPs of the light chain to 140, they went back to very low values, making the CC_mask go worse (although still > 0.7). I also tried increasing the number of iterations to 600, no success. I'm considering placing Q-scores in the ADP column, as I believe that would be more realistic. Any strong opinions about that? _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s