[ccp4bb] mixed cleavage states of RNA: not exactly multiple conformations

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Postdoctoral position. RNA crystallography
From: Alfonso Mondragon a-mondragon {- at -} NORTHWESTERN {- dot -} EDU
Date: 2007-05-14

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From: Vineet Gaur vineetgaur1982 {- at -} GMAIL {- dot -} COM
Date: 2007-05-15

Subject: mixed cleavage states of RNA: not exactly multiple conformations
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2007-05-14

I have a partially cleaved RNA, so I would like to try refining with
two different dinucleotide segments embedded in the model, one of
which has a broken backbone and 2',3'-cyclic phosphate, and the other
with a standard phosphodiester backbone. This should be analogous to
having two conformations but the covalency would be different.

I'd like to do this in refmac but if it can be done in phenix or CNS
that would be ok I guess too.

Any suggestions? The only thing I have come up with is two have the
end nucleotides at the cleavage site each in two conformations, and
then impose a link on one of these to "fake" the phosphodiester, but
this seems like an ugly hack (and I can't seem to get it to work
anyway).

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Postdoctoral position. RNA crystallography
From: Alfonso Mondragon a-mondragon {- at -} NORTHWESTERN {- dot -} EDU
Date: 2007-05-14

Next message:
Subject: intel Xeon vs AMD Opteron for crystallographic applications
From: Vineet Gaur vineetgaur1982 {- at -} GMAIL {- dot -} COM
Date: 2007-05-15