cctbx.miller problem

李选选

5 Dec 2017 5 Dec '17

9:01 a.m.

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 http://img.chem.ucl.ac.uk/sgp/large/227az2.htm.

Looking forward to your response.

Thanks, Xuanxuan

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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 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 [email protected] 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 PHENIX: http://www.phenix-online.org CAMERA: http://camera.lbl.gov/ -----------------------------------------------------------------

Haiguang Liu

6 Dec 6 Dec

12:48 a.m.

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 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 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 [email protected] 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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Petrus Zwart

5:27 a.m.

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 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 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 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 [email protected] 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/ -----------------------------------------------------------------

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

Graeme.Winter＠diamond.ac.uk

6:14 a.m.

If you want to compute all possible Miller indices to a given resolution, for a unit cell, without considering symmetry something like this is what you need: def generate_reflection_indices(uc, dmin): maxh, maxk, maxl = uc.max_miller_indices(dmin) indices = [] for h in range(-maxh, maxh + 1): for k in range(-maxk, maxk + 1): for l in range(-maxl, maxl + 1): if h == 0 and k == 0 and l == 0: continue if uc.d((h, k, l)) < dmin: continue indices.append((h, k, l)) return indices This does however mean that systematically absent reflections will be included - you would need to also test this with the space group object Cheers Graeme On 6 Dec 2017, at 00:48, Haiguang Liu mailto:[email protected]> 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 mailto:[email protected]> 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 mailto:[email protected]> 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 [email protected]mailto:[email protected] 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 9246tel:(510)%20289-9246 PHENIX: http://www.phenix-online.org http://www.phenix-online.org/ CAMERA: http://camera.lbl.gov/ ----------------------------------------------------------------- _______________________________________________ cctbxbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/cctbxbb _______________________________________________ cctbxbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/cctbxbb -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Graeme.Winter＠diamond.ac.uk
Haiguang Liu
Peter Zwart
Petrus Zwart
李选选