Fetch PDB flatfile from RCSB server

Created: 2008-01-25 11:52:38      Last updated: 2008-03-05 16:11:13

Given aPDB identifier such as '1crn', this workflow fetches the PDB format flatfile from the RCSB

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Review Title: works!

Rating: 5 out of 5

Created: 2008-08-06 22:29:58 | Updated: 2008-08-06 22:29:58

I am now nesting two of these for my workflow. It is dead simple: PDB ID in, structure out. And it was damn quick, too! Tested with 1.7.0.

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  • Sunday 02 November 2008 10:13:13 (UTC)

    It would be good to have some sort of md5 check - because when you use batch downloads, sometimes you can have network problems and not be aware of it.

    Also, you can save the date of the download and the version of pdb database, to make the experiment easier to reproduce.

  • Sunday 02 November 2008 10:15:07 (UTC)

    Also, it could give an error message when the pdb protein doesnt' exists (e.g. un-existing ids, keywords, etc..)

  • Wednesday 18 May 2011 09:17:08 (UTC)

    I agree with Giovanni on the error message / early failure. Still, something like this workflow should be immediately available at startup of Taverna. The novice Taverna user should not need to despair over not finding such basic routines. Same for sequences.

  • Wednesday 18 May 2011 14:11:41 (UTC)

    No idea if this already worked for Taverna 1.7 but for 2.x I am definitely missing an example value for the input port, i.e. 1crn.

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