[phenixbb] Validation of structure with modified residue

Wed Apr 20 23:06:58 PDT 2022

Thank you for your feedback.

@Paul, I’ve run the « Prepare model for deposition » with the option modified residue (SLG). Not sure it will change if I change the name as it is already the PDB database, but I will give it another try.

I think that I will have to describe only the ligand and add some parameters restricting distance and angles between the OG of SER and the ligand, I think this is right way.
@ Nigel, is that what you mean with « details » ? If you have any other « tips/tricks » they are welcome.

Best
Xavier

> Le 21 avr. 2022 à 02:47, Nigel Moriarty <nwmoriarty at lbl.gov> a écrit :
> 
> Xavier
> 
> Paul's point is very valid because the "Prepare for Deposition" step is what generates the sequence (which is the crucial point here) for deposition. However, because you have "created" a new amino acid, there will still be issues as highlighted by Pavel. It is a corner case. 
> 
> One small addition point is that SLG is already taken in the PDB Ligand list. There are tools in Phenix to find an used code.
> 
> Can you re-engineer it with SER+ligand? This will solve the problem using the current Phenix version. I can help with the details if needed.
> 
> Cheers
> 
> Nigel
> 
> ---
> Nigel W. Moriarty
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> 
> 
> On Wed, Apr 20, 2022 at 5:02 PM Paul Adams <pdadams at lbl.gov <mailto:pdadams at lbl.gov>> wrote:
> 
> 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 at gmail.com <mailto: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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