[chimerax-users] Placing a ligand in a protein structure from PDB

[Elaine Meng]

> On Nov 30, 2022, at 7:41 AM, Amit Kugler <amit.kugler at kemi.uu.se> wrote:
> 
> Hej Elaine,
> 
> I found you on the ChimeraX website, and I have a question.
> 
> I have a PDB file of my protein, but not showing a ligand.
> 
> I am wondering if there a way I can add a ligand to the active site of the protein and write out the new PDB file on ChimeraX?
> 
> Best regards,
> Amit
> 
Hi Amit,
We recommend sending questions to chimerax-users at cgl.ucsf.edu (CC'd here) to make it more likely you get a response.

Not sure what you mean by add a ligand.  Sure you can open a file of a ligand and open a file of the protein, and then combine them into one model, and then save.  But probably you want to put the ligand in some sensible position, which could be done by moving it individually by hand, or by using some docking program.  ChimeraX does not do docking.  You would have to use some docking program (Glide, DOCK, Gold, Autodock, Autodock Vina, etc.) and then open the output from that docking program in ChimeraX.

Moving models by hand, see this previous post:
<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2017-November/000157.html>

There is a "combine" command to combine the two separate models into a new single model, and "save" (or menu File... Save) to save the resulting combined model as a PDB file.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb>

Or maybe you don't have a structure of the ligand.  If there is some other PDB structure that contains it you can open that structure and delete all the rest of the atoms, or if you can find it in PubChem you can try fetching by PubChem ID into ChimeraX, e.g. command

open pubchem:12120

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco