[phenixbb] Re: Zero B-factors

Dear Guillaume, Martin, Pavel and Wladek, Many thanks for your replies. I used the averaged half maps and the B-factors are now OK suggesting over-sharpening of the deposited PDB map as you wrote. This can really be of help to others. Best, Pascal

Le 16 oct. 2025 à 10:20, Guillaume Gaullier a écrit :

Hi Pascal,

How exactly did you change the atomic B-factors in the model? If you re-refined the model against the map, it is possible that the map was over-sharpened in some regions (if the local resolution is heterogeneous across the map, then sharpening with a single global sharpening B-factor will be sub-optimal at some locations and might well cause under- or over-sharpening at places). Over-sharpening artificially drives the refined atomic B-factors to lower values (and they can in fact reach 0 in extreme cases). So, if this is how you did it, I suggest repeating it as follows: download the two half-maps from EMDB, average them to obtain the un-sharpened full map (ChimeraX can do that), then repeat the model refinement against this raw map.

The EMDB doesn't specify what the "main map" (the one you get by default when fetching an EMDB entry) should be: in some entries it is a sharpened map, in others it is a raw map. It is not always clearly documented in the entry's annotation, or even in the article describing the structure. This is unfortunate. But at least, deposition of raw half-maps is mandatory, so one can always generate a full raw map from them.

I hope this helps,

Guillaume From: [email protected] Sent: Thursday, October 16, 2025 9:29:53 AM To: [email protected] Subject: [phenixbb] Zero B-factors

Hi,

I have a large structure for which I just want to update B-factors. Unfortunately, I get zero values for some B-factors.

Basically, I modified coordinates of a PDB deposited file and used the deposited cry-EM map. Is there something in the header (present or missing) that could influence the outcome of such a calculation ?

Thanks,

Pascal _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

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