Search found 27 matches
- Tue Dec 20, 2022 7:29 pm
- Forum: Main Forum
- Topic: MSTA issue
- Replies: 5
- Views: 713
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 ********************...
- Sat Dec 17, 2022 9:18 pm
- Forum: Main Forum
- Topic: MSTA issue
- Replies: 5
- Views: 713
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.
- Sat Dec 17, 2022 2:06 pm
- Forum: Main Forum
- Topic: MSTA issue
- Replies: 5
- Views: 713
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?
- Tue Jul 05, 2022 4:07 pm
- Forum: Main Forum
- Topic: 3D Structure of Methylated DNA
- Replies: 1
- Views: 532
Re: 3D Structure of Methylated DNA
We do not have programs to predict DNA structure. Sorry.
- Thu Jun 23, 2022 8:46 pm
- Forum: Main Forum
- Topic: ThreaDom Processing (Job T11532)
- Replies: 4
- Views: 1165
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.
- 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: 640
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.
- Fri Jun 03, 2022 6:15 pm
- Forum: Main Forum
- Topic: Active and inactive states of the predicted model
- Replies: 1
- Views: 580
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.
- Tue May 31, 2022 6:00 pm
- Forum: Main Forum
- Topic: ERROR! NO XSCORE results for Edock
- Replies: 1
- Views: 479
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.
- Sun May 22, 2022 5:57 pm
- Forum: Main Forum
- Topic: Use FUpred to split protein domain
- Replies: 3
- Views: 634
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.
- 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