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Re: [dddwg] To contribute to Open Science using Zenodo Ifound quite straightforward

Kamil
If you take a look at the nexus nxmx format you should see that most of this is solved. Indeed it was resolved 20 years ago but no one used imfCIF...
That said the list of software which will natively process this data is not long...
Zip of images does actually work though I agree is far less elegant a solution
Best wishes Graeme
On 27 Sep 2016, at 17:12, Kamil Dziubek <rumianek@amu.edu.pl<mailto:rumianek@amu.edu.pl>> wrote:
Simon -
- thanks for the update. Your example may be just a model solution for the commercial diffractometer companies software managers on how to format the diffraction data for the purpose of data sharing (and it can actually encourage them to add an 'export button' in data collection/reduction programs!) Just we need to be sure that your data could be easily imported by anyone, even without access to the commercial software you were using for data analysis. Not only the image format is important, also axes description.
I am afraid I do not remember if the standard setting of goniometer geometry was unanimously decided. I remember the paper(s) by Loes and John but here the situation is more complicated - multiple runs, description and rotation sense of the axes, the difference between the kappa-axis geometry and Eulerian craddle machines, etc.
Best wishes,Kamil
Sent from my iPhone
On 28 Sep 2016, at 00:42, Coles S.J. <S.J.Coles@soton.ac.uk<mailto:S.J.Coles@soton.ac.uk>> wrote:
Thanks everyone – I’ll have a play around (particularly when I am not at home on a ‘rural’ network!).
My example is a small molecule single crystal diffraction experiment on a commercial diffractometer (although it is far from being a small structure!!). We have the bulk of the paper written so I just need to ‘top and tail’ it, sort out ESI and put it into a template and I will then upload raw data to get a citable DOI (all this depends on how well I cope with the start of the academic year!). Zenodo certainly looks like a good option, but I cant see a way of bulk downloading files? Graeme’s suggestion, blended with Andy’s, would seem to be the approach that should be “recommended” ie take the images from each run and wrap in HDF5 container (although I will have to put some more effort in to make the latter happen!).
All the best,Simon.
Simon Coles FRSC, SFHEA.Professor of Structural Chemistry.Director, UK National Crystallography Service.Chemistry, Faculty of Natural and Environmental Sciences,University of Southampton.Southampton, SO17 1BJ. UK.+44(0)2380596721Staff Page: http://www.soton.ac.uk/chemistry/about/staff/sjc5.pageNCS: http://www.ncs.ac.uk | Southampton Diffraction Centre: http://www.soton.ac.uk/sdcResearcherID: http://www.researcherid.com/rid/A-1795-2009 | ORCID: http://orcid.org/0000-0001-8414-9272

From: Kamil Dziubek <rumianek@amu.edu.pl<mailto:rumianek@amu.edu.pl>>Date: Tuesday, 27 September 2016 at 15:56To: "mail=s. uk" <S.J.Coles@soton.ac.uk<mailto:S.J.Coles@soton.ac.uk>>Cc: "john.helliwell@manchester.ac.uk<mailto:john.helliwell@manchester.ac.uk>" <john.helliwell@manchester.ac.uk<mailto:john.helliwell@manchester.ac.uk>>, "dddwg@iucr.org<mailto:dddwg@iucr.org>" <dddwg@iucr.org<mailto:dddwg@iucr.org>>Subject: Re: [dddwg] To contribute to Open Science using Zenodo I found quite straightforward

