[Chimera-users] Adding Heme ligand to protein pdb

Yangqi Gu yangqi.gu at yale.edu
Wed Dec 26 21:20:26 PST 2018

Thank you very much!

On Wednesday, December 26, 2018, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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 at 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


Yangqi Gu
Graduate Student
Malvankar Lab
Yale University, West Campus
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