[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!


> 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
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