Motto =mitti in predictive text! On Thu, 26 Aug 2021 at 16:52, Eleanor Dodson <[email protected]> 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 <[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/
