Search found 28 matches

by zcx@umich.edu
Fri Feb 03, 2023 5:34 pm
Forum: Main Forum
Topic: crash on biolip web site and a site at position 0
Replies: 2
Views: 116

Re: crash on biolip web site and a site at position 0

We have fixed the issue for 8gwo:G. The webpage you mention should now work. u0 is not a mistake. If you check line 22085 to line 22104 of the PDB format file for 8gwo at https://files.rcsb.org/view/8GWO.pdb, you will notice that residue 0 of chain G is ribonucleotide U, while the remaining residues...
by zcx@umich.edu
Tue Dec 20, 2022 7:29 pm
Forum: Main Forum
Topic: MSTA issue
Replies: 5
Views: 816

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: 816

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: 816

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: 554

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: 1232

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: 654

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: 588

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: 487

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: 647

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.