Yes. I tried to weight those B values by occupancies, but the result is still not the same as the value reported by refmac5.
Qixu Cai Email: caiq...@gmail.com Eleanor Dodson <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> 于2023年11月6日周一 14:04写道： > Are there some atoms with occupancies < 1.0 ? > You would need to weight those Bs by occ > > On Sun, 5 Nov 2023 at 11:34, Ian Tickle <ianj...@gmail.com> wrote: > >> 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 >> > > ------------------------------ > > 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/
