On Wed, 2011-04-20 at 13:57 +0100, david lawson (JIC) wrote:
> I am building and refining a protein-DNA complex at 3 Ang resolution
> and having a bit of trouble with side-chains that interact with DNA.
> In particular Arg side-chains that H-bond to the phosphate backbone
> tend to get dragged into the phosphate density when I do real space
> refinement. I have tried playing about with the weight matrix in the
> R/RC menu, but this doesn’t seem to help much. I am running version
> 0.6 for Mac (Miramar revision 2540).
Look at Extensions->Maps->Mask map by atom selection. This should
exclude phosphates from the map.
But if these arginines do not have "their own" density to latch on, some
people would say you should not model them at all.
Good luck,
Ed.
--
"Hurry up before we all come back to our senses!"
Julian, King of Lemurs
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