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

Terwilliger, Thomas Charles terwilliger at lanl.gov
Sun Apr 23 07:35:55 PDT 2017

Hi Alex,

The notation that

This NCS object does not contain point group symmetry
This NCS object does not contain helical symmetry.

means that the NCS itself is not point-group or helical symmetry  (not including any space-group symmetry).
 For crystallographic data this summary is usually not useful because it doesn't include space-group symmetry in the calculation.

You can probably tell if your NCS is similar to the 2-fold axis in P 3(2) 2 1 that goes along (1,1,0) by examining the NCS log file.  It will have a summary of point-group symmetry like this:

 Analysis of NC symmetry using cutoff of   0.10 A as maximum
 distance between intersecting elements

Looking for point-group symmetry among  the            2 NC elements that might be members

 This point group is a rotation about  a line going through the point
 xyz (orthogonal A) =   12.858 -10.339  23.956
 xyz (fractional)=       0.224  -0.175   0.213
 in the direction of xyz (orthogonal A) =    0.807   0.294   0.513

In your case you are looking for this kind of point-group symmetry where the line goes through something like (0,0,0) or (0,0,0.5) and the direction is something like (0.866,0.50,0), corresponding to a line going half-way between the X and Y axes, where this 2-fold belongs in P 3(2) 2 1. (I could have some angles mixed up here but if you get  +-0.866 and +/- 0.5 in some order for x and y and 0 along z it's probably this 2-fold).

I'll be happy to look at your log file if you do this.

All the best,
Tom T

From: phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> on behalf of Alex Lee <alexlee198609 at gmail.com>
Sent: Saturday, April 22, 2017 5:18 PM
To: PHENIX user mailing list
Subject: [phenixbb] Can I use PHENIX "Find NCS" tool to verify space group ?

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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