Conformation Explorer

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:

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.

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 . 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.


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?

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

We are trying out Genodock on But unfortunately none of the models worked.

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 runserver >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 runserver
root 25968 25966 2 2020 ? 1-05:19:32 /usr/bin/python3.6 runserver

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:

Server errors on molmovdb

I was trying a couple of tools: Morph Server and RigidFinder and in both cases I get a server error indicating that files could not be written. Specifically, RigidFinder complains: "Cann’t write to file ‘/tmp/rid74285/upfile1.pdb’." and Morph Server says "Can’t create morph directory!". If this site is still being maintained, please consider addressing these issues.

Thank you for your interest in our servers and for letting us know of
problems you’ve encountered.

Rigidfinder’s disk filled up. I cleared some space and it should be
working again.

Molmovdb, however, is a more complicated issue. It needs an upgrade
since it is more than 15 years old. Occasionally, we simply roll back
to a previous version but then any submissions would be lost. We also
cannot guarantee when the next roll back would be.

We apologize for any inconvenience this may have caused. We provide
related software in our FAQs for those who are interested.

Yale Morph Server job not being completed

I uploaded my PDB files on the multi-chain morph server, the job ID is b499364-832. It has been two days but the results page still says that the job is not yet complete. Is there any problem with my morph? I understand that my files are very large so it may take a long time to finish, but is it possible that it takes this long? I would really appreciate your assistance.

Files generated by the multi-chain server can be found in<job ID>/
Yours are in

Looking at it, some files seem to be missing.
For e.g., a complete run would look like

There is a job running and it seems to be related to yours
"/usr/bin/perl ./ b499364-832 –chains=WCBAXHGFEDJLMNOPQRYAIS
–nframes=8 –email=seiga –engine=CNS –debug"

The short of it is that your job is probably stuck since you seem to
have submitted it 6 days ago judging from the submit time. Note that
we cannot guarantee the full functionality of this service as it is
from 2005 and has not been fully maintained since. Occasionally, we
may roll back but that would mean you will need to resubmit your job.

MorphServer job

I am trying to use Morph Server, my job ID: b198308-29491
It has been running for 5 days and is still not completed. Could you please check?

The files in the folder of your jobs seems to indicate that it
finished successfully. You can find the files using

So yours would be in

Unfortunately, some of the other features of the web interface need

Supplementary data of Architecture of the human regulatory network derived from ENCODE data

I recently read the ENCODE paper "Architecture of the human regulatory network derived from ENCODE data", and I realized that the supplementary data will greatly help me to refine projects results, in particular those files related to the K562. Unfortunately, I found that all the supplementary data files are not available to download, since both of the following sites can’t be reached.

In particular, the second link is active, but if I try to download one of the files, it points to the first link and the download is interrupted. I am writing to ask if there are any other ways to access the files.

A: should be back up now. Let us know

Request about Pubnet

I am looking for an easy-to-handle application to analyse collaborative networks in science, and I am very interested by Pubnet, that you published quite a while ago. Unfortunately, event if it looks very simple to use the web interface, after submitting a query with a author name, I always have a page indicating the pubmed xml was generated, but it is never analysed. It always blocks as this: (see image)

We’ve managed to revive pubnet. Please check it out.