Search found 27 matches

by zcx@umich.edu
Tue Dec 20, 2022 7:29 pm
Forum: Main Forum
Topic: MSTA issue
Replies: 5
Views: 720

Re: MSTA issue

I test US-align on your model and do not observe any issue: curl "https://zhanggroup.org/forum/download/file.php?id=60&sid=e7d55819c30ec4ed7cf974e16cdc5b4e" -o dino_models.zip unzip dino_models.zip USalign -dir dino_models/ dino_models/input_list -suffix .pdb -mm 4 ********************...
by zcx@umich.edu
Sat Dec 17, 2022 9:18 pm
Forum: Main Forum
Topic: MSTA issue
Replies: 5
Views: 720

Re: MSTA issue

You issue may be related to https://github.com/pylelab/USalign/issu ... 1356474145 where your pdb file does not have standard atom name. Please check if this is the case.
by zcx@umich.edu
Sat Dec 17, 2022 2:06 pm
Forum: Main Forum
Topic: MSTA issue
Replies: 5
Views: 720

Re: MSTA issue

Can you attach the content of "dino_models/" as a zip archive in your next post so that we can check what the issue is?
by zcx@umich.edu
Tue Jul 05, 2022 4:07 pm
Forum: Main Forum
Topic: 3D Structure of Methylated DNA
Replies: 1
Views: 536

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: 1194

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: 642

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: 583

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: 481

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: 637

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: 467

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