Along similar lines, if you happen to be working in the DIALS ecosystem there
is the dials.damage_analysis program, which takes the scaled data (scaled.expt,
scaled.refl) and computes a number of statistics including Rd as discussed
below, and the cumulative-pairwise R factor Rcp, which
Hi
I’ve never actually used it in anger (one should never be angry when processing
data…), but doesn’t AutoProc, developed by the good folks at Global Phasing do
a lot of these analyses? Clemens, Claus etc may have something pertinent to say.
Harry
> On 30 Oct 2023, at 13:23, Jorge Iulek
Dear Jorge,
the plots available from XDSGUI in the "statistics" tab are helpful in this
respect (see https://journals.iucr.org/j/issues/2023/05/00/yr5110/index.html
and in particular Fig 4). In particular, delta-CC1/2 and R_d are sensitive to
radiation damage.
Pls note that sometimes a few
Dear Jorge,
If you are using XDS for data processing, XDSCC12 and XDSSTAT (developed
by Kay Diederichs) provide very useful guidance as to where to truncate
your dataset in the rotation dimension. In particular, have a look at
the R_d metric provided by XDSSTAT.
These analyses can also be
Dear all,
I have found many fundamental studies on image processing and
refinement indexes concerning the decision on cutting resolution for a
dataset, always meant to get better models, the final objective. Paired
refinement has been a procedure mostly indicated.
I have been searching
padu 2017 12:01:43
Komu: CCP4BB@JISCMAIL.AC.UK
Předmět: [ccp4bb] Radiation damage to the FAD in enzyme structure
Dear colleagues,
I am investigating a structure of a FAD-dependent enzyme. The electron density
map suggests radiation damage to the FAD. It apparently is different from
s
<malym...@fjfi.cvut.cz>
Reply-To: Martin Malý <malym...@fjfi.cvut.cz>
Date: Tuesday, 7November, 2017 at 05:16
To: "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Radiation damage to the FAD in enzyme structure
Dear Ilme,
thank you for your answer. We ar
,
Martin Maly
Od: Ilme Schlichting <ilme.schlicht...@mpimf-heidelberg.mpg.de>
Odesláno: 6. listopadu 2017 12:38:17
Komu: Martin Malý
Předmět: Re: [ccp4bb] Radiation damage to the FAD in enzyme structure
Hello,
Are you sure you had full occupancy to begin wit
Dear Martin,
A more bleeding-edge type of experiment in the vein David is
indicating would be to use a "rotation SFX" protocol to record
complete data off one or very few crystals that will be completely
exempt from radiation damage, as described in doi:10.1038/nmeth.2962
and in doi:
Some alternative interpretations have been suggested, but if you think
you are seeing radiation damage, you could try collecting data on
several crystals and binning it by dose received. For comparison see:
The catalytic pathway of horseradish peroxidase at high resolution.
Berglund, et al.
..@fjfi.cvut.cz>
Date: Monday, 6November, 2017 at 03:01
To: "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] Radiation damage to the FAD in enzyme structure
Dear colleagues,
I am investigating a structure of a FAD-dependent enzyme. The electron density
map su
Dear Martin,
we experienced the butterfly-like structure of FAD in monoamine oxidases
but this was observed also in other flavoenzymes. Whether this is an
intrinsic feature of these enzymes or something due to radation damage is
not clear for each case. However, in our experience this bent
Dear Martin,
a couple of years ago we had a similar problem with FAD degradation. In
our case it was not caused by radiation damage, but we saw different
ratios of intact and degraded FAD depending on the age of the crystals
[Winkler et al., Nat. Chem. Biol. 4, 739-741 (2008)].
Best
Dear colleagues,
I am investigating a structure of a FAD-dependent enzyme. The electron density
map suggests radiation damage to the FAD. It apparently is different from
simple change of the redox state and "butterfly"-like structure. We did not
find in literature possible products of
of George Sheldrick
[gshe...@shelx.uni-ac.gwdg.de]
Sent: Saturday, April 29, 2017 2:14 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] radiation damage-induced phasing (RIP) tutorial
Dear Murpholino,
I must apologize, there was a mistake in may last email. The critical
parameter is, as you
Dear Murpholino,
I must apologize, there was a mistake in may last email. The critical
parameter is, as you correctly pointed out, DSCA not RIPW and it is
necessary to try a range of values for DSCA. For this reason I am CCing
this to CCP4bb.
As you will be discovering, RIP phasing is not
, April 28, 2017 9:16 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] radiation damage-induced phasing (RIP) tutorial
That's more like a tutorial for XDS :P (thanks though)
The problems:
1) It uses autorickshaw (which is a black box ...guess I'll read the paper
today) ...
and
2) my files were
Dear Murpholino,
I suspect that the pipelines in CCP4i and CCP4i2 do not include RIP
phasing (perhaps they should) but you can also run the SHELX programs
from a command line since you don't like black boxes. SHELXC reads
XDS_ASCII.HKL files and has some special facilities for RIP, you can
That's more like a tutorial for XDS :P (thanks though)
The problems:
1) It uses autorickshaw (which is a black box ...guess I'll read the paper
today) ...
and
2) my files were not recognized (MTZ with proper labels ...even the
XDS_ASCII.HKL files ).
