Hello, what web server protein refinement tool can you recommend? I tried to use Galaxy Refine, but HADDOCK does not accept refined PDB. “ATOM/HETATM line does not meet the expected format” this is what pops up every time I use the refined PDB in HADDOCK.
Hello, HADDOCK refinement interface removes my protein bad angles and bonds. However, it does not improve my Ramachandran analysis result.
It is only a very short refinement… No miracles.
Check our article about refining complexes to get an idea of what can be done / achieved.
- T Neijenhuis, S.C. van Keulen and A.M.J.J. Bonvin. Interface Refinement of Low-to-Medium Resolution Cryo-EM Complexes using HADDOCK2.4. Structure 30, 476-484 (2022).