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

[Dom Bellini]

Dear Sagnik,

To make a covalent bond in Coot: Calculate -> Modelling... -> Male Link 
(click 2 atoms)...

HTH,

D

On 15/10/2025 16:19, Sagnik Sen via 3dem wrote:
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> 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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