Please also remember that you need to run “Prepare model for PDB deposition” (in the GUI under "PDB Deposition") on the mmCIF file you get from phenix.refine. This provides important information that is required for the deposition at the PDB. 

On Apr 20, 2022, at 1:58 PM, Xavier Brazzolotto <xbrazzolotto@gmail.com> wrote:

Dear Phenix users,

I don’t know if my problem is related to Phenix but for information I’m running Phenix 1.20.1-4487 under MacOS 12.3.1.

I’ve finalized a structure where a ligand covalently modified the protein.

I’ve generated the modified residue (named SLG for serine modified by ligand). For this I’ve generated the molecules in SMILES and used eLBOW to generate the restraints. Then I’ve modified the cif file defining the molecule as a L-peptide and replacing the atom names of the Serine part (CA, CB, OG, C, O, N, and OXT)
In coot (from CCP4 : 0.9.6 EL), I’ve used the modified cif file and it allowed merging of the modified residue into the polypeptide chain as expected and further refinements went without any issue in Phenix (providing the modified cif file of course). Everything seems well interpreted. So far so good.

However, now I would like to validate the structure and both Phenix validation tool and the PDB web server do not accept the final cif file.

Checking this file I’ve noticed that the protein seems split into 3 pieces (chain A, first residue up to the one before the modified residue; chain B the modified residue by itself described as HETATM and chain C the rest of the polypeptide up to the C-ter).
The PDB file presents only one chain A for the whole protein with the modified residue...

I don’t know if this is an issue with Phenix generating this final cif file in this specific case or if I need to modify this final file by hand ?

Any help is welcome.
Thanks

Xavier



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