Re: [COOT] problem with refining DNA

[Paul Emsley]

Miguel Ortiz Lombardia wrote:

Le 4 févr. 2010 à 04:37, Norman Zhu a écrit :

hello there

      I am in the process of refining a protein structure complexed to DNA
promoter site.  I ran into difficulty as i try to move a few bases into
patch of electron density that is obviously meant for them.  dragging the
bases with real space refine zone and/or regularize zone neither break open

the phosphate back bone bounds or turn everything into knots. I know there is nothing wrong with the naming convention of my bases since I changed them from DT to Td after similar blog. Any suggestion on this matter would be greatly appreciated.

Norm

Hi Norm,

Depending on the resolution of your data you may need to turn down the matrix 
weight in refinement parameters. I tipically put this down to 30 (compared to 
the default value of 60) and for really lower resolution (say 3 or worse) I may 
go as down as 20.

I frequently use 6.0 or even 2.0 sometimes.

Paul