Hello, You can at least browse the repository: https://github.com/MonomerLibrary/monomers Probably even search it, but it seems this only works when logged in with a GitHub account (can’t check now on a phone). You can also download the entire repository with git clone and update your copy later with git pull. This gives you direct access to the cif files. Cheers, Guillaume Typed on a phone On 17 Jan 2026, at 06:06, rainfieldcn wrote: Dear Martin, This AceDRG resource looks very useful. Is there a way to search this online monomer library? Or can I download the whole library? Thanks, Lei On 1/16/2026 5:26 PM, Martin Malý wrote: 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 _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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:

...

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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phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

Dear Nigel, I resolved this issue by manually editing the CIF restraint file. The problem occurred when I used an old version of phenix.elbow (1.19.2-4158) to generate the CIF file for ligand AJP. The resulting file contained incorrect geometry; for example, the C05-C06 bond distance was listed as 1.75 Å instead of the expected ~1.53 Å. The refinement succeeded after I corrected these values manually. Best, Lei On Sun, Jan 18, 2026 at 2:14 AM Nigel Moriarty wrote:

Lei

As the author of both eLBOW and ReadySet!, I'm sure I can help but I need more. If you wish to share the model and restraints (directly and privately) I can take a look otherwise there is nothing anyone can do with the information you have provided so far.

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 10:15 PM Lei Chen wrote:

...

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:

...

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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