Zhanglab forum

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...

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 ********************...

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.

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?

We do not have programs to predict DNA structure. Sorry.

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.

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.

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.

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.

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.