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Re: [ccp4bb]: refining NCS matrices

Any virus structure requires two sets of NCS matrices: 1) one set refers to the virus in a standard orientation in a hypothetical orthogonal h-cell. Standard orientation implies that the three orthogonal axes of the h-cell coincide with three of the  2-fold NCS axes of the virus particle 2) The other set of NCS matrices defines the virus particle in the actual crystallographic unit cell (or the u-cell).

If you already know the u-cell matrices accurately (as I understand from your email), then the simplest way to refine these matrices is to use 6d_improve in the RAVE package (Uppsaala software). Then, find out the transformation matrix (T) between the h-cell and the refined u-cell matrices using lsq option in O. Use the T-matrix along with the h-cell matrices in CNS. Remember to use u-cell coordinates of the virus asymmetric unit.

I hope that helps.

Sugoto
 

Deena Oren wrote:
 

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Hello all,

How would you recommend refining the NCS matrices to best agree with the
X-ray terms? I have 15 copies of the monomer in the asymmetric unit
(virus) and I have arrived at the matrices using the virus from a
different space group in O.
I must admit I am using cns for minimization so I am curious to know how
to perfect these matrices in cns, but I am open to suggestions in CCP4 as
well.

Thanks

Deena Oren, PhD                                  732-235-4498
Center for Advanced Biotechnology and Medicine
Rutgers University
679 Hoes ln                                 fax: 732-235-5669
Piscataway, NJ 08854                    oren@cabm.rutgers.edu

-- 
Sugoto Chakravarty, Ph.D.
Dept of Biochemistry & Molecular Biology
Baylor College of Medicine
One Baylor Plaza
Houston, TX-77030

Ph : 713-798 8432 (W)
Fax : 713-798 1625 (W)