Q:
I’m trying to use Conformation Explorer.

I have submitted a job, but looks like Proxy error. Is this server still working?

Server message:
The job ce199231-3887 is not yet completed. Please check again a few minutes to a day from the time of your initial submission.

The proxy server received an invalid response from an upstream server.
The proxy server could not handle the request GET /cgi-bin/morph.cgi.

Reason: Error reading from remote server

Here’s the URL and job ID: http://molmovdb.org/cgi-bin/morph.cgi?ID=ce199231-3887&type=choosehinge

Server message:
The job ce199231-3887 is not yet completed. Please check again a few minutes to a day from the time of your initial submission. If this job is older than a day or so, please contact the server administrator. Email: Mark.Gerstein _at_ yale.eduI wanted to know how conformation of protein changes due to ligand addition.

A:
Unfortunately, the server is experiencing problems and we do not have a developer maintaining this right now. All files generated and related to your submission are in http://www.molmovdb.org/uploads/ce199231-3887/ . The PDB movie file looks like it consists of one frame when viewed in VMD so I do not think a movie was successfully produced by the server.

Q1:
We are running some docking and would like to use genodock for some experiments too. Is it something that we can install on our servers to run? who should we talk to for more details? I have also noticed that the server is currently down. We would actually like to even run on our cloud environment for some more intensive computation. Is there a github or sth or any documentation about it? or would you happen to know more about it?

A1:
The webserver was in a hung state at the moment, but will be back up shortly.

Q2:
We are trying out Genodock on http://genodock.molmovdb.org/calculation/0. But unfortunately none of the models worked.

A2:
There’s enough file space in the device and nothing obviously and immediately stands out to me why the 77 print(….) line should fail. Nothing in his user history indicates that any other service should be running.

I restarted it and it now works. See below for details:

The error probably was due to the function ‘print’ which couldn’t find its stdout handle to log. I have restarted the server with this command:

nohup python3.6 manage.py runserver 0.0.0.0:80 >nohup.out 2>&1 </dev/null &

This should be the same as how the server previously started:
root 25966 25965 0 2020 ? 00:00:00 python3.6 manage.py runserver 0.0.0.0:80
root 25968 25966 2 2020 ? 1-05:19:32 /usr/bin/python3.6 manage.py runserver 0.0.0.0:80

Hopefully the nohup, redirects and background execution, which previously may or may not have it all, together can prevent this problem from happening again. You probably know but just fyi, the way that it started (which is now restarted) might not be fully production level:
https://docs.djangoproject.com/en/2.2/ref/django-admin/#runserver