[phenixbb] increasing NCS restraints

Mark van Raaij mjvanraaij at cnb.csic.es
Thu Oct 17 15:58:01 PDT 2013

Oops, 1 vote for making phenixbb default reply to sender only....

Mark van Raaij <mjvanraaij at cnb.csic.es> wrote: 

>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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