Hi Everyone, Thank you for your helpful input.. Below is a summary of my findings so far.
In P1, P21, or P212121, translational pseudo-symmetry is not detected, as the max off-origin peak is only 3% of the origin. Pointless still suggests twinning with <[L]> of ~0.18 and <L^2> of ~0.17 after processing and scaling in P21 with different b edges: 105.6 71.7 200.9 71.7 105.6 201.0 71.1 200.9 105.6 For the P1 unit cell, there are faint but present reflections along (0,k,0) at k = n. There are clearly no absences along (h,0,0), but I do see strong absences along (0,0,l) at l = n. I've noticed that my geometry is not so great when performing twin refinement in Refmac5 with NCS (~90.8% Ramachandran favored, ~1.7% outliers). Adding a weighting term of 0.3 (no NCS) seems to improve these (~95.0% favored, ~0.7% outliers) at the cost of Rwork/Rfree (from 15.5%/18.3% to 18.6%/21.5%). The same treatment with NCS enabled counteracts the geometry improvements (~91.1% favored, ~1.6% outliers) and does not really affect Rwork/Rfree. Thanks, Chris On 7/12/14, Isupov, Michail <[email protected]> wrote: > Dear Chris, > > If you have pseudo-translation in your data close to (0,0,0.5), for > instance, > you will have origin ambiguity and, therefore, two P212121 space groups > differing by a choice of origin. When ZANUDA reports P212121 as a correct > space group > it may be not the space group you have submitted. This is true only if you > have pseudo-translation, > which can be detected by calculation of the native Patterson. > > To check for it, in ccp4i choose > 'GENERATE PATTERSON' from 'EXPERIMENTAL PHASING/HEAVY METAL LOCATION' > submenu. > Choose > Run FFT to generate PATTERSON option and > look at at the PEAKMAX output at the end of the log file > > If there are peaks higher than 15 % of the origin (553.48 in the table > below), > you have pseudo-translation, In the example below peak at (0.5,0.5,0) is > around 30 % of the origin. > > > 1 1 1 553.48 0 0 0 0.0000 0.0000 0.0000 0.00 > 0.00 0.00 > 2 24 14 171.73 132 132 0 0.5000 0.5000 0.0000 100.96 > 100.96 0.00 > 3 4 4 10.20 6 2 0 0.0231 0.0084 0.0000 4.66 > 1.69 0.00 > > Alternatively, many programs, including MOLREP report pseudo-translation. > Origin ambiguity int the orthorhombic space group may happen when > pseudo-translation is close to half of one of your cell parameters. > > > If you do not have such pseudo-translation, your case is more complex and do > not waste time on ZANUDA. > > If you have pseudo-translation, try to refine the model output by ZANUDA in > P212121. > > Best, > > Misha > > ________________________________________ > From: Chris Fage [[email protected]] > Sent: 12 July 2014 00:33 > To: Isupov, Michail > Cc: [email protected] > Subject: Re: [ccp4bb] Proper detwinning? > > Nat and Misha, > > Thank you for the suggestions. > > Xtriage does indeed detect twinning in P1, reporting similar values > for <|L|>, <L^2>, and twin fraction as in P212121. > > The unit cell dimensions for the 2.0-A structure (P1) are: > 72.050 105.987 201.142 89.97 89.98 89.94 P 1 > > The unit cell dimensions for the 2.8-A structure (P212121) are: > 75.456 115.154 202.022 90.00 90.00 90.00 P 21 21 21 > > I have been processing in HKL2000, which only recognizes one set of > unit cell parameters for each Bravais lattice (does anyone know how to > change this?). Specifically, for a primitive monoclinic unit cell it > estimates: > 104.53 71.82 200.99 89.86 91.80 91.16 > This is the unit cell which refined to Rwork/Rfree ~ 27%/34%. > > Indexing in mosflm gives three options for primitive monoclinic: > 105.6 71.7 200.9 90.0 90.1 90.0 > 71.7 105.6 201.0 90.0 89.9 90.0 > 71.7 200.9 105.6 90.0 90.3 90.0 > Attempting to integrate in any of these space groups leads to a fatal > error in subroutine "MASKIT". I can also use the "index multiple > lattices" feature to get a > whole slew of potential space group; however, integrating reflections > leads to the same fatal error. > > Finally, Zanuda tells me that P212121 is the best space group, > according to R-factors. However, I do not believe P212121 is the > correct assignment. > > Best, > Chris > > > On 7/10/14, Isupov, Michail <[email protected]> wrote: >> I would recommend to run ZANUDA in the default mode from ccp4i or on CCP4 >> web server. >> ZANUDA has resolved several similar cases for me. >> >> Misha >> >> ________________________________________ >> From: CCP4 bulletin board [[email protected]] on behalf of Chris Fage >> [[email protected]] >> Sent: 10 July 2014 01:14 >> To: [email protected] >> Subject: [ccp4bb] Proper detwinning? >> >> Hi Everyone, >> >> Despite modelling completely into great electron density, Rwork/Rfree >> stalled at ~38%/44% during refinement of my 2.0-angstrom structure >> (P212121, 4 monomers per asymmetric unit). Xtriage suggested twinning, >> with <|L|> = 0.419, <L^2> = 0.245, and twin fraction = 0.415-0.447. >> However, there are no twin laws in this space group. I reprocessed the >> dataset in P21 (8 monomers/AU), which did not alter Rwork/Rfree, and >> in P1 (16 monomers/AU), which dropped Rwork/Rfree to ~27%/32%. Xtriage >> reported the pseudo-merohedral twin laws below. >> >> P21: >> h, -k, -l >> >> P1: >> h, -k, -l; >> -h, k, -l; >> -h, -k, l >> >> Performing intensity-based twin refinement in Refmac5 dropped >> Rwork/Rfree to ~27%/34% (P21) and ~18%/22% (P1). Would it be >> appropriate to continue with twin refinement in space group P1? How do >> I know I'm taking the right approach? >> >> Interestingly, I solved the structure of the same protein in P212121 >> at 2.8 angstroms from a different crystal. Rwork/Rfree bottomed out at >> ~21%/26%. One unit cell dimension is 9 angstroms greater in the >> "twinned" dataset than in the "untwinned". >> >> Thank you for any suggestions! >> >> Regards, >> Chris >> >
