Dear Grace,
There are two ways that you can do this. If you run POINTLESS/AIMLESS from iMosflm using the “Quickscale” option, you can tell POINTLESS to use the symmetry set at the indexing stage, using SETTINGS -> Processing options -> Sort Scale and Merge tab,, select the tick box “ Use iMosflm symmetry in Quickscale option”. So providing the C2 space group is selected at the indexing stage, it will keep that symmetry.
If running POINTLESS/AIMLESS through CCP4i, in the Data reduction - Pointless, Aimless, Ctruncate window, under the “Options for Pointless” box you can select an option:
Set primitive orthorhombic groups in cell length order (a<b<c) but always use C2 rather than I2”.
Either way should work!
Best wishes,
Andrew
> On 18 Jul 2017, at 20:17, Grace Beggs <[log in to unmask]> wrote:
>
> Thank you, Andrew. How do I tell POINTLESS to keep C2?
>
> Grace
>
> ____________________________________________________
> Grace Beggs
> Brennan lab
> Department of Biochemistry | Duke University
> Email: [log in to unmask] <mailto:[log in to unmask]>
>
>
> From: Andrew Leslie <[log in to unmask] <mailto:[log in to unmask]>>
> Sent: Tuesday, July 18, 2017 1:48:23 PM
> To: Grace Beggs; [log in to unmask] <mailto:[log in to unmask]> Laboratory
> Subject: Re: Indexing question
>
> Dear Grace,
>
> POINTLESS will convert a C2 cell into I2 if this results a beta angle closer to 90, so that the axes are closer to being orthogonal. All CCP4 programs should work with I2, so this should not cause any issues. If you want to keep the C@ space group, you can tell POINTLESS to keep C2 rather than changing to I2.
>
> Best wishes,
>
> Andrew
>
>> On 18 Jul 2017, at 18:42, Grace Beggs <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>>
>> To whom it may concern:
>>
>> I am using version 7.2.1 of iMosflm. I have indexed, refined and successfully integrated and scaled my data with the space group C 1 2 1. Although the log file output after running aimless states the space group as C 1 2 1, when I load the mtz file into Phenix it states the space group is I 1 2 1. Could imosflm be writing the mtz file as I 1 2 1? How does one correct this? I 1 2 1 is not a standard space group.
>>
>> Thank you,
>> Grace Beggs
>>
>> ____________________________________________________
>> Grace Beggs
>> Brennan lab
>> Department of Biochemistry | Duke University
>> Email: [log in to unmask] <mailto:[log in to unmask]>
