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Notes on Session 4
Leighton Pritchard edited this page Mar 7, 2018
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- comments in the JMol scripts to explain each step would be helpful
- more explanation of what is the biological intent/reasoning behind each action could help
- copy/paste of scripts slowed things down; can the scripts be saved as files and loaded into the script editor?
- the z-ordering of JMol was annoying! It was very difficult to follow when flicking between the windows. This might be avoided with a higher resolution projector/more screen real-estate
- it’s very much a point and click exercise; might it be good to include examples where we produce a f8nal figure for inclusion in a (fake) publication, including colouring and rotation of the structure
- the black background in JMol looks out of date, maybe setting the background to white would make it look more ‘modern’ and ‘clean’?
- JPred has a REST API, and it might be possible to demonstrate reproducibility with this in a notebook
- SWISS-MODEL has an API through which models/structures can be obtained for UniProt entries: https://swissmodel.expasy.org/docs/repository_help#smr_api - possible to integrate with/refer back to UniProt lesson?