[Chimera-users] Help on removing ligand on a pdb file with protein in complex with ligand and viewing the conformational change

Elaine Meng meng at cgl.ucsf.edu
Tue Dec 25 11:20:05 PST 2018

Dear Kei Onn,
When you open the structure in Chimera, the conformers are already separate submodels, and it looks like they are already superimposed.  Also you can delete the ligand residue in all submodels at the same time using the ligand residue name, which  is “PKA” according to the the information for this structure at the RCSB PDB:

I.e.Chimera command:
delete :pka

However, you need to consider what makes scientific sense.  If you just delete the ligand, Chimera is not going to predict the change in the rest of the structure, so it will just look exactly the same as it did before except without ligand.   

Instead you should search the PDB for a structure of the same or similar (e.g. homolog in different species) protein that has been solved without the ligand.  Then you would actually have something different to compare to the structure(s)with the ligand.  

One way to search is with Blast Protein in the Chimera menu under Tools… Sequence. You have to look through the results and figure out which ones do and don’t have ligand.

I’m sure there are other ways to look for related structures, so you could certainly use other programs or websites to do that.
I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Dec 24, 2018, at 6:55 PM, #LAI KEI ONN# <KEIONN001 at e.ntu.edu.sg> wrote:
> Dear Elaine,  Eric, Chimera Team and fellow users
> Thank you very much for the great work in developing Chimera!
> I was wondering if there's a way in Chimera for me to visualise my protein of interest without the ligand bound to it and for me to visualise it's original unbound conformation ( so that i can compare bound and unbound protein).
> In addition, i realised that the PDB file has 20 conformers of the protein-ligand complex.
> Therefore I thought that my steps/strategy would be 
> 	• split the 20 conformers into submodels
> 	• del ligand and to do a loop on it for the 20 submodels.
> 	• superimpose all 20 conformers (unbound) vs 20 conformers (bound with ligand)
> Please advice if my steps are right or I am missing something.
> PDB file is 2MGY
> Thank you!
> Once again really appreciate all the work and technical advice provided for Chimera
> Best
> Kei Onn

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