Dear Valérie,
Can you please share the model and reference model (off-list) that you
are using? Then I'll be able to tell exactly what is happening (files
will be treated confidentially).
For some reason Phenix does not believe they are close enough. That
could be because sequence is not similar enough. Renumbering the
residues normally won't change this fact. Reference chains needs to be
at least 0.85 sequence identical by default. This can be changed with
reference_model.search_options.chain_similarity_threshold=0.5
Best regards,
Oleg Sobolev.
On Wed, Apr 29, 2026 at 12:11 AM Valérie Biou via phenixbb
Dear all,
I would like to use a reference model to try to improve my cryo-em refinement geometry. I have an AF3 model that superposes with an RMSD of 1.4Å wrt my structure, and I renumbered the residues so they match with my structure. however, I get the message
Reference Model Matching Summary: reference file: renumbered.pdb Model: Reference: Total # of matched residue pairs: 0 Total # of reference model restraints: 0
input file list (truncated from the root) default_model = "RealSpaceRefine_72/rsr71_isolde1_real_space_refined_072.pdb" real_map_files = /cryosparc_P29_J343_010_volume_map_sharp.mrc" default_real_map = cryosparc_P29_J343_010_volume_map_sharp.mrc" restraint_files = eLBOW_46/elbow.P.P_pdb.001.cif" default_restraint = eLBOW_46/elbow.P.P_pdb.001.cif" phil_files = Phenix/.phenix/project_data/real_space_refine_88.eff" default_phil = Phenix/.phenix/project_data/real_space_refine_88.eff"
then : reference_model { enabled = True file = "renumbered.pdb" side_chain = False secondary_structure_only = True search_options { chain_max_rmsd = 3.0
Can you please help me with this? Kind regards
Valérie _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s