Is it working? Guess I'll try to contact the
There was a tutorial for MX including UV RIP available from the HZB in
Berlin (BESSY MX group). Have a look at there website. I'm sure it is
still available, or maybe they can send you the files on request.
Cheers
Christian
Am 28.04.2017 um 17:12 schrieb Murpholino Peligro:
Hi lads...
Do
Hi lads...
Do you know if there is a good tutorial for doing RIP somewhere on the
internet?
What programs can do RIP?
-SHELX
-AutoRickShaw
-?
Thanks
Dear colleagues,
I would like to draw your attention to an upcoming free, educational webinar to
be presented by Elspeth Garman, Ph. D. titled Radiation Damage in
Macromolecular Crystallography: What is it and why do we care? Radiation
damage inflicted during diffraction data collection in
.
Preben
On 04/10/2010, at 21.48, Jacob Keller wrote:
- Original Message - From: Poul Nissen p...@mb.au.dk
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, October 04, 2010 2:21 PM
Subject: Re: [ccp4bb] Radiation damage with crystals containing metal centers
(TaBr people chime in?)
[1
Hi all
I'm reading a recent review by Elspeth Garman regarding radiation
damage (Acta Cryst D) and in this she mentions two ideas regarding
metal centers:
[1] They (The metal complexes themselves) are quickly reduced
[2] Their absorption causes localized heating in the crystal. (This
The radiation damage with Ta6Br12 collected on the absorption edge is very
severe. There may be a case for avoiding the edge wavelength for this reason
Phil
On 4 Oct 2010, at 17:28, Francis E Reyes wrote:
Hi all
I'm reading a recent review by Elspeth Garman regarding radiation damage
Sent: Monday, October 04, 2010 9:29 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Radiation damage with crystals containing metal centers (TaBr
people chime in?)
Hi all
I'm reading a recent review by Elspeth Garman regarding radiation
damage (Acta Cryst D) and in this she mentions two ideas
[1] the signal from Ta6Br12 is enormous and one will typically focus on low
resolution (below 7 Å) so radiation sensitivity can be handled by a fairly low
dose data collection
We collected several data sets with Ta6Br12(2+) on the Na+,K+-ATPase (Morth JP
et al. 2007) and found that although we
- Original Message -
From: Poul Nissen p...@mb.au.dk
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, October 04, 2010 2:21 PM
Subject: Re: [ccp4bb] Radiation damage with crystals containing metal
centers (TaBr people chime in?)
[1] the signal from Ta6Br12 is enormous and one will typically
Two separate crystals, but very similar data collection strategies
P
On 04/10/2010, at 21.48, Jacob Keller wrote:
- Original Message - From: Poul Nissen p...@mb.au.dk
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, October 04, 2010 2:21 PM
Subject: Re: [ccp4bb] Radiation damage
I am pleased to announce that this year's ACA meeting (Chicago, IL, July
24-29, 2010) will include a return of the highly popular session on
radiation damage. We all know that damage can be a problem, but the
interesting developments over the last few years are that there are
finally some
As much as I hate to see the CCP4BB used for shameless self-promotion of
articles, I did just publish a Beginner's Guide to Radiation Damage:
http://journals.iucr.org/s/issues/2009/02/00/issconts.html
My answers to Paul and Michael's posts would be cut-and-pasted from it,
so I think it
I even made the cover! And I hope that (after looking at the cover) all you
BBers will forgive me just this once as this was clearly a once-in-a-lifetime
opportunity. Or, at least, I HOPE only once.
Congratulations, James. But surely you could have found a better example of
medical imaging?
Gerard DVD Kleywegt wrote:
Congratulations, James. But surely you could have found a better
example of medical imaging? For instance, here:
http://www.ibeatyou.com/competition/867945/craziest-x-ray/entry/be24b3/coke-bottle
--dvd
Unfortunately, (unlike the infamous coke bottle image),
Hi all,
I had an interesting experience, and wonder if others have seen
similar things.
I was collecting data from a crystal that contains an iodinated
macromolecule. After 2 days on a copper rotating anode, with the
crystal at 100 K, we experienced a detector problem, so I put the
)3 88 41 70 02
[EMAIL PROTECTED]
-Message d'origine-
De : CCP4 bulletin board [mailto:[EMAIL PROTECTED] la part de
Patrick Loll
Envoye : Monday, March 03, 2008 6:00 PM
A : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] radiation damage question
Hi all,
I had an interesting
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