[phenixbb] problems with phenix.refine and wwPDB deposition

Joel Tyndall joel.tyndall at otago.ac.nz
Tue Sep 21 15:12:27 PDT 2021

Have you tried PreparePDBDeposition under PDB deposition?

-----Original Message-----
From: phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> On Behalf Of Blazej Baginski
Sent: Wednesday, 22 September 2021 5:44 AM
To: phenixbb at phenix-online.org; blazej.baginski at irbbarcelona.org
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-extract.wwpdb.org%2F&amp;data=04%7C01%7Cjoel.tyndall%40otago.ac.nz%7C5ca9994acd1543b0d96608d97d27f41e%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637678433407092459%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=keM7zsTAH7sqirp0uR0TIab2uJkQC84aV1CfqMiWef0%3D&amp;reserved=0), 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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