qFit-protein is selecting conformers that are going into the density for the symmetry mate, thus leading to clashes with the symmetry mate structure.
Examples of such behavior are shown below, where orange conformers are the qFit model, green conformers are the original model, and light blue conformers are the original model's symmetry mate. Maps shown are the deposited 2Fo-Fc map at 1 sigma and the Fo-Fc map at 3 sigma.
PDB: 6YBO – Trp237
PDB: 3CX2 – Phe247
To Reproduce:
qfit_protein \
composite_omit_map.mtz \
-l 2FOFCWT,PH2FOFCWT \
6YBO_modified_refine_001.pdb \ (used refined model from PHENIX in above examples)
-p 20 \
--write_intermediate_conformers
qFit-protein is selecting conformers that are going into the density for the symmetry mate, thus leading to clashes with the symmetry mate structure.
Examples of such behavior are shown below, where orange conformers are the qFit model, green conformers are the original model, and light blue conformers are the original model's symmetry mate. Maps shown are the deposited 2Fo-Fc map at 1 sigma and the Fo-Fc map at 3 sigma.
PDB: 6YBO – Trp237
PDB: 3CX2 – Phe247
To Reproduce: qfit_protein \ composite_omit_map.mtz \ -l 2FOFCWT,PH2FOFCWT \ 6YBO_modified_refine_001.pdb \ (used refined model from PHENIX in above examples) -p 20 \ --write_intermediate_conformers
Software & OS Version: