Details
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Type: Improvement
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Status: Closed
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Priority: Blocker
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Resolution: Fixed
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Affects Version/s: None
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Fix Version/s: 2.8.2
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Component/s: data retrieval services, na
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Labels:None
Description
Fabrice Jossinet let me know about the new version of the paradise services for running RNAView:
Hi Jim,
i have released a public bitbucket project with documentation and source code samples to use the new RNA web services:
https://bitbucket.org/fjossinet/rna-js-clients/
Concerning the annotation of 3D structures, the URL is now:
http://arn-ibmc.in2p3.fr/api/compute/2d
the parameters are:
- tool=rnaview
- output=raw
- data=<the content of your pdb file> (for a POST request)
Just one remark. It returns you always a JSON array with all the 2D computed associated to a key "2D".
If you used output=raw, the value of the 2D is RNAML data. If you didn't precise any output format, the value of the 2D is JSON data.
You will get has many 2Ds as molecular chains you had in your PDB file.
Let me know if any problem.
This means jalview needs a Json parser now !
Hi Jim,
i have released a public bitbucket project with documentation and source code samples to use the new RNA web services:
https://bitbucket.org/fjossinet/rna-js-clients/
Concerning the annotation of 3D structures, the URL is now:
http://arn-ibmc.in2p3.fr/api/compute/2d
the parameters are:
- tool=rnaview
- output=raw
- data=<the content of your pdb file> (for a POST request)
Just one remark. It returns you always a JSON array with all the 2D computed associated to a key "2D".
If you used output=raw, the value of the 2D is RNAML data. If you didn't precise any output format, the value of the 2D is JSON data.
You will get has many 2Ds as molecular chains you had in your PDB file.
Let me know if any problem.
This means jalview needs a Json parser now !
Attachments
Issue Links
- blocks
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JAL-1028 use rnaview to retrieve annotated PDB entry as RNAML
- Closed