Hi Kay, Can you also comment on Rfree set selection? It seems thin shell might be preferred in these cases?
jbb Jeffrey B. Bonanno, Ph.D. Department of Biochemistry Albert Einstein College of Medicine 1300 Morris Park Avenue Bronx, NY 10461 off. 718-430-2452 fax. 718-430-8565 email jeffrey.bona...@einsteinmed.org -----Original Message----- From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Kay Diederichs Sent: Friday, August 27, 2021 9:16 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis? CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the "Phish Alert" button on the top right of the Outlook dashboard to report any suspicious emails. Dear Herman, there is no freedom to choose between twinned-P32 (5 chains) and untwinned-P3221 (2 chains plus 0.5 chain in two orientations) or even vote; it is either one or the other, and there should be a difference in R values. Why? A twin operator leads to addition of intensities whereas a spacegroup operator leads to addition of (complex) structure factors. They are not exchangeable. Both produce symmetry, but the math is different, and thus the resulting intensities are different. The correct spacegroup can only be found by trying all possibilities, and comparing R values. However, for a meaningful comparison of R values, one has to restrain the NCS (and one cannot strictly compare twinned refinement results with untwinned refinement, as noted earlier). best wishes, Kay On Fri, 27 Aug 2021 08:56:38 +0000, Schreuder, Herman /DE <herman.schreu...@sanofi.com> wrote: >Dear Peer and Eleanor, > >This is indeed what I am suspecting: If the "twinning operator" in P32 puts 4 >out of 5 protein chains on top of symmetry mates, is the "true" space group >then P32, with 5 twinned chains, or P3221 with 4 normal chains and 1 chain on >a special position? I would vote for the latter. > >Best, >Herman > >Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Peer >Mittl >Gesendet: Freitag, 27. August 2021 10:17 >An: CCP4BB@JISCMAIL.AC.UK >Betreff: Re: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis? > >Dear Eleanor, > >I indeed used r/tefmac for the refinement and it came up with the >values HKL (a=0.56), KH-L (a=0.44). It would be interesting to see if a >refinement in P3221 would come up with the same occupancies for the >alternative conformations for the "extra" chain on the 2-fold axis. It >seems as if the "well-ordered" chains (2 in P3221, 4 in P32) form a >sublattice with P3221 symmetry and it's just the "extra" chain, which >generates the twinning. > >All the best, >Peer > >On 26.08.2021 18:09, Eleanor Dodson wrote: >> Motto =mitti in predictive text! >> >> On Thu, 26 Aug 2021 at 16:52, Eleanor Dodson >> <eleanor.dod...@york.ac.uk >> <mailto:eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk%20%3cmailto:eleanor.dod...@york.ac.uk>>> >> wrote: >> >> Great, motto. I think you have nailed it! Did you use tefmac for >> twinned refinement? And if so what did it suggest the twin fraction >> is? >> >> On Thu, 26 Aug 2021 at 16:30, Peer Mittl <mi...@bioc.uzh.ch ><mailto:mi...@bioc.uzh.ch%0b>> <mailto:mi...@bioc.uzh.ch>> wrote: >> >> Yes, the data indeed seems to be twinned and the tNCS has masked the >> twinning statistics, which is why I haven't considered it so far. >> >> I have not tried twinned refinement in C2 and P1 yet, but refining 4 >> chains in P32 with twinning yields a difference ED map that clearly >> indicates one (and just on!) orientation for the 5th chain. Thank you >> all for your suggestions. >> >> Have a nice evening, >> Peer >> >> -----"CCP4 bulletin board" <CCP4BB@JISCMAIL.AC.UK ><mailto:CCP4BB@JISCMAIL.AC.UK%0b>> <mailto:CCP4BB@JISCMAIL.AC.UK>> >schrieb: ----- >> An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> >> <mailto:CCP4BB@JISCMAIL.AC.UK> >> Von: "Kay Diederichs" >> Gesendet von: "CCP4 bulletin board" >> Datum: 26.08.2021 16:41 >> Betreff: Re: [ccp4bb] chain on 2-fold axis? >> >> Dear Peer, >> >> I suspect that the true spacegroup has lower symmetry than P3221, and >> that there may be twinning masked by tNCS. >> Subgroups of P3221 are C2 and P32 ( >> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstr >> ucbio.biologie.unikonstanz.de%2Fxdswiki%2Findex.php%2FSpace_group_det >> ermination%23Subgroup_and_supergroup_relations_of_these_space_groups& >> amp;data=04%7C01%7Cjeffrey.bonanno%40EINSTEINMED.ORG%7C8cb9aec600e747 >> dd037808d9695cd888%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C63765 >> 6671517394475%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2l >> uMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=%2BaoWmkX1WjT3oD >> RZX6829YT47e%2BjVFSBb%2BXQ8X4lsjs%3D&reserved=0<https://nam04.saf >> elinks.protection.outlook.com/?url=https%3A%2F%2Fstrucbio.biologie.un >> ikonstanz.de%2Fxdswiki%2Findex.php%2FSpace_group_determination%23Subg >> roup_and_supergroup_relations_of_these_space_groups&data=04%7C01% >> 7Cjeffrey.bonanno%40EINSTEINMED.ORG%7C8cb9aec600e747dd037808d9695cd88 >> 8%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637656671517394475%7CU >> nknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1h >> aWwiLCJXVCI6Mn0%3D%7C1000&sdata=%2BaoWmkX1WjT3oDRZX6829YT47e%2BjV >> FSBb%2BXQ8X4lsjs%3D&reserved=0> >> <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fst >> rucbio.biologie.unikonstanz.de%2Fxdswiki%2Findex.php%2FSpace_group_de >> termination%23Subgroup_and_supergroup_relations_of_these_space_groups >> &data=04%7C01%7Cjeffrey.bonanno%40EINSTEINMED.ORG%7C8cb9aec600e74 >> 7dd037808d9695cd888%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C6376 >> 56671517404430%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2 >> luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=qe1uZNNLabPbmAf >> VdBs7bpp1RH98AIz1X%2BY05p4eShc%3D&reserved=0<https://nam04.safeli >> nks.protection.outlook.com/?url=https%3A%2F%2Fstrucbio.biologie.uniko >> nstanz.de%2Fxdswiki%2Findex.php%2FSpace_group_determination%23Subgrou >> p_and_supergroup_relations_of_these_space_groups&data=04%7C01%7Cj >> effrey.bonanno%40EINSTEINMED.ORG%7C8cb9aec600e747dd037808d9695cd888%7 >> C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637656671517404430%7CUnkn >> own%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWw >> iLCJXVCI6Mn0%3D%7C1000&sdata=qe1uZNNLabPbmAfVdBs7bpp1RH98AIz1X%2B >> Y05p4eShc%3D&reserved=0>> >> ) >> and of course P1. >> What I'd do is process the data, and solve (use the best chain of the >> refined P3221 model for MR) and refine the structure in these >> spacegroups. >> Inspect the results: If P1 is clearly better than P32 and C2, >> P1 is correct. >> If C2 (P32) is clearly better than P32 (C2), then P1 should give the >> same R-values as the better one; if so, P1 can be discarded. >> Try this with and without twin refinement - although it's hard to >> compare R-values of non-twinned and twinned refinements. >> >> The automatic way to do this is with Zanuda. If you run that locally, >> you can make refmac do twin refinement. >> >> For all resulting structures, I'd also feed the resulting Fcalc (!) >> into pointless. That should reveal that the packing is indeed close >> to P3221. >> >> Best wishes, >> Kay >> >> >> On Thu, 26 Aug 2021 11:54:06 +0200, Peer Mittl <mi...@bioc.uzh.ch >> <mailto:mi...@bioc.uzh.ch<mailto:mi...@bioc.uzh.ch%20%3cmailto:mi...@bioc.uzh.ch>>> >> wrote: >> >> >Der CCP4 community, >> > >> >Is there a refinement program that can handle protein >> monomers sitting >> >on crystallographic 2-folds? >> > >> >This is probably a strange question but we have the following >> situation. >> >We have a 2.6 Ang datasets in SG P3221 (Rpim=4%, Isa=19.6) >> and a clear >> >molrep solution with 2 chains, albeit with tNCS (0/0/0.5) >> that can be >> >refined to around 27/33% Rfactor. According to Vm a third >> chain could be >> >present. So far so good, but there is clear difference ED for >> a third >> >chain sitting exactly on the 2-fold. Since the protein has a >> peculiar >> >shape, one can tell even its orientation. I can relax the >> symmetry to >> >P32 (or even P1) and place the missing chain with 50% >> occupancy on the >> >2-fold. This model can be refined, but I do not like this >> work around, >> >because the data is clearly P3221. >> > >> >Any hints on similar crystal pathologies and how they have >> been handled >> >would be helpful. >> > >> >All the best, >> >Peer >> > >> >#################################################################### >> >#### >> > >> >To unsubscribe from the CCP4BB list, click the following link: >> >https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fww >> >w.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&a >> >mp;data=04%7C01%7Cjeffrey.bonanno%40EINSTEINMED.ORG%7C8cb9aec600e747 >> >dd037808d9695cd888%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C6376 >> >56671517404430%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV >> >2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=lM0fyxzsJhnTz >> >CUDEvp78iLoAgj%2FIrFIgaWpT4zGFhU%3D&reserved=0<https://nam04.saf >> >elinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk% >> 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