Christian

While there is the possibility to point to the CCP4 mon_lib from Phenix, it is generally better to generate the restraints because there are nuances. I would use the command

phenix.pdb_interpretation model.cif

to find the missing restraints and then

phenix.elbow --chemical_component=<XYZ>

with the optional

--final_geometry=<XYZ>

until you have the restraints needed.

I'm happy to help more with restraints if needed.

Cheers

Nigel

---
Nigel W. Moriarty
Building 91, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : NWMoriarty@LBL.gov
Web  : CCI.LBL.gov


On Tue, Dec 10, 2024 at 2:25 PM <christian.steinmetzger@imbim.uu.se> wrote:
Dear community,

I'm trying to work with a published ribosome structure (PDB 7K00, https://www.rcsb.org/structure/7k00 ) for example in phenix.combine_focused_maps or phenix.real_space_refine. Of course this structure contains a lot of modified residues and the monomer library in a fresh Phenix installation (version 1.21.2-5419) does not handle these out of the box.

Since a lot of publications have used 7K00 as a starting point for their work in Phenix and since the current CCP4 monomer library plays nice with this structure I would not have expected this. Am I missing something in my Phenix setup to make it recognize such "common" modified residues in a ribosome or do I indeed need to generate parameters myself using AceDRG, eLBOW, Grade2 etc.?

In the latter case, could I simply swap out the stock Phenix monomer library for the one from CCP4 as a drop-in replacement or would that be a bad idea?

Thank you!
Christian
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