Hi Yangqi,
Of course you can open multiple structures and move them how you like and and then save again as PDB or session.

See this previous post for “manual placement of ligand”
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-June/006473.html>

Another way is to open your protein pdb file, then open a similar pdb that does have the heme in it, superimpose the two models, and then delete the other protein atoms so that only the heme is left together with your protein. You could just save the PDB file with both models in it, or you could combine them into one model first. 

How to superimpose structures:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

Use menu: Help… Search Documentation to search for “delete” “combine” “save PDB” etc.

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

> On Dec 26, 2018, at 12:05 PM, Yangqi Gu <yangqi.gu@yale.edu> wrote:
>
> Dear Chimera users,
> I have a pdb file of my protein, but not showing the binding ligand (Heme). I know where the binding motif is and I am wondering is there a way I can add ligand to the binding motif and write out the new pdb file in Chimera?
> Best,
> Yangqi

_______________________________________________
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu
Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users