Dear all
Thanks for all the input both on- and off- the list. We shall definitely
look into these suggestions further and report again here in due course.
Kind regards
Sam
On Tue, 9 Oct 2018 at 19:12, Sam Tang wrote:
> Dear all
>
> Hello. We recently shot a crystal (a protein with small
raised previously on CCP4bb
From: Sam Tang
Sent: 09 October 2018 15:02
To: Nave, Colin (DLSLtd,RAL,LSCI)
Cc: ccp4bb
Subject: Re: [ccp4bb] Weird diffraction pattern
Hello Colin
Although the unit cell dimensions from mosflm should be largely unreliable in
this case, the software actually
Hello Colin
Although the unit cell dimensions from mosflm should be largely unreliable
in this case, the software actually returned a P2 space group with a=24.6,
b=7.5, c=69.5 where b is so short that it resembles a small molecule
crystal.
Regards
Sam
Sam
On Tue, 9 Oct 2018 at 20:53,
Sam
Would this unit cell index some of the spots?
a = 7.00 ± 0.04 A, b = 9.96 ± 0.05 A, c = 6.29 ± 0.04 A.
Colin
From: CCP4 bulletin board On Behalf Of Sam Tang
Sent: 09 October 2018 12:13
To: ccp4bb
Subject: [ccp4bb] Weird diffraction pattern
Dear all
Hello. We recently shot a crystal (a
Hello Tang,
1) For MR, you might want to try a range of homologs, or even a stack of
overlapping homologs. A normal modes server like elNemo might also help
if it can predict the "bend" your molecule undergoes upon binding. A
long shot perhaps, but stranger things have happened. You also
July 28, 2017 2:21 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] weird diffraction pattern
Hi,
Thanks to all who gave me suggestions concerning the weird diffraction pattern
and I really appreciate it that Kay Diederichs help me processing my data set
and answer my questions. Although the dat
Hi,
Thanks to all who gave me suggestions concerning the weird diffraction pattern
and I really appreciate it that Kay Diederichs help me processing my data set
and answer my questions. Although the data set can be processed using HKL3000,
XDS without problems, the Rwork/Rfree values are still
Dear Gerd,
I wasn't really giving much attention to the poke between the
ribs ;-) - for me the more serious matter was to see the merits of
pixel detectors over CCDs made light of, as if they didn't really make
much difference.
If some people get carried away in the way you describe,
Dear Gerard,
my "sound like a sales person" was meant as poking a little fun -
nothing serious, of course.
I and our users like our not-so-new-anymore Pilatus3 6M. It's a great
detector in many ways. But, there is a lot of hype that this detector
solves all-problem, for instance fine
Thanks for spelling it out!
Would that advice still hold if the mosaicity of the crystal is 0.7 degrees?
(I know, I should go read the paper., but . . .)
eab
On 07/13/2017 03:00 PM, Gerard Bricogne wrote:
Dear Gerd,
I can assure you that I have no shares in Dectris nor any
commecial
Dear Gerd,
I can assure you that I have no shares in Dectris nor any
commecial connections with them. What I do have is a lot of still
vivid memories of CCD images, with their wooly point-spread function
that was affected by fine-grained spatial variability as well as by
irredicible
Dear Gerard,
you sound like a sales person for Dectris. Fine slicing is perfectly
fine with CCD detectors - it takes a bit longer because of the step scan
instead of continuous scan. The read noise issue is often overstated
compared to the sample induced scatter background. If for fine
Hi Chenjun,
Few suggestions from my side. Process the data with XDS and look into
acentric intensity distribution (it indicates any twinning possibility).
Run XTRIAGE and SFCHECK to understand any twinning or pseudo translation
possibilities. Twinning can confuse the program and suggest you
- which may well be caused by your cryo-protection or flash-cooling procedure.
I'd try to collect a few images at room temperature to see how good the
crystals can be and if this procedure can be improved.
To prevent overlaps, it may help to find a way to collect the data with the
crystal
Dear Tang,
I noticed that your diffraction images seem to have been recorded
on a 3x3 CCD detector. With this type of detector, fine slicing is
often discouraged (because of the readout noise), and yet with the two
long cell axes you have, any form of thick (or only semi-fine) slicing
would
Hi Jacob,
I have tried seeding approaches but it didn't help.
All best,
Chenjun Tang
Hi David,
Thanks for your comments. Although the spots become streaky in certain
directions, I have processed the data in HKL3000 and imosflm, which suggested
the C2221 space group (66.59, 246.95 and 210.17). The Rmerge(0.14),
completeness(94.8%), redundancy(4.6) are OK. When I tried to run
You've got multiple lattices--try seeding approaches mentioned in a
recent/current thread.
JPK
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ???
Sent: Thursday, July 13, 2017 3:56 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] weird diffraction
Hi,
I'd need to see more processing stats to figure out your data issues. Streaky
spots in certain directions can be indicative of anisotropy and/or lattice
disorders.
However, if your Rfree is above 0.5, it is likely that your molecular
replacement solution is poor/bad/wrong.
HTH,
Dave
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