[cctbxbb] cctbx.miller problem

Haiguang Liu haiguang.liu at gmail.com
Tue Dec 5 16:48:31 PST 2017


Hi Peter,

Will the command ms.expand_to_P1() do the trick to generate all symmetry
peaks?

Best,
Haiguang

On Wed, Dec 6, 2017 at 2:13 AM, Peter Zwart <PHZwart at lbl.gov> wrote:

> Hi Xuanxuan,
>
> This:
>
>
> from cctbx import miller
> import cctbx
> from cctbx import crystal
>
> ms = miller.build_set(
>     crystal_symmetry=crystal.symmetry(
>         space_group_symbol='Fd-3m',
>         unit_cell=(5.4307,5.4307,5.4307,90.00,90.0,90.00)),
>     anomalous_flag=False,
>     d_min=0.4)
>
> for hkl in ms.indices():
>     print hkl
>
> gives:
>
> (0, 2, 2)
> .
> .
> .
> (1, 3, 3)
>
> etc
>
> 2,2,0 is related by symmetry to 0,2,2
>
> HTH-P
>
>
> On 5 December 2017 at 01:01, 李选选 <lixx11 at csrc.ac.cn> wrote:
>
>>
>> Dear cctbx developers,
>>
>> I’m Xuanxuan, and I’m using cctbx to develop a crystallography-related
>> algorithm. Recently, I found there is something wrong when I use miller
>> package to generate miller indices for given space group and unit cell
>> parameters. Maybe it’s my mistake, or it’s a bug.
>>
>> Here are some details. I just use the following code to generate a list
>> of miller indices for a Fd-3m crystal.
>>
>> ms = miller.build_set(
>>     crystal_symmetry=crystal.symmetry(
>>         space_group_symbol='Fd-3m',
>>         unit_cell=(5.4307,5.4307,5.4307,90.00,90.0,90.00)),
>>     anomalous_flag=False,
>>     d_min=0.4)
>>
>> And I found some reflections are missing, like 220, 311, which should
>> exist according to the reflection conditions listed in this page
>> http://img.chem.ucl.ac.uk/sgp/large/227az2.htm.
>>
>> Looking forward to your response.
>>
>> Thanks,
>> Xuanxuan
>>
>>
>>
>> _______________________________________________
>> cctbxbb mailing list
>> cctbxbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>
>>
>
>
> --
> -----------------------------------------------------------------
> P.H. Zwart
> Staff Scientist
> Molecular Biophysics and Integrated Bioimaging &
> Center for Advanced Mathematics for Energy Research Applications
> Lawrence Berkeley National Laboratories
> 1 Cyclotron Road, Berkeley, CA-94703, USA
> Cell: 510 289 9246 <(510)%20289-9246>
>
> PHENIX:   http://www.phenix-online.org
> CAMERA: http://camera.lbl.gov/
> -----------------------------------------------------------------
>
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