[phenixbb] Can I use PHENIX "Find NCS" tool to verify space group ?

Alex Lee alexlee198609 at gmail.com
Sat Apr 22 16:18:57 PDT 2017

Hi All,

I have a protein/dna dataset (3A resolution) with space group (SG)
ambiguity, it could be P32 with two copies of molecules  (one copy of
molecule composed of protein homodimer with asymmetric dsDNA)  in
asymmetric unit (ASU) or P3221 with one copy of molecule in ASU. Both SG
can give me MR solutions and after Refmac P32 Rfree is around 31% while
P3221 Rfree is around 34% (without any twin refine at this stage). Density
maps from both SG makes sense and they are similar by eye inspection.
Because of partial twinning of the dataset (estimation twin fraction alpha
around 0.22) , which confuse programs of assigning the correct SG.
Pointless and Xtriage suggests P6222, which we are sure it's not correct
(based on performance on both MR, Refmac and biology sense that dsDNA is
asymmetric, and if P6222 is true then based on Mathew coef. there will be a
monomer protein with single strand ssDNA in ASU). Zanuda suggests SG P32 in
both cases (input experimental data P32 or P3221 along with refined model).
However, Zanuda may not work well in twin case.  In short, the problem now
is to choose one SG from P32 or P3221.

There is one suggestion that try SG P32, as there are two copies of
molecules in ASU in P32 group, try find the NCS operator in P32 and check
if this operator is close to crystallographic symmetry operator or not, if
it is, then SG is P3221, if it's not, then SG is P32.

I did a few rounds of search in Internet, I found Phenix "Find NCS tool"
and input PDB of my refined structures from both P32 and P3221. For both
test, Find NCS tool did find NCS operator but in the end of the log file I
see the same results as below:
This NCS object does not contain point group symmetry
This NCS object does not contain helical symmetry.

I am asking: 1.  does "This NCS object does not contain point group
symmetry" from Find NCS tool mean that NCS operator in my PDB is not
crystallographic symmetry operator?

2. Is there a tool in Phenix which can find the NCS operator and check if
the NCS operator is close to crystallographic symmetry operator or not?

Thanks ahead.
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