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
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.
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
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 ./multi.pl 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.
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
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.
http://encodenets.gersteinlab.org should be back up now. Let us know
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.
image 2 1
screen shot 2019 07 12 at 2.49.53 pm
I tried to use the 3V (http://3vee.molmovdb.org/) server developed at your lab but I was not able to connect to it. Is the server still running? Would you help me find a way to run it?
It was up but unresponsive. It should be working now.
We could not access your 3V server listed in your paper below.
Link to such calculation of protein volume in the presence of probe with
Should be up now. We had to power down all our machines on Monday and
3vee went up but it was in a hung state.
I was wondering if asco.gersteinlab.org is still available or having issues?
It should be back online now.
Sorry for the inconvenience.