Discussion group for the ARIA software

[Benjamin Bardiaux <bardiaux AT pasteur.fr>]

Dear Julien,

You can have a look in temporary folder for refine.out files (actual CNS 
output).
I'm no expert google-drive ocamlfuse but maybe try also a local drive just to 
be sure.
Regarding ARIAweb, it should produce very similar results to the local 
version with the same data/paremeters.

Best,

Benjamin

On 05/10/2020 14:08, Julien CAPPELE wrote:
> Hello everyone,
>
> I am sorry to disturb again, as I encountered another error, and again I can't understand what is wrong. I didn't find 
> anything using google yet.
>
> I have been able to compile CNS 1.2 and now it can be launched correctly from the terminal. On my project this time (not 
> the tutorial of CcpNmr), I have set up an XML file for aria to work. Using the GUI, the project was completed and then I 
> used :
> $ aria2 -s test_aria.xml   # test_aria.xml is the name of the xml file that I 
> used
> $ aria2 test_aria.xml
> Everything started and the structure calculation began. However, a few minutes later, I received some messages saying 
> that the whole 20 structure calculation failed, and that I should check CNS output for errors. (I joined a screenshot in 
> png format for you to see the output).
>
> The thing is, the path to CNS output is empty. There are no cns files there. And I didn't find any files of use yet. Has 
> anyone encountered a similar error?
>
> There are multiple options that I can already consider :
>
> 1. I'm using google-drive ocamlfuse to work with my cloud, and maybe it is a problem for whatever reason. I can allocate 
> more space to my ubuntu partition and do copy all the files to a local space. But i'm skeptical about that, it shouldn't 
> be a problem.
>
> 2. CNS compiled without visible errors, but is not functional yet. I really don't know how to do better than I already 
> did with my last question.
>
> 3. I could stop using local Aria and try AriaWeb but as I am new to NMR structure calculation, I do not know how to set 
> up the parameters correctly. The jobs I tried to launch did not produce anything decent yet. My NMR supervisor also 
> tried with one of her older projects that resulted with a publishable structure on Aria2 locally, but with AriaWeb she 
> didn't get a good result either with the default parameters.
>
> I have been struggling with these NMR structure calculations for over a month now, and starting to lose faith. Please 
> help me, I don't really want to deal with bad x-ray diffraction nightmares again!
>
> Thanks again,
> ---------------------------------------------
> Julien Cappèle
> Doctorant - 3ème année - ED C2MP
> Université de Lorraine
> CRM² - UMR CNRS 7036
> julien.cappele@ <mailto:juliencappele AT gmail.com>univ-lorraine.fr 
> <https://urldefense.com/v3/__http://univ-lorraine.fr__;!!JFdNOqOXpB6UZW0!7eTTaYCuO-jM7ogG79OuK4eLEJkQBMwryMYzqu-3cvuOMNC4UztaXpBwiNs0pjcx3g$>*
> *
> Tel: (+33)6 99 18 59 03
> ---------------------------------------------


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Dr Benjamin Bardiaux      bardiaux AT pasteur.fr
Unité de Bioinformatique Structurale
CNRS UMR3528 - Institut Pasteur
25,28 rue du Docteur Roux 75015 Paris, France
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