[cctbxbb] cctbx.miller problem

Petrus Zwart phzwart at lbl.gov
Tue Dec 5 21:27:06 PST 2017


Yes, but then you loose the symmetry info. It is typically better to ensure
your reflections are all in the asymmetric the program uses.

use a

.map_to_asu()

on any set of miller indices you read in to make sure you are in the right
part of the ASU.

A map to ASU will generate the right indices you need, but the associated
epsilons, phase restrictions and reflection types (centric, acentric) will
be meaningless.
If you don't need those, it could be ok

P



On Tue, Dec 5, 2017 at 4:48 PM, Haiguang Liu <haiguang.liu at gmail.com> wrote:

> 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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>>
>>
>
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>


-- 
-----------------------------------------------------------------
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

PHENIX:   http://www.phenix-online.org
CAMERA: http://camera.lbl.gov/
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