[phenixbb] problems with phenix.refine and wwPDB deposition

Pavel Afonine pafonine at lbl.gov
Fri Sep 24 14:05:59 PDT 2021

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!

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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org

More information about the phenixbb mailing list