[Proteopedia] NMR format, bot tasks

Eran Hodis eran.hodis at weizmann.ac.il
Sun Feb 8 09:20:45 EST 2009

Hi Ralf,

On Feb 8, 2009, at 12:10 PM, Ralf Stephan wrote:

> Hello,
> first, to introduce myself, I'm an IT guy, privately interested
> in molecular biology. After writing some time for the german language
> Wikipedia, the lack of 3D visualisation for my protein pages drove
> me to Proteopedia. At the moment, I'm playing.
> Does someone of you know where code can be had that collects
> several structures into one, presumably using the NMR format?
> I know it's easy to do but why reinvent the wheel...
> The question, however, that's bothering me is that IMHO there should
> be a link from any structure page to that topic pages where the
> structure is used. It could be text like 'See also the topics:' at
> the top or a row in the info box 'Topic pages:' or a paragraph in
> the section 'About this structure' reading e.g. 'This structure is
> also used in the pages ...'
> Since it can't be relied on that authors do such backlinks, and this
> can be automatized, it should be automatized at some time.

That's a really great idea if it can be done well. How would you  
suggest doing this (of course automatically)?  Let's say you're on the  
page for 1ea5, do you want to list, on the page for 1ea5, all other  
pages that link to 1ea5?  Or all other pages that link to 1ea5 but are  
not PDB-entry pages?  I'm just worried that such an automatically  
generated list might, in some instances, be long and irrelevant.  Of  
course as you've said, the person who created the Topic page should  
link from the topic page to the PDB entry page and vice versa, but  
they will sometimes neglect to do this.

> On another note, I would like to see a list of all structure pages
> that have been enhanced by other authors than OCA. This should be
> automatized, too.

Eric, at one point you were interested in such a list -- what did you  

> Which leads me to the question, is there a way of running a bot like
> in Wikipedia? I have a one time experience with writing a bot and
> would be willing to write something that does the abovementioned
> tasks in Proteopedia.

Good to know! Let's brainstorm this idea a bit further before talking  
about implementation. As Jaime said, there are currently no user-owned  
bots on Proteopedia, so, at least for now, we would run your bot for  

> Regards,
> ralf
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Eran Hodis
eran.hodis at weizmann.ac.il

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