[phenixbb] Heme geometry restraint

Nigel Moriarty nwmoriarty at lbl.gov
Tue Jul 21 10:50:13 PDT 2020


@ 3.6Å resolution, you would almost certainly not have enough information
to suggest anything but planar geometry. I'm happy to take a look if you
send me the model and restraints directly.



Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Sun, Jul 19, 2020 at 5:24 PM Yangqi Gu <yangqi.gu at yale.edu> wrote:

> Dear all,
> I have a question regarding the heme c geometry restraint. I am aware that
> heme c could undergo distortion when bound to protein, but I am not sure at
> what resolution I could claim such distortion (such as
> ruffling/bending/doming). I have a map at 3.6 A resolution and whenever I
> did the refinement in phenix with real space refinement, some of the hemes
> are distorted and I am wondering if it is justified to leave it that way or
> do I have to impose the flat plane geometry. If so, how should I proceed to
> impose such geometry? Thank you in advance!
> Best,
> Yangqi
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