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 <[log in to unmask]> 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 [[log in to unmask]]
> Sent: 12 July 2014 00:33
> To: Isupov, Michail
> Cc: [log in to unmask]
> 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 <[log in to unmask]> 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 [[log in to unmask]] on behalf of Chris Fage
>> [[log in to unmask]]
>> Sent: 10 July 2014 01:14
>> To: [log in to unmask]
>> 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
>>
>
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