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 <[email protected]> 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" <[email protected]> schrieb: ----- > An: [email protected] > 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 > ) > 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 <[email protected]> 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 > > > >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/ > > ######################################################################## > > 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/ > > ######################################################################## > > 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/ > ######################################################################## 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/
