Search found 42 matches

by robpearc
Sun May 09, 2021 3:53 pm
Forum: Main Forum
Topic: run a query using partial sequences/partial alignments
Replies: 2
Views: 1030

Re: run a query using partial sequences/partial alignments

Hello, Yes, this is possible. If you know the alignment between your protein sequence and the template structure, you may specify this under Option 1: Assign additional restraints and templates to guide I-TASSER modeling. When you click on this option, there will be an explanation link that you can ...
by robpearc
Fri May 07, 2021 1:43 pm
Forum: Main Forum
Topic: iTASSER unexpected result
Replies: 1
Views: 772

Re: iTASSER unexpected result

When the same amino acid sequence is submitted twice, it will refer you back to the previous submission as the results should be identical. The reason the models are so different is the mutant closely resembles the template 6npyA, while the wild-type closely resembles 6w2sS. However, if you look at ...
by robpearc
Wed May 05, 2021 11:34 pm
Forum: Main Forum
Topic: I-TASSER: Change default number (14) of independent runs
Replies: 2
Views: 1080

Re: I-TASSER: Change default number (14) of independent runs

Hello, There is currently no command line option for modifying the number of simulation trajectories. However, these parameters can be modified by changing the parameters in the runI-TASSER.pl file between lines 1613-1629 in the "decide number of runs section", so it will require some more...
by robpearc
Wed May 05, 2021 4:39 am
Forum: Main Forum
Topic: Delay ModRefiner for 3D protein refinement
Replies: 3
Views: 1055

Re: Delay ModRefiner for 3D protein refinement

It looks like M30440 has finished and is available at https://zhanglab.dcmb.med.umich.edu/Mod ... ut/M30440/. M30441 is currently in the queue waiting to run.
by robpearc
Wed May 05, 2021 4:36 am
Forum: Main Forum
Topic: Delay ModRefiner for protein dimer
Replies: 5
Views: 1852

Re: Delay ModRefiner for protein dimer

Hello,

It looks like your job was just submitted and is currently in the queue. We are currently working on catching up on many jobs that were submitted since our web server failure, so there may be additional delays, but we are working on processing your request ASAP.

Thanks!
Robin
by robpearc
Wed May 05, 2021 4:34 am
Forum: Main Forum
Topic: IonCom issues
Replies: 5
Views: 1900

Re: IonCom issues

Thank you for the notification. We are working on fixing the issue ASAP, which arose during our transition to our new web server.
by robpearc
Mon May 03, 2021 8:42 pm
Forum: Main Forum
Topic: Delay in I-TASSER and LOMETS server
Replies: 1
Views: 836

Re: Delay in I-TASSER and LOMETS server

Yes, we have been experiencing delays due to a hardware failure on our web server as well as some recent maintenance on our backend cluster. We are currently catching up with old jobs, and it looks like your modeling results have finished, but the biological function prediction is currently running....
by robpearc
Mon May 03, 2021 8:39 pm
Forum: Main Forum
Topic: Delay ModRefiner for 3D protein refinement
Replies: 3
Views: 1055

Re: Delay ModRefiner for 3D protein refinement

Yes, ModRefiner was down due to server issues. It should be back up and running and catching up on older jobs. If you have your job id or email used for submission, I can check on the status for you.
by robpearc
Mon May 03, 2021 1:41 am
Forum: Main Forum
Topic: I-TASSER: bzip2: Can't open input file rep*.tra: No such file or directory.
Replies: 3
Views: 1362

Re: I-TASSER: bzip2: Can't open input file rep*.tra: No such file or directory.

The error appears to be due to the I-TASSER folding simulations failing to generate the structure decoy files (rep*.tra), although the exact error for this isn't apparent from the output. If you zip your data directory and send it to robpearc@umich.edu, I will look at the issue further.
by robpearc
Sun May 02, 2021 6:01 pm
Forum: Main Forum
Topic: Delay ModRefiner for protein dimer
Replies: 5
Views: 1852

Re: Delay ModRefiner for protein dimer

We apologize for the delay. If you have your job id or email used for submission, I will check on the status for you.