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 VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

Dear Pascal, Did you use the deposited half maps for B-value refinement? Unwanted effects, including unrealistically low B-values, can happen when a postprocessed or sharpened map is used. Cheers, Martin On 16/10/2025 08:29, [email protected] wrote:

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