[phenixbb] centered triclinic lattice
cathy.lawson at rcsb.org
Wed Dec 14 08:49:10 PST 2022
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.
> 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.
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