Hi Rangarajan, Yes, you should be able to keep the hydrogens...add these commands to your script (note that there are two levels of quotes in the resolve_command_list command): resolve_command_list=" 'keep_hydrogen' 'n_template_atom 9' " refine_ligand=false You need to specify the number of atoms in your ligand (including H atoms) with n_template_atom along with specifying keep_hydrogen. the refine_ligand=False is in case the hydrogens prevent refinement from working. You can just refine afterwards in that case. Let me know if that does not do it! All the best, Tom T On Mon, Jan 18, 2021 at 12:55 PM Rangarajan Erumbi wrote:

Hi,

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.

Rangarajan.

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