Search found 24 matches

by zcx@umich.edu
Tue Jul 05, 2022 4:07 pm
Forum: Main Forum
Topic: 3D Structure of Methylated DNA
Replies: 1
Views: 367

Re: 3D Structure of Methylated DNA

We do not have programs to predict DNA structure. Sorry.
by zcx@umich.edu
Thu Jun 23, 2022 8:46 pm
Forum: Main Forum
Topic: ThreaDom Processing (Job T11532)
Replies: 4
Views: 607

Re: ThreaDom Processing (Job T11532)

Unfortunately, your job was not correctly parsed by our server due to internal bug. I have already resubmitted your protein as job T11532. If you did not receive result by next week, please let us know.
by zcx@umich.edu
Fri Jun 03, 2022 6:22 pm
Forum: Main Forum
Topic: Error in final PDB model generated by I-TASSER standalone program
Replies: 2
Views: 513

Re: Error in final PDB model generated by I-TASSER standalone program

This is an issue related to the EMrefinement.pl script of I-TASSER. Could you send us the closc*pdb, combo*pdb and model*pdb files of your job as a zip file? We can further check what the issue is.
by zcx@umich.edu
Fri Jun 03, 2022 6:15 pm
Forum: Main Forum
Topic: Active and inactive states of the predicted model
Replies: 1
Views: 445

Re: Active and inactive states of the predicted model

I-TASSER does not explicitly consider ligand, just like almost any protein structure prediction program. Therefore, the predicted structure are usually the apo (i.e., ligand-free) conformation of the protein.
by zcx@umich.edu
Tue May 31, 2022 6:00 pm
Forum: Main Forum
Topic: ERROR! NO XSCORE results for Edock
Replies: 1
Views: 372

Re: ERROR! NO XSCORE results for Edock

Your EDock job is now fixed. There will be no xscore as it cannot parse the FE atom. Nonetheless, you should be able to get the docking pose.
by zcx@umich.edu
Sun May 22, 2022 5:57 pm
Forum: Main Forum
Topic: Use FUpred to split protein domain
Replies: 3
Views: 470

Re: Use FUpred to split protein domain

This is just a warning from the contact predictor used by FUpred. It uses JIT compiler from numba. Without numba, the program will still run correctly, albeit slower.
by zcx@umich.edu
Sat May 21, 2022 3:45 pm
Forum: Main Forum
Topic: Regarding the second iteration of the TASSER program in the I-TASSER standalone
Replies: 2
Views: 329

Re: Regarding the second iteration of the TASSER program in the I-TASSER standalone

The second round of simulation is performed by I-TASSERmod/EMrefinement.pl which is called by line 1915 of I-TASSERmod/runI-TASSER.pl
by zcx@umich.edu
Tue Apr 19, 2022 6:35 pm
Forum: Main Forum
Topic: Differences in the predictions by I-TASSER web server and standalone package
Replies: 5
Views: 760

Re: Differences in the predictions by I-TASSER web server and standalone package

The online web server contains some component that we unfortunately cannot redistribute with the standalone package due to license issue. For example, the template identification by LOMETS uses HHsearch, which is only used by web server but not standalone package. In most cases, this does not have a...
by zcx@umich.edu
Sun Apr 17, 2022 12:59 am
Forum: Main Forum
Topic: Job is not complete
Replies: 1
Views: 321

Re: Job is not complete

According to our system record, job S680633 is already deleted by the user. Please also note that the estimated queue time is only a very rough approximation. It is very possible that some proteins would take longer than expected, e.g. due to heavy load of the supercomputer cluster. In your case, yo...
by zcx@umich.edu
Wed Apr 13, 2022 4:40 pm
Forum: Main Forum
Topic: iTASSER job remains in queue ??
Replies: 3
Views: 682

Re: iTASSER job remains in queue ??

Your jobs should have been completed a few days ago at https://zhanggroup.org/I-TASSER/output/S679460/