The arithmetic mean B value from the structure as quoted everywhere is pretty meaningless anyway and 10 Ang.^2 either way is probably not significant. Let's say some waters or LYS side-chains or whatever have B = 1000 Ang.^2. That will bias the mean B upwards, but those atoms do not contribute significantly to the total scattering except at very low resolution and might as well not be there, so they should not be included in the mean. A better method would be to weight the mean by the scattering power at the resolution limit. That should more closely match the B value from the Wilson plot.
Cheers Ian On Sun, 5 Nov 2023, 10:45 Qixu Cai, <caiq...@gmail.com> wrote: > Dear all, > > I found that the "Mean B value (OVERALL, A**2)" reported by refmac5 in the > head region of pdb file is 62.76. However, I calculated the average B value > of all B factors from all atoms and the result is 67.7. What makes the > difference? The canonical restrained refinement mode was used in refmac5. > When we prepare the Table 1 of manuscript, which one is correct for the > "average B value"? > > Thanks and best regards, > Qixu Cai > Email: caiq...@gmail.com > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
