***
James Holton jmhol...@lbl.gov
Sent by: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK
01/28/2009 09:59 PM
Please respond to
James Holton jmhol...@lbl.gov
To
CCP4BB@JISCMAIL.AC.UK
cc
Subject
Re: [ccp4bb] small lines in diffraction pattern
I'm sure Gloria would be delighted
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)
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
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
http
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
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
out, to my opinion, since the lines appeared on different
...@jiscmail.ac.uk] On Behalf Of Margriet 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
...@astex-therapeutics.com]
Sent: Thursday, January 29, 2009 12:53 PM
To: Schreuder, Herman RD/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 the case of true
; 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 antisense
strand in position 2
B
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?
]
Sent: 29 January 2009 16:26
To: herman.schreu...@sanofi-aventis.com; Ian Tickle
Cc: 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
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
Margriet
This looks like stacking or shift disorder which can occur when perfect
3 dimensional order breaks down. For example one can have a situation
where the lattice is preserved in 2 dimensions but the planes can slide
with respect to one another destroying the order in the 3rd dimension,
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,
Couldn't the lines be explained most simply by extreme mosaicity, perhaps
severely anisotropic? If not, why not? What were the values obtained in
integration?
Jacob
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
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
...@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 values obtained
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) what detector are you using, 2) are
reflections
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
...@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
***
- Original Message -
From: James Holton jmhol...@lbl.gov
To: CCP4BB@JISCMAIL.AC.UK
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
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
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
...@northwestern.edu
***
- Original Message - From: James Holton jmhol...@lbl.gov
To: CCP4BB@JISCMAIL.AC.UK
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
...@northwestern.edu
***
- Original Message - From: James Holton jmhol...@lbl.gov
To: CCP4BB@JISCMAIL.AC.UK
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
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
: 773.608.9185
email: j-kell...@northwestern.edu
***
- Original Message - From: James Holton jmhol...@lbl.gov
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, January 28, 2009 12:20 PM
Subject: Re: [ccp4bb] small lines in diffraction pattern
Hmm. I don't remember
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