[phenixbb] Validation of structure with modified residue

[Nigel Moriarty]

Xavier

I'm sure others can solve this problem but it adds to my point that if you
have a covalently bound ligand to an amino acid that does not change the
main chain, it is generally "better" to maintain the, in this case SER, and
generate the ligand and links to the side chain.

Just one of a number of reasons.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909      Web  : CCI.LBL.gov
ORCID : orcid.org/0000-0001-8857-9464


On Wed, Apr 20, 2022 at 2:02 PM Xavier Brazzolotto <xbrazzolotto at 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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