XCA feedback from Kate Kot

mwinokan commented 4 months ago

Summarising XCA Feedback provided by Kate Kot in a word document. Likely will need several spin-out tickets.

Getting started

[x] Clearer "outside of Diamond" instructions. E.g. how to install conda & use python 3.10 (partially done, but might need more detail, @mwinokan to ask Kate)

config.yaml

[x] Explicitly specify the need for creation of the output/xchemalign file for the output_dir
[ ] Outdated config-example.yaml

assemblies.yaml

[x] Explain how to get symmetry operator from coot
[ ] The difference between biomol and chains is not clear:

I could not put together an assemblies file myself. A,B,C and C,E,A in example look the same to me, I do not understand the example. Also A and B in mediumcell look the same as A and Asymm in smallcell. I am happy to sit down with someone who knows what’s going on, if they teach this to me I can try and make a more intuitive illustration.

[x] Include yamlchecker.com in the user guide

collating and aligning

[x] Explicitly specify changing to the output/xchemalign folder
[x] Specify that the config and assemblies yaml's should be in the above folder
[x] Better XCA collation errors when CIF's are missing because of data archival (wontfix)
[x] Warn users that the collation step may take long
[x] More verbose XCA aligning output (progress bar?): @tdudgeon says there's plenty of output

Upload into Fragalysis

[x] Docs: explain difference between staging and production
[x] Instructions on how to fill in the upload form (maybe this should be on the loader screen)
[x] Explain how to track the progress of the upload:

Make instructions about how to fill out the upload form e.g. fill in target access string, email, attach zipped folder and click post. Leave media type and content box empty. After clicking post a url is generated which should be posted into new tab after “xchem.fragalysis.diamond.ac.uk/” to see progress of the upload. All of that is not obvious and not stated anywhere in the user guide.

[x] Explain how target access is linked to ISpyB proposals to reassure users their data is not open to the public

mwinokan commented 4 months ago

@mwinokan to take care of the docs changes, @ConorFWild can help explain the biomol/chains on Friday

mwinokan commented 3 months ago

@ConorFWild please add comments/docs for the following two points:

[x] Explain how to get symmetry operator from coot
[ ] The difference between biomol and chains is not clear:

mwinokan commented 3 months ago

Sat down with @ConorFWild and looked at the documentation, we think it is sufficient for now, and confusion from future users is best resolved in one to one conversations as the docs couldn't cover all the edge cases.

mwinokan commented 1 month ago

@mwinokan to fix the example config.yaml (check with @tdudgeon if needed)

@Waztom please show the latest diagram to @phraenquex

m2ms / fragalysis-frontend