Have you tried PreparePDBDeposition under PDB deposition?
-----Original Message-----
From: [email protected] On Behalf Of Blazej Baginski
Sent: Wednesday, 22 September 2021 5:44 AM
To: [email protected]; [email protected]
Subject: [phenixbb] problems with phenix.refine and wwPDB deposition
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://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpdb-extrac...), 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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