[phenixbb] increasing NCS restraints

Mark van Raaij mjvanraaij at cnb.csic.es
Thu Oct 17 14:52:46 PDT 2013

Dont worry about it, we are alli diots...even without commuting 4 hrs a day

Yarrow Madrona <amadrona at uci.edu> wrote: 

>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
>phenixbb mailing list
>phenixbb at phenix-online.org

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