hi Chris
Can you send the date-stamped log file (called something like mosflm_20140712_140235.lp, I.e. with the year, month, date, etc when you ran the program) to me directly (i.e. not to the BB, since it's likely to be of little interest to all the other subscribers...) so I can have a look at the results of indexing, and the processing that led up to the MASKIT error?
Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
> On 12 Jul 2014, at 00:33, Chris Fage <[log in to unmask]> wrote:
>
> 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
>>
|