Hello Simon,
Good to hear from you! Is your example a small molecule crystallography experiment carried out using a commercial diffractometer? Since all the other examples so far have concerned biocrystallography, I would be delighted to see it, especially the way of addressing different experiment strategies (series of omega and phi scans, etc.) In what format are you going to store the images?
Best regards and wishes,
Kamil
On 2016-09-27 23:27, Coles S.J. wrote:John,
This is very good to hear!
I personally have an example where I wish to make the images available for a data collection associated with a remarkable structure we are going to submit to an IUCr journal quite soon. The primary reason I want to make the raw data available is so that others can take them and 'have a go themselves' to see if they can come up with a different / better model.
All fine – but I note you uploaded individual images? Or did Zenodo unpack a zipfile? I don't want to go through the effort of uploading 300 individual files – and I'm absolutely sure nobody wants to go through the effort of downloading 300 individual files to reprocess and reuse the dataset! Is there a reason for this - why not bundle them together in a package of some sort (Zip too big)? Or am I missing something?
Thanks!Simon.
Simon Coles FRSC, SFHEA.Professor of Structural Chemistry.Director, UK National Crystallography Service.Chemistry, Faculty of Natural and Environmental Sciences,University of Southampton.Southampton, SO17 1BJ. UK.+44(0)2380596721Staff Page: http://www.soton.ac.uk/chemistry/about/staff/sjc5.pageNCS: http://www.ncs.ac.uk | Southampton Diffraction Centre: http://www.soton.ac.uk/sdcResearcherID: http://www.researcherid.com/rid/A-1795-2009 | ORCID: http://orcid.org/0000-0001-8414-9272

From: dddwg <dddwg-bounces@iucr.org<mailto:dddwg-bounces@iucr.org><mailto:dddwg-bounces@iucr.org>> on behalf of "john.helliwell@manchester.ac.uk<mailto:john.helliwell@manchester.ac.uk><mailto:john.helliwell@manchester.ac.uk>" <john.helliwell@manchester.ac.uk<mailto:john.helliwell@manchester.ac.uk><mailto:john.helliwell@manchester.ac.uk>>Date: Tuesday, 27 September 2016 at 14:48To: "dddwg@iucr.org<mailto:dddwg@iucr.org><mailto:dddwg@iucr.org>" <dddwg@iucr.org<mailto:dddwg@iucr.org><mailto:dddwg@iucr.org>>Subject: [dddwg] To contribute to Open Science using Zenodo I found quite straightforward
Dear Colleagues,I imagine that it will be of general interest that to contribute to "OpenScience" harnessing Zenodo is quite straightforward ie:- preprint and raw data uploaded and assigned dois on Sept 24th 2016 and then for good measure announced on my twitter account @HelliwellJohn on Sept 25th 2016:-
#OpenScience Our atomic resolution cisplatin lysozyme study; the dois are here:- http://doi.org/10.5281/zenodo.155068 http://doi.org/10.5281/zenodo.154704
The PDB code (5LXW) is cited in the preprint at the first Zenodo doi above. My instruction to PDB to release the entry 5LXW I made on Sept 25th 2016.
Greetings,John
Emeritus Prof of Chemistry John R Helliwell DSc_PhysicsPerspectives in Crystallography<https://outlook.manchester.ac.uk/owa/redir.aspx?SURL=JLjRW0_uSO2uCWXoeK-_YEiBuCJ_wkHJ5QxVDbIIAj0l57JRLfrSCGgAdAB0AHAAcwA6AC8ALwB3AHcAdwAuAGMAcgBjAHAAcgBlAHMAcwAuAGMAbwBtAC8AUABlAHIAcwBwAGUAYwB0AGkAdgBlAHMALQBpAG4ALQBDAHIAeQBzAHQAYQBsAGwAbwBnAHIAYQBwAGgAeQAvAEgAZQBsAGwAaQB3AGUAbABsAC8AOQA3ADgAMQA0ADkAOAA3ADMAMgAxADAAOQA.&URL=https%3a%2f%2fwww.crcpress.com%2fPerspectives-in-Crystallography%2fHelliwell%2f9781498732109>
Skills for a Scientific Life<https://www.crcpress.com/Skills-for-a-Scientific-Life/Helliwell/p/book/9781498768757>_______________________________________________dddwg mailing listdddwg@iucr.org<mailto:dddwg@iucr.org><mailto:dddwg@iucr.org>http://mailman.iucr.org/cgi-bin/mailman/listinfo/dddwg



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