: [ccp4bb] Babinet solvent correction [WAS: R-free flag
problem]
Dear Tim,
Interesting discussion, and I agree with your last description of the issues.
When I started playing with this for oxymyoglobin [J. Mol. Biol. 142, 531-544
(1980)]
it seemed immediately apparent (i.e. by thinking about it
On Thu, 28 Oct 2010 16:56:42 +0200
Dirk Kostrewa wrote:
>
> In the Babinet bulk solvent correction, no bulk solvent phases are
> used, it is entirely based on amplitudes and strictly only valid if
> the phases of the bulk solvent are opposite to the ones of the
> protein. And as Sasha Urzhumtsev
Hi Tim,
sorry for my late reply - I just came back to the lab.
In the Babinet bulk solvent correction, no bulk solvent phases are used,
it is entirely based on amplitudes and strictly only valid if the phases
of the bulk solvent are opposite to the ones of the protein. And as
Sasha Urzhumtsev
3 October 2010 21:14
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Babinet solvent correction [WAS: R-free flag problem]
On Sat, 23 Oct 2010 10:05:15 -0700
Pavel Afonine wrote:
> Hi Tim,
>
> ...but I hope this answers the question:
> Babinet's vs. the flat model? Use them toge
On Sat, 23 Oct 2010 10:05:15 -0700
Pavel Afonine wrote:
> Hi Tim,
>
> ...but I hope this answers the question:
> Babinet's vs. the flat model? Use them together! ;)
>
>
> thanks a lot for your reply.
>
> Could you please explain the *physical* meaning of using both
> models togethe
Hi Tim,
...but I hope this answers the question:
Babinet's vs. the flat model? Use them together! ;)
thanks a lot for your reply.
Could you please explain the *physical* meaning of using both models
together? Flat (mask-based) bulk solvent model has clear physical meaning
and its adv
On Fri, 22 Oct 2010 13:38:07 -0700
Ethan Merritt wrote:
>
> Unfortunately for the current discussion, I do not find any practical
> comparison to Babinet models in either paper. Both start with the
> implicit assumption that a flat, masked model is better and then
> proceed to explore how best t
Hi Ethan,
Do you know of any published or unpublished results that compare
> the R factors achieved by Babinet treatment with those obtained from the
> state-of-the-art mask models?
>
I afraid I don't know about published ones, and I see Sacha replied for
unpublished one.
I could spend a few h
Dear Ethan,
Just answering your last remarks,
very many years ago I've done tests (unpublished) where I tried to estimate the
magnitudes Fbulk and PHASES Pbulk for the reflections due to bulk solvent. It
came out that :
- for high-resolution reflections the magnitudes are small (everybody knows
On Fri, Oct 22, 2010 at 11:01 AM, Ed Pozharski wrote:
> Ethan pointed out to me that Babinet-principle based solvent correction
> is not always inferior to mask-based approach.
On Friday, October 22, 2010 11:17:53 am Pavel Afonine wrote:
> Hi Ed,
>
> may be "not always" (in a sense that mask-ba
Hi Ed,
may be "not always" (in a sense that mask-based one sometimes may leave a
negative footprint in areas where there is no solvent), but I still want to
remind this paper where there is some discussion about exponential vs
mask-based bulk solvent model:
http://journals.iucr.org/d/issues/2002/
Ethan pointed out to me that Babinet-principle based solvent correction
is not always inferior to mask-based approach. My belief was based on
some old observations which were in fact made prior to mask
implementation in refmac and thus not exactly side-by-side comparisons.
I hereby recant my prior
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