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 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: http://img.chem.ucl.ac.uk/sgp/large/001bz1.htm

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.

Thanks for chiming in Randy. We could consider reindexing. The goal is to update the entry in such a way that “round trip” refinement becomes possible using modern software. Phenix is not the only program that cannot handle “A 1”. Can you suggest software that can assist in identifying reindexing strategy for merged amplitudes?

On Dec 14, 2022, at 15:50, Randy John Read wrote:

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 mailto:[email protected]> 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 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 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: [email protected] mailto:[email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk http://www-structmed.cimr.cam.ac.uk/