Hi Sam,
> Hi, the question may be a bit weird, but how do you define 'over-fitting'
> in the context of structure refinement? From users' perspective the
> practical aspect is to 'fit' the model into the density. So there comes
> this question from our juniors: fit is fit, how is a model
On Monday, 19 October 2020 20:27:04 PDT Sam Tang wrote:
> Hi, the question may be a bit weird, but how do you define 'over-fitting'
> in the context of structure refinement? From users' perspective the
> practical aspect is to 'fit' the model into the density. So there comes
> this question from
Hi, the question may be a bit weird, but how do you define 'over-fitting'
in the context of structure refinement? From users' perspective the
practical aspect is to 'fit' the model into the density. So there comes
this question from our juniors: fit is fit, how is a model over-fit?
BRS
Sam
Hi All,
there was a bug at some point that could potentially lead to this.
This all should be fixed in current Phenix nightly builds:
http://phenix-online.org/download/nightly_builds.cgi
If not, get back to us (phenixbb or Phenix help lists or reply directly to
me).
Pavel
On Mon, Oct 19, 2020
I've seen a similar behavior when, for the Phenix.refine refinement
strategy, I accidentally selected both XYZ (reciprocal-space) and XYZ
(real-space) at the same time. As well as a Phe jumping out of density
in one NCS copy, planarity was very poor for several sidechains (but
no obvious
Dear Michael
I would carefully check the backbone region around the tyrosine and make sure
it’s correct as errors there might be the issue.
Regards
Christine
Sent from my iPhone
> On Oct 19, 2020, at 11:52 AM, Boniecki, Michal
> wrote:
>
>
> Hello,
> I have a problem during refining with
As Paul observes, there's a bona fide email list for phenix, but in fact
comparing REFMAC to phenix.refine might be useful to see if this really is a
program bug or if it's a bug in the model. Sometimes one is better than the
other.
For phenix.refine:
Put the Tyr in the "right" place and
You dont say what resolution your data goes to - certainly REFMAC and I
guess PHENIX have restraints to prevent van der waal clashes.
If there is high resolution data then these restraints can be overridden to
some extent. Maybe set the occupancy of the PRO C=O to 0.0 and see where
the TYR
On 19/10/2020 19:52, Boniecki, Michal wrote:
I have a problem during refining with one of the Tyr residues. It is
constantly pushed out of the position during refinement in all 4
chains in ASU.
I have tried to exclude it from refinement in phenix but it is refined
anyway out of the position
You are invited to participate in the Center for BioMolecular Structures
Solution Scattering - LIX (morning) and Macromolecular Crystallography - MX
(afternoon) Workbenches, November 3 through 5. The main goal of these
workshops is to provide an opportunity to get acquainted with the method
Thanks for the info. Will forward it to my colleague.
Best,
JP
From: Jon Cooper
mailto:jon.b.coo...@protonmail.com>>
Reply-To: Jon Cooper
mailto:jon.b.coo...@protonmail.com>>
Date: Friday, October 16, 2020 at 5:13 PM
To: "Xiong, Jian-Ping"
mailto:xi...@helix.mgh.harvard.edu>>,
Dear all,
Sorry for the off-topic question. I need to prepare an heterodimeric protein
complex for an immunisation, and I would like to make sure that the dimer will
be stable and it won't dissociate after injection.
I am wondering if any of you has a mild cross-linking protocol (and
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