[phenixbb] centered triclinic lattice
Randy John Read
rjr27 at cam.ac.uk
Wed Dec 14 12:50:54 PST 2022
Hi Cathy,
Presumably you’re trying to keep the original cell, which is why you haven’t reindexed to a smaller P1 cell?
We’ve run into this problem when we wanted to test whether pseudo-centering in a P1 crystal was really a centering operator. Is that what you’re trying to do? If so, I can’t help because we gave up and just reindexed!
Randy
> On 14 Dec 2022, at 16:49, Cathy Lawson <cathy.lawson at rcsb.org> wrote:
>
> Thanks Pavel.
>
> I tried adding _struct_ncs_oper matrices to the input cif file but got a phenix error that an identity rotation with non-zero translation elements was improper.
> It would be great if the code could be modified to accept this transformation.
>
>> On Dec 14, 2022, at 11:25, Pavel Afonine <pafonine at lbl.gov> wrote:
>>
>> Hi Cathy,
>>
>> making the 2nd copy and working in P1 seems as fine option to me. And no, cctbx doesn't know A1.
>>
>> If this is for refinement you can use NCS constrains which will enforce the strict symmetry on everything: coordinates, occupancies, B factors.
>>
>> Pavel
>>
>>
>> On 12/14/22 07:31, Cathy Lawson wrote:
>>> Looking for suggestions — cctbx/phenix seems not to be able to handle a triclinic lattice with centering.
>>>
>>> Specific Example: PDB entry 1LKS with cell parameters/space group “A 1”: CRYST1 31.970 65.080 27.250 94.57 111.56 82.98 A 1 2
>>>
>>> A 1 diagram: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimg.chem.ucl.ac.uk%2Fsgp%2Flarge%2F001bz1.htm&data=05%7C01%7Crjr27%40universityofcambridgecloud.onmicrosoft.com%7C27a6359621024bb8b37208daddf37afd%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C638066335049293047%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=VvbkrtwH9AdH1irFnag8F4vCnMfDVib%2F%2B7VutLIVdmw%3D&reserved=0
>>>
>>> Are there any other options for working with this data in phenix other than creating an explicit 2nd copy of the coordinates at x, 1/2+y,1/2+z and setting space group to primitive lattice P 1?
>>>
>>> Thanks in advance.
>
>
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-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building Fax: +44 1223 336827
Hills Road E-mail: rjr27 at cam.ac.uk
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
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