[ccp4bb] Mean B value in refmac5
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 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/
Re: [ccp4bb] Mean B value in refmac5
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, 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/
Re: [ccp4bb] About model building
Dear all Thanks for all the input. I will definitely try out in the coming couple of days. To provide more information: - the data was checked in Xtriage and no major pathology was found. Completeness was 99.2% with multiplicity of >13. Mean I/sigma(I) 18.8, CC1/2 for outer shell 0.902. - After one round of refinement, the R-factor was around 0.5, which looked reasonable given the incorrect B-chain was not removed and sequence deviations in chain A not yet rectified. - While I said Arp/warp failed to rebuild the model, it did return 3 helices in chain A and one in chain B when I ran in the QuickFold mode (secondary structure tracing) later on. So I am going to start with the helix in chain B and see how further manual rebuild goes. Thanks again and I shall send an update for any progress. Kind regards Sam On Sun, 5 Nov 2023 at 06:26, Firdous Tarique wrote: > Do the mass spec of your crystal to identify the other protein. Once done > solve your structure and build the complete model. This should be straight > forward and quick. > > Best Wishes > > On Sat, 4 Nov 2023, 09:05 Sam Tang, wrote: > >> Dear community, >> >> I am solving the structure of a complex between proteins A and B, where A >> is a protein with known homologs and B is a novel protein isolated from >> plant. The diffraction data was at 1.9 Ang collected in-house, indexed to >> P321. Using A as the search model, we have got a reasonable solution where, >> after one round of refinement, the A chain fits the map pretty well. What's >> left was to extend the termini and fit a few rotamers. >> >> For protein B (B chain) I have tried the web version of ARP/wARP but the >> outcome was not really good. The model was not successfully built as >> indicated by low model completeness and score. The tricky thing may be that >> we do not have the complete sequence information of this protein B in-hand. >> (The other way round, we more or less wish to rely on the high resolution >> data to confirm its sequence.) What approach would you then recommend to >> build the B chain in this scenario? >> >> Thanks in advance and best regards, >> >> Sam >> >> -- >> >> 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/
Re: [ccp4bb] About model building
Hmmm - r 50% rather suspect.. do the MR solutions from phaser and molten agree? Eleanor On Mon, 6 Nov 2023 at 05:10, Sam Tang wrote: > Dear all > > Thanks for all the input. I will definitely try out in the coming couple > of days. To provide more information: > - the data was checked in Xtriage and no major pathology was found. > Completeness was 99.2% with multiplicity of >13. Mean I/sigma(I) 18.8, > CC1/2 for outer shell 0.902. > - After one round of refinement, the R-factor was around 0.5, which looked > reasonable given the incorrect B-chain was not removed and sequence > deviations in chain A not yet rectified. > - While I said Arp/warp failed to rebuild the model, it did return 3 > helices in chain A and one in chain B when I ran in the QuickFold mode > (secondary structure tracing) later on. So I am going to start with the > helix in chain B and see how further manual rebuild goes. > > Thanks again and I shall send an update for any progress. > > Kind regards > > Sam > > > On Sun, 5 Nov 2023 at 06:26, Firdous Tarique > wrote: > >> Do the mass spec of your crystal to identify the other protein. Once done >> solve your structure and build the complete model. This should be straight >> forward and quick. >> >> Best Wishes >> >> On Sat, 4 Nov 2023, 09:05 Sam Tang, wrote: >> >>> Dear community, >>> >>> I am solving the structure of a complex between proteins A and B, where >>> A is a protein with known homologs and B is a novel protein isolated from >>> plant. The diffraction data was at 1.9 Ang collected in-house, indexed to >>> P321. Using A as the search model, we have got a reasonable solution where, >>> after one round of refinement, the A chain fits the map pretty well. What's >>> left was to extend the termini and fit a few rotamers. >>> >>> For protein B (B chain) I have tried the web version of ARP/wARP but the >>> outcome was not really good. The model was not successfully built as >>> indicated by low model completeness and score. The tricky thing may be that >>> we do not have the complete sequence information of this protein B in-hand. >>> (The other way round, we more or less wish to rely on the high resolution >>> data to confirm its sequence.) What approach would you then recommend to >>> build the B chain in this scenario? >>> >>> Thanks in advance and best regards, >>> >>> Sam >>> >>> -- >>> >>> 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/
Re: [ccp4bb] Mean B value in refmac5
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 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, 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 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/
