[phenixbb] Re: Obtaining standard cif restrain file for ligand in PDB

The error I got was about bond length. The chirals are OK. Thank you though. Best, Lei On Sat, Jan 17, 2026 at 2:17 AM Nigel Moriarty wrote:

You can also send the files directly to me so I can investigate. AJP has a 38 chiral restraints requiring a match between the input model and the restraints.

Cheers

Nigel

--- Nigel W. Moriarty Building 91, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : [email protected] Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464

On Fri, Jan 16, 2026 at 8:53 AM Pavel Afonine wrote:

...

Hi Lei,

eLBOW or ReadySet! are the tools for this, so you are on the right track.

Failing PDB validation can mean two things, with a 50/50 chance: Phenix is wrong or PDB is wrong. So here, you are on the wrong track by blindly assuming Phenix is wrong.

The command

mmtbx.where_is_that_cif_file AJP

shows that Phenix has AJP in its library. This means you do not even need to generate restraints for it using eLBOW or ReadySet! If you have correctly defined AJP in your model file (correctly means atom names conform with the library), you should be golden.

Good luck! Pavel

On 1/16/26 00:32, Lei Chen wrote:

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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

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