[3dem] Seeking guidance regarding fitting a small molecule ligand to a protein , using a cryoEM map

[Sagnik Sen]

Dear all,

We have a sample where a small molecule ligand is bound to a homodimer
protein. It forms covalent bonds with the Sulfur of a Cysteine on both the
chains. We currently have a cryoEM map of 2.5 Å and we can clearly see the
ligand density on both the chains, after fitting the protein model to the
map.

We are also able to roughly fit the ligand using Coot but seek inputs with
respect to forming the bond. Placement of the ligand in the density near to
the Cysteine and doing real space refinement does not make the bond.

We do have a PDB and restraints file for the ligand, made using Phenix
eLBOW. Do we need to edit the PDB files for both the protein and the ligand
to make the link? IF so, what is a good way to do that?

Or is there a way to fit this using Phenix?

Thanks and best regards,
Sagnik
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