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move where we add hydrogens to after while loop #296

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Dec 15, 2022
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move where we add hydrogens to after while loop #296

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16 changes: 8 additions & 8 deletions scripts/post/qfit_final_refine_xray.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -138,14 +138,6 @@ phenix.refine "${multiconf}.f_modified.updated.pdb" \
"${pdb_name}_refine.params" \
--overwrite

#__________________________________ADD HYDROGENS__________________________________
# The first round of refinement regularizes geometry from qFit.
# Here we add H with phenix.ready_set. Addition of H to the backbone is important
# since it introduces planarity restraints to the peptide bond.
# We will also create a cif file for any ligands in the structure at this point.
phenix.ready_set hydrogens=true pdb_file_name="${pdb_name}_002.pdb"
mv "${pdb_name}_002.updated.pdb" "${pdb_name}_002.pdb"

#__________________________________REFINE UNTIL OCCUPANCIES CONVERGE__________________________________
# Write refinement parameters into parameters file
echo "refinement.refine.strategy=*individual_sites *individual_adp *occupancies" > ${pdb_name}_occ_refine.params
Expand Down Expand Up @@ -188,6 +180,14 @@ while [ $zeroes -gt 1 ]; do
((i++));
done

#__________________________________ADD HYDROGENS__________________________________
# The first round of refinement regularizes geometry from qFit.
# Here we add H with phenix.ready_set. Addition of H to the backbone is important
# since it introduces planarity restraints to the peptide bond.
# We will also create a cif file for any ligands in the structure at this point.
phenix.ready_set hydrogens=true pdb_file_name="${pdb_name}_002.pdb"
mv "${pdb_name}_002.updated.pdb" "${pdb_name}_002.pdb"

#__________________________________FINAL REFINEMENT__________________________________
cp -v "${pdb_name}_002.pdb" "${pdb_name}_004.pdb"

Expand Down