r 27, 2018 5:41 AM
To: Whitley, Matthew J
Cc: ccp4bb
Subject: Re: [ccp4bb] Off topic: 'Difficult' Datasets for Processing Practice
Dear Matthew,
I am also late in responding to this, but as part of a
Nature Protocols paper on iMosflm (Supplementary Information for Na
Hi Matthew, I am also a bit late in responding, I have a few
incommensurately modulated protein crystal datasets that you would be
welcome to use in your course. It would be neat for students to at
least know that this type of diffraction exists. As far as I know,
they can only be processed
Dear Matthew,
I am also late in responding to this, but as part of a
Nature Protocols paper on iMosflm (Supplementary Information for Nature
Protocols 12, 1310-1325, 2017) I provided a number of examples of “problem
datasets”. Some of these are just two images, to show
For some reason, the September 19th ccp4bb digest got caught in my spam filter
and didn't come through until a few minutes ago, so I didn't see several
responses concerning interesting datasets for processing until just now.
Therefore, thanks also to Kay Diederichs, Eugene Osipov, and David
Hi Matthew,
I'm a little late to the thread, but I thought I would still like to add
DPF3b, kindly provided by Wolfram Tempel. This dataset is available on
zenodo and forms the basis of a tutorial for using DIALS:
Dear colleagues,
I want to thank the following people for providing suggestions and comments
about ‘difficult’ datasets suitable for teaching data processing:
Tim Craig
Jacob Keller
Graeme Winter
Aleksandar Bijelic
Clemens Vonrhein
Loes Kroon-Batenburg
James Holton
If anyone else has
It was brought to my attention that the link to the preprint I provided
below doesn't work, but this one does:
https://www.biorxiv.org/content/early/2018/08/18/394965
Thanks to Folmer Fredslund for pointing this out to me!
-James Holton
MAD Scientist
On 9/21/2018 3:50 PM, James Holton wrote:
Hi James,
you’re probably aware of this but you can edit CBF headers in place with
sed. That’s what I do when I make the detector on my diffractometer go
closer than the hardware limit.
All best - Andreas
On Sat, 22 Sep 2018 at 00:51, James Holton
wrote:
> For teaching purposes I have found
For teaching purposes I have found that controlled pairs of data sets
are most instructive. You are right that an easy one-button-push
processing run tells you nothing, but so does a bang-it-crashed-now-what
data set. Most useful are two data sets that are identical in every
respect but one,
Dear Matthew,
In my search for the validity of meta data, I went through several data
sets in SBGrid and proteindiffraction.org (IRRMC), especially those
where automatic processing did not succeed are gave different results
with different processing software. We reprocessed those data sets
Hi Matthew,
I have some notes which indicate that SBgrid data sets 5, 62, 78, 117, 218
posed problems for "automatic" processing using generate_XDS.INP / XDS when I
saw them for the first time.
Some of these problems (mainly the conversion of header values to ORGX ORGY)
are taken care of in
Matthew,
One SBGrid example I used for a workshop was
https://data.sbgrid.org/dataset/218/
This has the “wrong” beam centre as understood by (me/dials/xia2) which causes
a certain amount of fun, nice example for use of the reciprocal lattice viewer
and image viewer in DIALS to make sensible
: [ccp4bb] Off topic: 'Difficult' Datasets for Processing Practice
Dear colleagues,
For teaching purposes, I am looking for a small number (< 5) of macromolecular
diffraction datasets (raw images) that might be considered 'difficult' for a
beginning crystallography student to process. By 'diff
Dear colleagues,
For teaching purposes, I am looking for a small number (< 5) of
macromolecular diffraction datasets (raw images) that might be
considered 'difficult' for a beginning crystallography student to
process. By 'difficult' I generally mean not able to be processed
automatically by
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