-ccp...@jiscmail.ac.uk]
On
Behalf Of James Holton
Sent: 29 January 2010 09:43
To: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Refining against images instead of only
reflections
All I'm saying is that when I calculate the average general scattering
from 8192 random configurations
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
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 with
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] Refining against images instead
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
crystallographers produce a pseudo rigid body motion (or static
disorder) model described by TLS parameters
Dear James,
Am 27.01.10 10:08, schrieb James Holton:
snip
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,
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:
snip
I'm still not
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
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
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 a
Of
James Holton
Sent: 21 January 2010 08:39
To: CCP4BB@jiscmail.ac.uk mailto:CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Refining against images instead
of only reflections
It is interesting and relevant here I think
...@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 enjoyed your simulations.
Thank you!
Re your conclusion:-
However
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
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 of
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 reflections
-Original Message
...@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.uk
[mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of James Holton
...@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
categories:
The ice rings. Now if you can model
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.uk
-
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.uk
[mailto:owner
-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
It is interesting and relevant
!
-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
] 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 think that if you
measure background-subtracted spot intensities you actually
are measuring the AVERAGE
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
***
- 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 exploring how
Dear Crystallographers,
One can see from many posts on this listserve that in any given x-ray
diffraction experiment, there are more data than merely the diffraction
spots. Given that we now have vastly increased computational power and data
storage capability, does it make sense to think
] Refining against images instead of only reflections
Dear Crystallographers,
One can see from many posts on this listserve that in any given x-ray
diffraction experiment, there are more data than merely the diffraction
spots. Given that we now have vastly increased computational power and data
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[
.
-
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jacob
Keller
Sent: Wednesday, January 20, 2010 9:47 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Refining against images instead of only reflections
Dear
] Refining against images instead of only reflections
Dear Crystallographers,
One can see from many posts on this listserve that in any given x-ray
diffraction experiment, there are more data than merely the
diffraction spots. Given that we now have vastly increased
computational power
detector
which makes the process of analyzing images moot.
--Paul
--- On Wed, 1/20/10, Jacob Keller j-kell...@md.northwestern.edu wrote:
From: Jacob Keller j-kell...@md.northwestern.edu
Subject: [ccp4bb] Refining against images instead of only reflections
To: CCP4BB@JISCMAIL.AC.UK
Date
images instead of only reflections
Dear Crystallographers,
One can see from many posts on this listserve that in any given x-ray
diffraction experiment, there are more data than merely the diffraction
spots. Given that we now have vastly increased computational power and
data
storage capability
-
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 crystallography business.
While you have
!
-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
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 structures. Much of what you see
...@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: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refining against images instead of only
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