Dear Lei, It sounds to me that you did everything alright (but I didn't see the refined structure obviously). From my experience, there are still some limitations in ligand validation in the PDB deposition. So if you are sure that your restraint file is good and refinement result makes sense, then do not worry much about reported outliers in the PDB deposition. (This may be a bit controversial opinion and someone can disagree.) (I should note that the PDB team is making a lot of effort to improve the ligand validation and is getting better and better. It's very appreciated. So may change my controversial opinion in the near future.) You can also try to use a restraint file from the CCP4 monomer library which was generated in AceDRG: https://raw.githubusercontent.com/MonomerLibrary/monomers/refs/heads/master/... Or you can generate a restraint file using GRADE server of Global Phasing. Then you can check how consistent are you refinement results while using restraints generated in different programs - if you had any doubts. Best wishes, Martin On 16/01/2026 08:32, Lei Chen wrote:
Dear all,
I am building a model of a digitonin molecule into the density map. Several released PDB entries contain digitonin (ligand code: AJP).
However, I could not find the corresponding mmCIF restraint file (AJP.cif) for refinement. I generated one using phenix.elbow, but it failed PDB validation, likely because the generated parameters differ from the standard reference.
Could you please advise on where I can obtain the standard restraint file for AJP? I have checked the RCSB PDB website, but it appears to provide coordinate files rather than refinement restraints.
Thank you for your help.
Best regards, Lei _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s