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C Squire csquire at CCU1.AUCKLAND.AC.NZ
Mon Jan 22 18:53:34 EST 1996



Hello,

I am attempting to refine a DNA octamer originally refined using
NUCLSQ.  The space group is P 43 21 2 and the asymetric unit contains 
a single strand of DNA.  The second strand is produced by 2-fold rotational
symmetry.  For NUCLSQ, a whole duplex was refined with
half occupancies and the 2 strands were averaged periodically throughout
the refinement. 

*******************************************************************
* What is the best way to deal with this refinement using X-PLOR? *
*******************************************************************

I am not very experienced in using x-plor but I have tried a couple of 
things with limited success:

1) I have tried using a single strand as the model but this results 
   in problems with the complementary strand being so close to 
   the first and being hydrogen bound.

2) I have also tried using a duplex as the model with half occupancies
   and using the NCS command with the 2 strands selected as the NCS related
   groups.  This appeared useful at first but then resulted in 
   the R-factor doubling from 25% to 50% at later stages in rigid body 
   refinement (this occurred at the same time as the rms deviation 
   between the 2 strands became significantly lower).


I would greatly appreciate any help!

Chris Squire.


/////////////////////////////////////////
/ Chris Squire                          /
/ Chemistry Dept.                       /
/ University of Auckland                /
/ Auckland                              /
/ New Zealand                           /
/                                       /
/ E-mail: csquire at ccu1.auckland.ac.nz   /
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