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
>
