lerskating
***
James Holton
Sent by: CCP4 bulletin board
01/28/2009 09:59 PM
Please respond to
James Holton
To
CCP4BB@JISCMAIL.AC.UK
cc
Subject
Re: [ccp4bb] small lines in diffraction pattern
I'm sure Gloria would be delighted if that were the case, but I don'
, January 29, 2009 5:26 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Small lines in diffraction pattern (more info)
Ian and Herman,
does one want to convolute the electron density at all? I was under the
impression that current thinking favors convolution of the model instead, i.e.
placing
So it would seem that the five-fold periodicity in the spot intensities
along the long axis is probably due to a short-range, 34 Ang pseudo-repeat
(the decamer) along the true 170 Ang cell axis (170 = 34 x 5).
I do not think that the streaks are helical layer lines, because the spacing
on the
FILETIME=[831110D0:01C9822E]
Yes I agree with that!
-- Ian
> -Original Message-
> From: Andreas Förster [mailto:docandr...@gmail.com]
> Sent: 29 January 2009 16:26
> To: herman.schreu...@sanofi-aventis.com; Ian Tickle
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [cc
Ian and Herman,
does one want to convolute the electron density at all? I was under the
impression that current thinking favors convolution of the model
instead, i.e. placing both the helices in both orientations at partial
occupancy and letting the refinement program figure things out?
An
riet.ova...@chem.kuleuven.be; CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] Small lines in diffraction pattern (more info)
Dear Margriet,
From your description and what James Holton wrote, it seems
that you have 2 types of unit cells:
A: with the "sense" strand in position 1 and the "
...@astex-therapeutics.com]
Sent: Thursday, January 29, 2009 12:53 PM
To: Schreuder, Herman R&D/DE; margriet.ova...@chem.kuleuven.be;
CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] Small lines in diffraction pattern (more info)
Hi Herman
Aren't detwinning methods appropriate only in th
leuven.be; CCP4BB@JISCMAIL.AC.UK
> Subject: RE: [ccp4bb] Small lines in diffraction pattern (more info)
>
> Dear Margriet,
>
> From your description and what James Holton wrote, it seems
> that you have 2 types of unit cells:
> A: with the "sense" strand in position 1
argriet Ovaere
Sent: Thursday, January 29, 2009 10:45 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Small lines in diffraction pattern (more info)
Dear all,
There were some comments about detector issues, but these can be ruled
o
The 34-34-34 cell does not predict all the spots, does it?
from the diffraction pattern it seems only the 34-34-170 or 34-34-340
cell can predict all spots, so the structure should be solved in the
one that predicts all spots.
The procedure I would use is to take a 180º dataset, sacrificing so
Colin
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Jacob Keller
Sent: 28 January 2009 18:05
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] small lines in diffraction pattern
Acta Cryst. (1998). D54, 848-853[ doi:10.1107/S0907444998001875
Dear all,
There were some comments about detector issues, but these can be
ruled out, to my opinion, since the lines appeared on different
beamlines.
Default settings of mosflm (spot picking) finds the cell 34 34 34 90
90 90 (pointless indicating P41212)
Structure was solved by SAD ph
Hi Stephan,
If there were overflows on the detector, which cause lines due to the
spill over of the wells of the CCD, the lines would be visible in the
readout direction of the CCD detector, which generally is from bottom to
top or top to bottom. You can also see this with your own (pocket)
c
Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
***
- Original Message ----- From: "James Holton"
To:
Sent: Wednesday, January 28, 2009 12:20
I'm sure Gloria would be delighted if that were the case, but I don't
think this is an incommensurate lattice. These actually don't so much
give you diffuse scattering as little satellite spots near the main
spots at spacings that don't make any sense given the lattice repeat.
My understandin
s Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
***
- Original Message - From: "James Holton"
To:
Sent: Wednesday, January 28, 2009 12:20 PM
Subject: Re: [ccp4bb] small lines in diffraction pattern
H
s Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
***
- Original Message - From: "James Holton"
To:
Sent: Wednesday, January 28, 2009 12:20 PM
Subject: Re: [ccp4bb] small lines in diffraction pattern
Hi James,
what your descriptions aims at is I think shown in this publication
Borgstahl, G. E. O. "Incommensurate Crystallography by Sander van
Smaalen" Crystallography reviews 14 , 259-260 (2008).
Or am I misunderstanding something here ?
Jürgen
On 28 Jan 2009, at 12:39, James Holton wrot
I'm coming in late here, having only now found time to look at the images.
It's facinating, isn't it?
Since the lines are not arcs centered on the origin, this isn't mosaic
spread.
For those who haven't seen the image and the zoom, the diffraction pattern
clearly shows one very long axis and
***
- Original Message -
From: "James Holton"
To:
Sent: Wednesday, January 28, 2009 12:20 PM
Subject: Re: [ccp4bb] small lines in diffraction pattern
Hmm. I don't remember that thread. However, I personally think it is a
good idea to keep the "mosaic crystal&
Hmm. I don't remember that thread. However, I personally think it is a
good idea to keep the "mosaic crystal" as Ewald and Darwin defined it.
Just because current integration software lumps things together into a
"mosaicity" does not mean that every mechanism contributing to the
rocking widt
...@northwestern.edu
***
- Original Message -
From: Jacob Keller
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, January 28, 2009 11:57 AM
Subject: Re: [ccp4bb] small lines in diffraction pattern
I had thought that in a previous thread, we had all come to a
Re: [ccp4bb] small lines in diffraction patternI had thought that in a previous
thread, we had all come to a consensus that actually the largest source of what
is normally explained as "mosaicity" is really differences in unit cell size,
due perhaps to uneven shrinkage in crystals upon freezing
Sent: 28 January 2009 17:43
> To: Margriet Ovaere; CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] small lines in diffraction pattern
>
> Hi Such line can occur on a CCD detector if reflection
> are saturating a pixel and is generally in the direction of
> the detector readout. 1)
mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jacob
Keller
Sent: 28 January 2009 17:05
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] small lines in diffraction pattern
Couldn't the lines be explained most simply by extreme mosaicity, perhaps
severely anisotropic? If not, why not? What were the val
I recommend you have a look at a book from OUP called "Diffuse X-Ray
Scattering and Models of Disorder" by T. R. Welberry. The first chapter
explains quite well (I think) where all these streaky things come from.
It will also make you feel better about having it when you see all the
small mol
ry 28, 2009 7:51 AM
Subject: [ccp4bb] small lines in diffraction pattern
Dear all,
In the diffraction pattern of crystals of an RNA decamer, small lines
appeared (see pictures attached). We've tried different crystals but they all
showed the same small lines. �Has anybody seen this
Hi Margriet
It's almost certainly due to diffuse scattering as a result of
correlated atomic displacements. See this:
http://www.nature.com/nsmb/journal/v1/n2/pdf/nsb0294-124.pdf .
Are they lines or sheets, in other words do they appear only on one
image, or are they also on adjacent images, i.e
uk] On Behalf Of
Margriet Ovaere
Sent: 28 January 2009 13:52
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] small lines in diffraction pattern
Dear all,
In the diffraction pattern of crystals of an RNA decamer, small lines
appeared (see pictures attached). We've tried different crystals but
they all
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