Search found 28 matches

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: 471

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: 935

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: 413

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: 845

Re: iTASSER job remains in queue ??

Your jobs should have been completed a few days ago at https://zhanggroup.org/I-TASSER/output/S679460/
by zcx@umich.edu
Wed Apr 13, 2022 4:39 pm
Forum: Main Forum
Topic: Job is not completing
Replies: 2
Views: 490

Re: Job is not completing

Your job should have been completed a few days ago at https://zhanggroup.org/I-TASSER/output/S679460/
by zcx@umich.edu
Sat Apr 09, 2022 6:48 pm
Forum: Main Forum
Topic: Job is not completing
Replies: 2
Views: 490

Re: Job is not completing

The job you just submitted 2 days ago does not seem to have particular issue. Your protein is long (891 residues). So it will take time to complete it. THe queue information is just a very rough estimate.
by zcx@umich.edu
Tue Mar 29, 2022 5:30 pm
Forum: Main Forum
Topic: Generate Protein
Replies: 8
Views: 3997

Re: Generate Protein

If the DNA contains an ORF, you may use ExPASy translate (https://web.expasy.org/translate/) to obtain the translated protein sequence from DNA. If your DNA is in NCBI, it should have annotations of translated protein sequences in its GenBank format.
by zcx@umich.edu
Tue Mar 29, 2022 5:27 pm
Forum: Main Forum
Topic: COACH job still pending
Replies: 6
Views: 1090

Re: COACH job still pending

Dear all, the COACH server is currently heavily loaded due to I/O issues. We are working on resolving the issues and apologize for any inconveniences this causes.
by zcx@umich.edu
Thu Mar 24, 2022 5:56 pm
Forum: Main Forum
Topic: converting .sdf files to .pdb/.pdbqt
Replies: 1
Views: 409

Re: converting .sdf files to .pdb/.pdbqt

We are not maintainer or developer of OpenBabel and are not entitled to assist you with the issue. You should ask your questions at http://openbabel.org/wiki/Help
by zcx@umich.edu
Wed Mar 23, 2022 2:22 pm
Forum: Main Forum
Topic: BioLiP coordinates
Replies: 2
Views: 436

Re: BioLiP coordinates

If you need to download BioLiP dataset, you may want to use https://zhanggroup.org/BioLiP/download.html rather than "browse".