Hi Randy,
Question regarding your reply to Pavel:
>That may well involve the French & Wilson algorithm, but can take advantage of
>whatever is understood by the program (e.g. anisotropy and >translational
>non-crystallographic symmetry, both of which in principle can be modeled
>better as the atomic model improves).
I may have misunderstood you completely, but do you mean that the Fobs's will
be recalculated as the model improves (this is where French-Wilson comes into
effect, right)? Or only once during refinement?
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Randy Read
[rj...@cam.ac.uk]
Sent: Wednesday, December 03, 2014 12:46 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Intensities and amplitudes
Hi Pavel,
We were chatting with Phil Evans the other day about things like this, and
generally we were in agreement that any programs that need amplitudes (and
you’re right of course, you have to have some sort of amplitude to calculate a
map!) should be able to compute them on the fly. That may well involve the
French & Wilson algorithm, but can take advantage of whatever is understood by
the program (e.g. anisotropy and translational non-crystallographic symmetry,
both of which in principle can be modeled better as the atomic model improves).
I haven’t really worried about R-factors. We could learn to embrace the
R-factor on intensity that small molecule crystallographers are comfortable
with but, as you say, people are not used to these. If we compute amplitudes
on the fly, with a French & Wilson algorithm that is calibrated better as the
model improves, the R-factors will be calculated with a changing set of Fobs.
This would probably be a minor effect, but it’s slightly disconcerting.
Randy
-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills Road E-mail:
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.
www-structmed.cimr.cam.ac.uk
On 2 Dec 2014, at 21:44, Pavel Afonine <pafon...@gmail.com> wrote:
> Hi Randy,
>
> I can see all good reasons for using intensities! What about maps and
> R-factors? I guess you still need F to compute them (I realize you can
> compute R(I) but this is not what people are used to do in general), and if
> that's the case then I->F is still inevitable (at least for some purposes).
>
> Thanks,
> Pavel
>
> On Tue, Dec 2, 2014 at 1:26 PM, Randy Read <rj...@cam.ac.uk> wrote:
> Dear Mohamed,
>
> At the moment, a lot of programs require amplitudes, but I believe that they
> should all eventually be updated to use intensities. In fact, we’re in the
> end stages of a large project to switch Phaser from using amplitudes to using
> intensities. There are a number of reasons why, in principle, it’s better to
> work in terms of intensities. One is that it’s perfectly reasonable to have
> a negative observed intensity, which can come from subtracting a background
> estimate with measurement errors from a very weak peak with its own
> measurement errors. That, of course, is where the French and Wilson
> algorithm comes in, allowing an amplitude to be estimated without simply
> taking a square root. However, the problem with the French and Wilson
> algorithm is that it loses information, i.e. you can’t reconstruct the
> intensity and its standard deviation. What you get out of French & Wilson
> depends on the estimate of the expected intensity for a reflection, which is
> typically taken from the mean in the resolution shell but should vary with
> direction for crystals suffering from anisotropic diffraction and should be
> modulated for crystals with translational non-crystallographic symmetry.
>
> Another reason it’s better to work in terms of intensities is that it’s
> reasonable to assume that the measurement errors for intensities are
> Gaussian, but then less reasonable to assume that for amplitudes
> (particularly with the problem that amplitudes can’t be negative).
>
> For now, you need amplitudes for a lot of purposes and then the French &
> Wilson algorithm is useful. But what I would strongly recommend is that you
> hang on to the intensities and you make sure that the intensities are
> deposited at the PDB. It’s a pity that many PDB depositions only have
> amplitudes that have been through French & Wilson, so that new procedures
> based on intensities won’t be able to be applied with their full power.
>
> Best wishes,
>
> Randy Read
>
> -----
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: +44 1223 336500
> Wellcome Trust/MRC Building Fax: +44 1223 336827
> Hills Road E-mail:
> rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
> On 1 Dec 2014, at 20:49, Mohamed Noor <mohamed.n...@staffmail.ul.ie> wrote:
>
> > Dear crystallographers
> >
> > Is there any reason for using one data type over the other? Are there any
> > errors associated with the French and Wilson I-to-F conversion step?
> >
> > Thanks.
> > Mohamed
>
