[phenixbb] increasing NCS restraints

Yarrow Madrona amadrona at uci.edu
Thu Oct 17 13:53:01 PDT 2013

Hi Dale,

That is right! And that is what I concluded yesterday yet I somehow forgot
all that overnight. Starting a new job and commuting 4 hours a day has
taken a toll on my brain. I am an idiot.


>    I'm puzzled.  Didn't you say that the translation of your ncs
> two-fold was not equal to half the "a" cell edge?  If it is not
> a translation of 1/2 (in fractional coordinates) then it cannot
> be a crystallographic symmetry element and your space group cannot
> be P212121.  Unless this condition is met, the similarity of your
> molecules is unimportant.
> Dale Tronrud
> On 10/17/2013 12:48 PM, Yarrow Madrona wrote:
>> I am doing restrained NCS refinement and would like to know how to set
>> the
>> target weight of the cartesian restraint in the command line? I also
>> found
>> a sigma value in the GUI. I read that I can decrease it in order to
>> increase the NCS restraints. However, I have seen this under Torsional
>> restraints. Does this also apply to cartesian restraints?
>> I am doing this so that I can look at the differences in position and
>> B-factors of two molecules in the ASU that I am trying to determine are
>> related by a perfect or imperfect 2(1) screw axis. (I posted a question
>> about this on the CCP4 bullitan board.) If the values between molecules
>> are exactly the same then presumably the space group is actually P212121
>> with 1molecule in the asu instead of P21 with two molecules. I already
>> know that the P21 dimer superimposes almost exactly on the P212121
>> monomer
>> and it's symmetry mate. I just don't know how "perfectly" they align and
>> I
>> am hoping this approach will tell me. I hope this makes some sense.
>> -Yarrow
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Yarrow Madrona

Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697

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