[phenixbb] Retaining hydrogen in ligand while carrying out automatic ligand fitting.

Rangarajan Erumbi rerumbi at scripps.edu
Mon Jan 18 11:55:01 PST 2021


I am using phenix.ligandfit to automatically fit a ligand in to the ligand site of a protein model using the experimentally derived structure factors for the complex.  The ligand pdb and restraints are created using phenix.elbow which contains the hydrogen atoms.  However, after phenix.ligandfit the coordinates that are derived is stripped of all the ligand hydrogens. I want to retain the hydrogens only on the ligand during the refinement to preserve the overall geometry of the ligand. I am trying to do this automatically over several datasets with different ligands. I don’t see any specific parameter in the phenix.ligandfit that would specifically allow me to retain the ligand hydrogens. Phenix.reduce or phenix.ready_set does add hydrogens to entire coordinates including protein residues and so could not use it directly.

Is there a way to get this accomplished in a simple way?

Thanks in advance and appreciate your suggestions.


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