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The WHAT IF list files may contain residues for which certain properties could not be calculated, e.g. it makes no sense to calculate accessibility if the residues have atoms with zero occupancy. WHAT IF now includes these residues in the acc list file with the reason between quotes. We have to find a way to show this to the user.

Suggestion:

• The 'reason' not in the parsed accessibility value range, and should therefore not be within the color range. Instead, the residue should have a distinct color saying "I don't have an acc value".
• A tooltip can say WHY (the reason) doesn't have an acc value.
• The acc values passed to cmbi/proseqjs must either be the acc values or the reason

The user should be able to select either pdb or pdb_redo as a source.

See xssp-rest for the correct implementation to log to the console. This fixes the issue where the supervisor logs are mostly empty.

There are some bugs in the ACC regex. For example, chain can be a number or lowercase character. I will look into this.

The paths for the data files are hardcoded. These should be a setting in the Flask config. It should be a list because for each file type there could be multiple folders. @touwwouter will confirm this and also determine which will have priority.

No log messages are appearing. See cmbi/xssp-api#46 for more details.

YASARA, Yasara, yasara

The output page should also contain links to yasara scenes.

Update the dockerfiles and docker-compose files to match hope, also utilising the scripts for running a development and test environment. This means:

• Use depends_on intead of links in docker-compose file
• Add a dev docker-compose file and run_dev.sh script
• Add a run_tests.sh script
• Put the command in the docker-compose file

Upgrade to proseq 0.0.2.

When a DSP or ACC file isn't found, provide a link to why not

Ensure the bower.json file references 0.0.3.

Add text to the index page describing the service.

All residues show the '^' indicating solvent accessibility, which is incorrect.

The user should be made aware of the tooltip. This can be done at the homepage or with a help button (in this case the other explanations will partly be moved to the help section).

We are behind a reverse proxy. This requires the ReverseProxied middleware (as in bdb_web and xssp-rest) to correctly generate URL's and redirects.

What is supposed to be a download link to a YASARA scene, is plain text.

The .acc and .dsp files must both exist in order for a visualisation to be made. Moreover, if one doesn't exist, it's fatal.

Instead, the visualisation using proseq should be skipped and the error message shown in its place. This means the user still has access to the yasara scenes.

site.css cannot be found and results in an internal server error (500). This is in contrast to a not found (404) error which you would expect.

Despite not being found, there's no obvious problem with the pages, so perhaps the css isn't even needed. Check this.

pdb-vis was introduced in the new facilities paper
http://dx.doi.org/10.1093/nar/gku1028