ined before is locally uniform and
therefore can be fitted by a planar background function.
Cheers
-- Ian
-Original Message-
From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
Behalf Of James Holton
Sent: 29 January 2010 09:43
To: CCP4BB@jiscmail.ac.uk
efore can be fitted by a planar background function.
Cheers
-- Ian
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of James Holton
> Sent: 29 January 2010 09:43
> To: CCP4BB@jiscmail.ac.uk
> Subject: Re: [ccp4bb]
> I believe he means something that is relevant to real life where
> crystals are small, diffraction weak, and background high, i.e. a
> quantity that can realistically be extracted from the crap we get on
our
> images.
Frank, my point was that in the presence of DS (which for protein
crystals mea
All I'm saying is that when I calculate the average general scattering
from 8192 random configurations of one disordered atom per unit cell:
http://bl831.als.lbl.gov/~jamesh/diffuse_scatter/xtal_diffuse.gif
and then subtract from that the general scattering from an
"occupancy-weighted model" wit
On 28/01/2010 20:20, Ian Tickle wrote:
On another point you said you wanted an 'operational' definition of
I(Bragg). I'm not entirely clear what you mean by that. Are you saying
I believe he means something that is relevant to real life where
crystals are small, diffraction weak, and backg
> If all cells are completely unsynchronized, then the
occupancy-weighted
> average electron density map of all the conformers will fully explain
> the background-subtracted spot intensities, but if there is
> cell-to-cell synchronization: it won't!
This is not correct: as I tried to explain in
On Thursday 28 January 2010 09:57:31 John Badger wrote:
> Hi Ethan,
> Your effort to play devils advocate is appreciated - I have not seen much
> debate on the applicability of TLS so at risk of diverging into a separate
> thread:
>
> I would not argue that TLS is necessarily a valid model for c
John Badger wrote:
Diffuse scatter patterns were compared to simulations of correlated motions
that were long-range (say, the size of the whole molecule) ...
This is exactly not the point I was trying to make. Anything confined
to a single unit cell is not what I would call "long range".
Hi Ethan,
Your effort to play devils advocate is appreciated - I have not seen much
debate on the applicability of TLS so at risk of diverging into a separate
thread:
I would not argue that TLS is necessarily a valid model for correlated motion
in
proteins because it 'works' in fitting the ava
This is the basis of the TAILS "correction" in Scala, but I'm not convinced it
works very well, particularly if you don't have lots of fully recorded
reflections
Phil
On 28 Jan 2010, at 15:41, Dirk Kostrewa wrote:
> Dear James,
>
> Am 27.01.10 10:08, schrieb James Holton:
>
>> I'm still no
Dear James,
Am 27.01.10 10:08, schrieb James Holton:
I'm still not really sure what the difference is between a Bragg spot
and a feature "under" it. Why not define a "Bragg intensity"
operationally? Subtracting local background with a least-squares
plane is pretty much universally done, and
: Re: [ccp4bb] Refining against images instead of only
> reflections
>
> On Wednesday 27 January 2010, John Badger wrote:
> > Colin,
> >
> > Your point:
> > "I think the point here (probably the one you are making)
> is that if
> > crystallograp
On Wednesday 27 January 2010, John Badger wrote:
> Colin,
>
> Your point:
> "I think the point here (probably the one you are making) is that if
> crystallographers produce a pseudo rigid body motion (or static
> disorder) model described by TLS parameters then it would make specific
> predictions
Colin,
Your point:
"I think the point here (probably the one you are making) is that if
crystallographers produce a pseudo rigid body motion (or static
disorder) model described by TLS parameters then it would make specific
predictions of diffuse scatter. These predictions could be used to test
th
[mailto:ccp...@jiscmail.ac.uk] On
> Behalf Of James Holton
> Sent: 27 January 2010 09:09
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Refining against images instead of only
> reflections
>
> John R Helliwell wrote:
> >
> > Dear James,
> > I enjoy
s instead of
only reflections
> -Original Message-
From: owner-ccp...@jiscmail.ac.uk
<mailto:owner-ccp...@jiscmail.ac.uk>
[mailto:owner-ccp...@jiscmail.ac.uk
<mailto:owner-ccp...@
alled "mosaicity" and use learned
>> profiles derived from nearby stronger spots (ignoring the fact that the
>> intrinsic profiles of a hkl and a 6h 6k 6l reflection will be closely
>> related). The normal procedure is obviously very good but we don't know
>>
inal Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On
Behalf Of Ian Tickle
Sent: 22 January 2010 10:54
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refining against images instead of only
reflections
> -Original Message-
From: owner-ccp...@jiscmail.ac.
