P1 is always a "correct" answer but this data says there is a three fold axis. Twinning generates an apparent 2 fold in the diffraction pattern, and with four of the five molecules obeying that 2fold, and twin factors 0.56/0.44 that will appear pretty exact..
And the NC transl;ation disguises the twin analyses.. So it isnt as weird as Mitti first thought .. Eleanor (I have seen this behavior before - we processed data as I422 then realised about 15% of the residues could not obey the 4 fold axis, and we had to back off to I222...) On Fri, 27 Aug 2021 at 12:56, Oganesyan, Vaheh < vaheh.oganes...@astrazeneca.com> wrote: > How P3221 can be an option if it assumes chain on axis? I guess I’m > missing something, but per my belief only those sg will be possible for > which there is no axis going through the extra molecule. P1 sg looks the > only correct option here in my humble opinion. > > Democracy (voting) depends on science. However, the reverse is not, > thankfully. > > > > Vaheh > > > > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> * On Behalf Of *Peer > Mittl > *Sent:* Friday, August 27, 2021 6:32 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on > 2-fold axis? > > > > Dear Herman, > > The answer probably depends on the impact of the "extra" chain on the > sublattice. If there is no impact the "true" space group is P3221 with > one chain on the special position. If the swapping of the extra chain > influences the sublattice P32 (or C2 or P1, as pointed out by Kay) > twinned to P3221 might be the better description. > > All the best, > Peer > > On 27.08.2021 10:56, Schreuder, Herman /DE 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 > <eleanor.dod...@york.ac.uk%20%3cmailto:eleanor.dod...@york.ac.uk%20%0b>> < > mailto:eleanor.dod...@york.ac.uk%20%3cmailto:eleanor.dod...@york.ac.uk > <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 > <mi...@bioc.uzh.ch%0b>> <mailto:mi...@bioc.uzh.ch%0b > <mi...@bioc.uzh.ch%0b>>> <mailto:mi...@bioc.uzh.ch > <mi...@bioc.uzh.ch%20%0b>> <mailto:mi...@bioc.uzh.ch <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 > <CCP4BB@JISCMAIL.AC.UK%0b>> <mailto:CCP4BB@JISCMAIL.AC.UK%0b > <CCP4BB@JISCMAIL.AC.UK%0b>>> <mailto:CCP4BB@JISCMAIL.AC.UK > <CCP4BB@JISCMAIL.AC.UK%20%0b>> <mailto:CCP4BB@JISCMAIL.AC.UK > <CCP4BB@JISCMAIL.AC.UK>>>> schrieb: ----- > > > An: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK > <CCP4BB@JISCMAIL.AC.UK>> > > <mailto:CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK > <CCP4BB@JISCMAIL.AC.UK%20%3cmailto: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://strucbio.biologie.unikonstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups > > < > https://strucbio.biologie.unikonstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups > > > > > > > < > https://strucbio.biologie.unikonstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups > > < > https://strucbio.biologie.unikonstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups > >> > > > ) > > > 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 > <mi...@bioc.uzh.ch%20%3cmailto:mi...@bioc.uzh.ch%20%0b>> < > mailto:mi...@bioc.uzh.ch%20%3cmailto:mi...@bioc.uzh.ch > <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://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> > > > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > <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 <http://www.jiscmail.ac.uk/CCP4BB> > > <http://www.jiscmail.ac.uk/CCP4BB <http://www.jiscmail.ac.uk/CCP4BB>>, > > > a mailing list hosted by www.jiscmail.ac.uk <http://www.jiscmail.ac.uk > 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<http://www.jiscmail.ac.uk/CCP4BB>>, > > > a mailing list hosted by www.jiscmail.ac.uk <http://www.jiscmail.ac.uk > > > > > <http://www.jiscmail.ac.uk <http://www.jiscmail.ac.uk>>, terms & > > conditions are available > > > at https://www.jiscmail.ac.uk/policyandsecurity/ > > <https://www.jiscmail.ac.uk/policyandsecurity/> > > > <https://www.jiscmail.ac.uk/policyandsecurity/ > > <https://www.jiscmail.ac.uk/policyandsecurity/>> > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> > > > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>> > > > > > -- > > **************************** > > Peer Mittl, PD Dr. > > Biochemisches Institut > > Universität 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