Hi Blazej, have you tried to contact PDB support team to see if they can provide you with an explanation why your files are being rejected? If this is a Phenix error, please let us know and we will address it promptly. However, note there are many thousands of structures in PDB that were refined with phenix.refine, so if the problem was at our end we'd probably know about it by now. Good luck! Pavel On 9/21/21 10:43, Błażej Bagiński wrote:

Dear fellow Phenix bulletin boarders, I'd like to ask for help with refinement-deposition file conflict. I 'finished' solving the structure (protein, 1 chain, 2 ligands), doing the final refinement in phenix.refine. Structure looks okay and does not report any errors in phenix/coot.

I than started the deposition with the wwPDB OneDep System.After long check, my files were rejected (multiple errors, with the best one being "coordinates not found"). Following the FAQ, I run the prepare_pdb_deposition, but the results were the same. I also tried using PDB_Extract (https://pdb-extract.wwpdb.org/), with its result file also generating plethora of errors.

As a control, I put the same phenix.refine file into the PDB-REDO server, and its results finished wwPDB validation successfully. Trouble is, PDB-REDO is quite aggressive and messed up one ligand, occupancies and two loops, so I would prefer to not submit it for anyone to see.

How do you make refinement output compatible with wwPDB? Is there a way to run PDB-REDO without the REDO?

Kind regards, Blazej Baginski

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