to:ccp...@jiscmail.ac.uk] On
> Behalf Of Pierre Rizkallah
> Sent: 24 January 2010 00:55
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Refining against images instead of only
> reflections
>
> Hi Colin,
>
> I was slightly disappointed you missed out one thing in your
> cat
ries plus other comments welcome
Regards
Colin
> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On
> Behalf Of Ian Tickle
> Sent: 22 January 2010 10:54
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Refining against images
plus other comments welcome
Regards
Colin
> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On
> Behalf Of Ian Tickle
> Sent: 22 January 2010 10:54
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Refining against images instead of only
> ref
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk
> [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of James Holton
> Sent: 21 January 2010 08:39
> To: CCP4BB@jiscmail.ac.uk
> Subject: Re: [ccp4bb] Refining against images instead of only
> reflections
>
estern.edu
***
- Original Message -
From: John R Helliwell
To: CCP4BB@JISCMAIL.AC.UK
Sent: Thursday, January 21, 2010 3:49 AM
Subject: Re: [ccp4bb] Refining against images instead of only reflections
Dear Jacob,
Your approach I think it is a sound one for explor
Dear Jacob,
Your approach I think it is a sound one for exploring how to gain a
significant potential improvement by harnessing the diffuse diffraction,
which looks rich and varied in many cases ie must surely contain good
structural information. The separation of the various experimental and
cryst
Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On
> Behalf Of James Holton
> Sent: 21 January 2010 08:39
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Refining against images instead of only
> reflections
>
> It is interesting and relevant here I thin
Fax: (716) 898 8660
Skype: eddie.snell Email: esn...@hwi.buffalo.edu
Telepathy: 42.2 GHz
Heisenberg was probably here!
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf
Of Paul Smith
Sent: Wednesday, January 20, 2010 3:00
Fax: (716) 898 8660
Skype: eddie.snell Email: esn...@hwi.buffalo.edu
Telepathy: 42.2 GHz
Heisenberg was probably here!
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf
Of Paul Smith
Sent: Wednesday, January 20, 2010 3:00 PM
To:
ct: Re: [ccp4bb] Refining against images instead of only
reflections
Hi Jacob,
I see you're still in the crystallography business.
While you have an interesting idea, I doubt refining structures
against entire images would be of any use in obtaining higher
quality macromolecular str
bably here!
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Paul
Smith
Sent: Wednesday, January 20, 2010 3:00 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refining against images instead of only reflections
Hi Jacob,
I see you're stil
!
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Paul Smith
Sent: Wednesday, January 20, 2010 3:00 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refining against images instead of only reflections
Hi Jacob,
I see you're still in the crysta
Jacob-
Based on your question, you would likely be interested in doing some
literature searches for the pioneering work of George Phillips and the
utilization of diffuse scattering information. What you are thinking
about has already been broached - nearly 20 yrs ago. It is likely that
a revisit
Hi Jacob,
I see you're still in the crystallography business.
While you have an interesting idea, I doubt refining structures against entire
images would be of any use in obtaining higher quality macromolecular
structures. Much of what you see on the screen is a function of parameters
complet
I agree with Bernhard -- both on the soundness of the idea and on
the difficulty in finding the right home for it in NSF or NIH, but
I would suggest giving it a try. -- Herbert
=
Herbert J. Bernstein, Professor of Computer Science
Dowling C
Dear Jacob:
I think the main impediment is that more diffuse scattering, for example, isn't
as easy to model as Bragg crystalline diffraction. But it is definitely useful.
One example is tRNA:
http://scripts.iucr.org/cgi-bin/paper?am0009
Acta Cryst. (1994). D50, 210-218[ doi:10.1107/S0907
I think these arguments for image conservation and image *use* are well
taken.
The best source of information of what is going on my be the imgCIF
people, - I'd start with Andy Howard and Herbert Bernstein.
I think that image data (after detector- and configuration-specific
corrections to the raw
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