Thanks for the advice Pavel!
I don't want to celebrate prematurely, but I just re-ran the same
refinement in both the stable and in nightly 4070, and it _seems_ to be
corrected in the nightly. Will let you know if it pops up again.
- Igor Petrik, PhD
On Thu, Dec 3, 2020 at 9:16 AM Pavel Afonin
Thanks Nigel,
I will put together the input and output file from my latest refinement and
send them to you and Pavel later today.
- Igor Petrik, PhD
On Wed, Dec 2, 2020 at 9:46 PM Folmer Fredslund wrote:
> Dear Igor
>
> There's a phenix bulletin board for question like this, which is where yo
Hi Folmer,
I would choose to not do the real space refinement in phenix.refine during
> the last rounds of refinement of a model, when sidechain positions are
> essentially correct.
>
by design it is supposed to place and fit side chains as good as possible,
satisfying both map fit and geometry c
Dear Igor
There's a phenix bulletin board for question like this, which is where you
should post the question. ( I crosspost here)
I would choose to not do the real space refinement in phenix.refine during
the last rounds of refinement of a model, when sidechain positions are
essentially correct
Igor
There is a Phenix BB for your Phenix related questions. You can subscribe
here.
http://www.phenix-online.org/mailman/listinfo/phenixbb
In the meantime, please send the Phenix version and OS to myself and Pavel
privately and I'm sure we can help. We may also need the inputs (privately,
of co
I am refining a 1.71A X-ray structure with phenix refine. I have everything
modelled in - ~150 residues in the ASU and a heme - and my R-work/R-free is
0.17/0.22. But when I went to deposit it, PDB pointed out that two of my
sidechains have distorted geometries. One is a His, and looking at it in
C
