Thanks for your reply. Does the refmac5 program weight the mean B value by the resolution?
Qixu Cai Email: caiq...@gmail.com Ian Tickle <ianj...@gmail.com> 于2023年11月5日周日 19:34写道： > 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/
