cmbi / bdb-web Goto Github PK

Calpha only Boolean not shown on bdb metadata page.

tlsanl_log and b_plots raise valueerrors with invalid pdb identifiers.
Incorporate exception handling in next release

Perhaps we should include the number of skttls outliers (listed in the tlsanl.log files, see cmbi/bdb/issues/17) on the bdb pages.

Change POST to GET search

Even though this should be prevented in b_plot.py, the following Exception is raised sometimes:

Exception on /bplot/2wja.png [GET]

Traceback (most recent call last):
File "/srv/www/bdb-web/.virtualenvs/bdb-web/local/lib/python2.7/site-packages/flask/app.py", line 1817, in wsgi_app
response = self.full_dispatch_request()
File "/srv/www/bdb-web/.virtualenvs/bdb-web/local/lib/python2.7/site-packages/flask/app.py", line 1477, in full_dispatch_request
rv = self.handle_user_exception(e)
File "/srv/www/bdb-web/.virtualenvs/bdb-web/local/lib/python2.7/site-packages/flask/app.py", line 1381, in handle_user_exception
reraise(exc_type, exc_value, tb)
File "/srv/www/bdb-web/.virtualenvs/bdb-web/local/lib/python2.7/site-packages/flask/app.py", line 1475, in full_dispatch_request
rv = self.dispatch_request()
File "/srv/www/bdb-web/.virtualenvs/bdb-web/local/lib/python2.7/site-packages/flask/app.py", line 1461, in dispatch_request
return self.view_functionsrule.endpoint
File "/srv/www/bdb-web/bdb-web/bdb_web/views.py", line 50, in bplot
fig = b_plot.show(pdb_id, ca=False)
File "/srv/www/bdb-web/bdb-web/bdb_web/b_plot.py", line 112, in show
canvas.print_png(output)
File "/srv/www/bdb-web/.virtualenvs/bdb-web/local/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", line 505, in print_png
FigureCanvasAgg.draw(self)
File "/srv/www/bdb-web/.virtualenvs/bdb-web/local/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", line 446, in draw
self.renderer = self.get_renderer(cleared=True)
File "/srv/www/bdb-web/.virtualenvs/bdb-web/local/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", line 465, in get_renderer
self.renderer = RendererAgg(w, h, self.figure.dpi)
File "/srv/www/bdb-web/.virtualenvs/bdb-web/local/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", line 84, in init
self._renderer = _RendererAgg(int(width), int(height), dpi, debug=False)
ValueError: width and height must each be below 32768

B-factors are 'likely residual' according to PDB remediations, not just 'residual'. Change accordingly, details matter.

Safari on iphone: does not render \rangle and \langle
Chromium: does not support mathml, only in version 24 (not lower/higher).
Internet Explorer does not support MathML natively. MathPlayer plugin needed.

Change back to mathjax and update pandoc on server?

Either github or tar.gz

Normalize per chain instead of per structure

e.g. 2lt9 (NMR) or 2vv8 (no BDB)

The flask-wtf session secure Form class with CSRF protection is used. Therefore cookies are required.

Explain that the overall scale may or may not be included in the B-factors of some files and provide references.

The top link, named after the id, directly under 'BDB Metadata', should be text only when the BDB file is unavailable.

Incorrect order of refinement program versions on bdb metadata page. Should be consistent with order of refinement programs obviously.

Use a rolling log file handler for production.

Include assume_iso in bdb template and somehow indicate how the information in the tables was derived (e.g. calculated from coordinates or parsed from remark 3 records).
Example: 4k6k has residual B-factors according to REMARK 3, but the current version of the bdb decision tree decides full B-factors are already present as the B-values can all be reproduced from the ANISOU records.

B-factors might still be on the U^2 scale (8*pi^2 smaller than normal) even though nothing is mentioned in the remarks.
Example: 1amm.

Now an empty search field redirects to the homepage.

An invalid or absent pdbid will lead to a bdb page with a link to WHY_NOT. Maybe catch the ValueError later on and use it to provide the user with info?

Currently, the pdb id is not passed to the WHY NOT search function correctly according to WHY NOT.

Now:
WHY_NOT_SEARCH_URL = "http://www.cmbi.ru.nl/WHY_NOT2/search/pdbid/"
results in "No value specified for parameter pdbid".
This used to work.

WHY NOT issue?

Large plots can take (too) much time

e.g. 3a07, 1zv4
138 seems a maximum on a 23x12 ca plot.