Hi Ed,
I didn't really open a can of worms... Sorry if I did!
But there are many things affecting R-factors not
being reported. Do I have to deposit the bulk solvent mask?
Not that many and most of them are reported (at least those that may
affect the R-factor "significantly"). The model
On Thu, 2008-12-18 at 10:15 -0800, Ethan A Merritt wrote:
> The riding-hydrogen treatment is definitely part of the model.
> But the number of parameters associated with it is not derived from the
> number of individual hydrogen atoms and their coordinates, it is
> limited to the number of paramete
> - "bond length restraints" do not contribute to the scattering and
> hence do not affect the R-factors, while H atoms do contribute to
> scattering and therefore R-factors computed from the model with or
> without hydrogens can be different (I spent a couple of months
> implementing it in PHENIX
On Thursday 18 December 2008, Ed Pozharski wrote:
> > > Riding hydrogens are *not* part of your model,
> >
> > The fact that you don't see H in your fo-fc map due to limited
> > resolution and high level of noise does not mean that H atoms are not
> > present in actual real structure -:)
> >
>
On 12/18/2008 8:23 AM, Ed Pozharski wrote:
Riding hydrogens are *not* part of your model,
The fact that you don't see H in your fo-fc map due to limited
resolution and high level of noise does not mean that H atoms are not
present in actual real structure -:)
Let me ask you this
> > Riding hydrogens are *not* part of your model,
>
> The fact that you don't see H in your fo-fc map due to limited
> resolution and high level of noise does not mean that H atoms are not
> present in actual real structure -:)
>
Let me ask you this - are bond length restraints part of the *mo
Dear Ed,
> Riding hydrogens are *not* part of your model, they are part of the
> algorithm used to predict observations.
As a diversion from PDB-ology I would point out that, according to
Bayesian statistics, of which the maximum-likelihood method is a rough
On 12/18/2008 7:23 AM, Ed Pozharski wrote:
Riding hydrogens are *not* part of your model,
The fact that you don't see H in your fo-fc map due to limited
resolution and high level of noise does not mean that H atoms are not
present in actual real structure -:)
There are definitely some (ma
Jon,
Riding hydrogens are *not* part of your model, they are part of the
algorithm used to predict observations. Thus, the information is
automatically included when you report the software used for refinement.
There are definitely some (many) parameters that are never included in
the deposited
Hi Jon,
- obviously, the model should not be manipulated once the final
statistics is obtained, or if it is manipulated, then the final
statistics must be re-calculated;
- I can't imagine someone thinking that hydrogens were refined
individually in a X-ray structure say at 2A resolution.
-
On Wednesday 17 December 2008 15:53:42 Jonathan Winger wrote:
> Hi all-
>
> Just wondering what the consensus is - should a structure refined with
> riding hydrogens be deposited with the coordinates for the hydrogens
> included? One could argue that, since they were used in the
> refinemen
Hi all-
Just wondering what the consensus is - should a structure refined with
riding hydrogens be deposited with the coordinates for the hydrogens
included? One could argue that, since they were used in the
refinement to obtain the model and statistics reported, they should be
included
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