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intermine / bluegenes-protein-visualizer

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Explain what the colors mean #11

Closed heralden closed 4 years ago

heralden commented 4 years ago

Display a link (or legend) explaining what the different colors in the viewer signify.

We would probably have to dig into bio-pv to find this information. https://pv.readthedocs.io/en/v1.8.1/

akshatbhargava123 commented 4 years ago

Hi @uosl , actually I couldn't find color significance on the pv docs page. Could you please have a look at this (https://www.rcsb.org/pages/help/3dview), the color scheme section if that helps.

heralden commented 4 years ago

Thanks for looking! The By Element/CPK color scheme is actually correct, and you can find a more exhaustive reference on Wikipedia.

It seems the PV documentation also mentions this page, under pv.color.uniform which I assume is the default coloring. https://pv.readthedocs.io/en/v1.8.1/coloring.html#available-color-operations

If you could take the table from Wikipedia, (just remove the third column, as having the color and the name of the gases should be enough) make it small and compact and perhaps put it at the bottom of the PV, it would make a great solution.

PS: Rachel said it would be very useful to also support coloring by secondary structure. I'll create a new issue for this with more information, so don't worry about this now.

bistaastha commented 4 years ago

@uosl @akshatbhargava123 Hi! Can I work on this?

akshatbhargava123 commented 4 years ago

@bistaastha sure, that would really help!