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

Tom Terwilliger tterwilliger at newmexicoconsortium.org
Mon Jan 18 17:52:35 PST 2021

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'  "

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 <rerumbi at scripps.edu>

> 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.
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org

Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilliger at newmexicoconsortium.org
Tel: 505-431-0010
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20210118/6894dccd/attachment.htm>

More information about the phenixbb mailing list