[phenixbb] Validation of structure with modified residue

[Pavel Afonine]

Hi Xavier,

I remember we had a similar case in January and had a long conversation 
about it between Nigel, Oleg and me. The solution at that time was to 
update Phenix library with that non-standard amino-acid-like entity so 
that Phenix produces mmcif file that is legible by PDB.

In your case it does seem you have "SER plus something" as the modified 
residue. I think the easiest way for you to proceed is to follow Nigel's 
suggestion.

Pavel

On 4/20/22 14:10, Nigel Moriarty wrote:
> 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 <http://CCI.LBL.gov>
> ORCID : orcid.org/0000-0001-8857-9464 
> <https://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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