[phenixbb] Low resolution structure

Kendall Nettles knettles at scripps.edu
Thu Mar 11 13:56:38 PST 2010

Hi Pavel,
Thanks for getting back to me. I think this could be quite useful, if for example you wanted to fix one end of a helix and allow the other end to move around during rigid body refinement. In my case, I'd ideally like to fix one end, and also limit the disulfide bond in the middle of the helix to some range (2-3 angstroms?). Any chance of this in the future?
Best regards,

On 3/11/10 4:03 PM, "Pavel Afonine" <PAfonine at lbl.gov> wrote:

Hi Kendall,

by the way, we now have secondary structure restraint which is expected to be useful at low resolution refinement, and they are generated automatically. So now you don't need to do this tedious work manually.

> I have a few questions related to a 3.5 angstrom structure. I have
> one helix that I am having trouble placing accurately. It does have
> a cysteine that disulfide bonds with the same residue in a symmetry
> related molecule. Can I restrain this distance during a rigid body
> refinement of the helix? How do I do this? What kind of parameters
> would be appropriate for the disulfide?

Just discussed it with Ralf. Not sure you can do it currently. I guess the rigid body refinement will just stop is  it noticed an atom at special position within a rigid group.

Good luck!

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