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
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