mmCIF 6mit hangs

[tic20@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-957.10.1.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.9 (2019-04-03)
Description
ChimeraX hangs when trying to open 6mit from the .cif file (whether using `open 6mit` to fetch from the wwPDB, or using `open 6mit.cif` to open a local copy). Opening from the PDB file appears to work fine.

OpenGL version: 3.3.0 NVIDIA 415.27
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Eric Pettersen]

opening 6mit did not hang on my mac, nor on two Ubuntu 18.04 boxes I tried, using the current daily build

[Tristan Croll]

Still happening on my CentOS machine, using today's RedHat RPM. Seems specific to 6mit.cif - everything else seems to open just fine. It's a true hang - i.e. top reports zero CPU usage for ChimeraX. I wonder if it's timing out trying to fetch some component from the CCD?

[Tristan Croll]

Still hanging after ~20 minutes (although now I see ~2% CPU use). Will see if I can add a little logging to see where it's hanging).

[Tristan Croll]

... and now it's working (and continues to work if I delete ChimeraX's download cache in ~/Downloads). Go figure...

I did notice that there's no timeout specified in chimerax.core.fetch.retrieve_url() - my understanding is that in this case the Python default is to never time-out. Might be behind it?

[Greg Couch]

Added timeout to fetch_file. Using a minute as the default, and 15 seconds for CCD files.