[ccp4bb] General interest re research data

2020-09-01 Thread John R Helliwell 
Dear Colleagues,
A couple of research data matters that I imagine will be of general interest I 
have placed at the IUCr CommDat Forum:-
The Photon and Neutron EU Facilities Open Science Cloud announced their “doi 
per experiment” described in this 3 minutes youtube movie clip
https://forums.iucr.org/viewtopic.php?f=39=431

Secondly, the Swiss Universities Bulletin have produced a special issue on 
Research Data Management, to which I have contributed an article on Open 
science and the reproducibility of the scientific record
https://forums.iucr.org/viewtopic.php?f=39=432

Best wishes,
John 
Emeritus Professor John R Helliwell DSc
Chairman of the IUCr Committee on Data





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[ccp4bb] PDBe API webinar series - starts September 15th 2020

2020-09-01 Thread John Berrisford 
Dear CCP4BB

 

We are excited to be offering a 6-part PDBe API webinar series, introducing
different levels of programmatic access at PDBe, starting on the 15th
September.

 

This webinar series will range from basic data retrieval and search using
the PDBe API to more advanced features, including access and reuse of PDBe
data visualisation components.

The webinars are free to attend but the number of registrations are limited,
therefore it is recommended that you sign up in advance to avoid
disappointment. Each webinar has its own individual registration so please
sign up for all those that you wish to attend.

 

For more details about the webinars and to register, please visit

https://www.ebi.ac.uk/pdbe/about/events/pdbe-api-webinar-series

 

Kind Regards,

John

 

--

John Berrisford

PDBe

European Bioinformatics Institute (EMBL-EBI)

European Molecular Biology Laboratory

Wellcome Trust Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

  http://www.pdbe.org

 
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Re: [ccp4bb] Problems with iMosflm under CCP4i2

2020-09-01 Thread Harry Powell - CCP4BB 
Hi folks

Thank for the name-check Jon - I haven’t been employed on the Mosflm project 
since 2016, but it’s nice to be remembered.

The place to look for a more definitive answer to the problem is in the 
date-stamped mosflm.lp file (called something like mosflm_202008319_124743.lp) 
which will give more information. It’s also worth looking at the History->Log 
tab in iMosflm (which gives a nice Tektronix 4010 rendering…) which may also 
indicate problems.

The current version of CCP4 is distributed with the current iMosflm version 
(version 7.3.0, built by Charles Ballard on Thursday, May 07 2020 at 16:24) - 
so the first thing I would check is that your installed (and running…) version 
of CCP4 is the latest (use the update manager) - until I updated this morning 
it seemed to be running iMosflm 7.2.2 (which is obsolete and will probably give 
the “…detector type MAR” error).

The second thing I’d do after that is download and run the definitive iMosflm 
from the MRC website:

> https://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver730/introduction.html


and see if the problem persists with that. If it does, the best thing to do 
then is to discuss it with Andrew…

Harry

> On 30 Aug 2020, at 22:43, Jon Cooper 
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Re: "I think MAR is the default detector, so I guess for some reason the 
> image header is not getting read correctly or is missing..."
> 
> Thanks for the proper explanation, Mark. 
> 
> Indeed the manual says:
> 
> "Default: DETECTOR defaults to MAR"
> 
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
> 
> 
> 
> 
> 
>  Original Message 
> On 30 Aug 2020, 18:20, Mark J van Raaij < mjvanra...@cnb.csic.es> wrote:
> 
> Hi Jon,
> I think MAR is the default detector, so I guess for some reason the image 
> header is not getting read correctly or is missing...
> (I wrote this to Yahui also)
> 
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> 
> 
> 
>> On 30 Aug 2020, at 19:16, Jon Cooper 
>> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> Apologies, I see that MAR now sell the Pilatus 200K detector, which may 
>> partly explain things.
>> 
>> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>> 
>> 
>> 
>> 
>> 
>>  Original Message 
>> On 30 Aug 2020, 18:03, Jon Cooper < 
>> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> Hello, have you installed the latest version of ccp4 or could you post the 
>> version number for mosflm that you are using? I know Harry has a penchant 
>> for detectors of all ages: 
>> https://doi.org/10.1080/0889311X.2019.1615483
>> 
>> but I have no idea why mosflm would think yours is one of these as they have 
>> not really been around for some time:
>> 
>> https://1.bp.blogspot.com/-Y3HEe2KTczg/X0rPRm3ffNI/AfQ/EeSLElXobsUG-uIlWpU4BruLO3J6CChjACLcBGAsYHQ/s2048/IMG_1032.JPG
>> 
>> (Picture c/o P. McArdle)
>> 
>> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>> 
>> 
>> 
>> 
>> 
>>  Original Message 
>> On 30 Aug 2020, 13:09, Yahui Liu < liuyahui1...@gmail.com> wrote:
>> 
>> Dear CCP4er,
>> I have some problem in loading the data(taken with a Dectris Pilatus 200K 
>> detector) with iMosflm.
>> The iMosflm showed the error message  “Error reading image header. Message 
>> from Mosflm is Incorrect size of image for detector type MAR” first (see the 
>> attachment), and  quit directly.
>> 
>> After that, I got another error in CCP4i2(the second attachment).
>> 
>> Dr.Andrew Leslie was kind and test my data with iMosflm alone, it was 
>> totally fine for him to open my images.  
>> It seems like this only happened when we start iMosflm in CCP4i.
>> 
>> Any one has some suggestions?
>> 
>> 
>> Best
>> Yahui
>> 
>> 
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> 
> 
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