[Chimera-users] Transfer of docked substrate co-ordinates

Elaine Meng meng at cgl.ucsf.edu
Sat May 8 08:08:04 PDT 2021

Hello Chittari Jaya Shree,
You would just open your file two times and match one copy "backwards" so that the ligand part goes into the other chain of the first copy.

More details:
I see your file has protein (with chains A and B) as one model and the ligand as another model.  If you open it in Chimera it is model #0 with submodels #0.1 protein and #0.2 ligand.   Open the file again so that you also have model #1,  #1.1 protein and #1.2 ligand.  Then you can use Matchmaker "specific chain to specific chain" option to match #1 protein chain A (with ligand) onto #0 chain B (which was empty).  You could use Matchmaker GUI, or the command to do the same thing:

mm #0.1:.A #1.1:.B pair ss


Then close the second copy of protein so you are just left with one copy of protein but with ligands in both sites, for example command:

close #1.1

That may be all you need to do if you are just using Chimera on the results, e.g. for analysis or making figures.  However, if you are planning to export to other programs you may want to combine the three models you have left (#0.1, #0.2, #1.2) into a single model before writing out the file.  For example, see instructions in this recent post on how to combine the models before saving:

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

> On May 7, 2021, at 9:31 PM, Jayashree Chittari <jayashreechittari27 at gmail.com> wrote:
> Respected sir/ma'am
> Greetings for the day!!!
> I have docked ligand into an enzyme which contains two active sites. My docked ligand is in one active site. I want to transfer the ligand conformation from one active site pocket to another using superimpose option in chimera. 
> Find herewith the attached file of PDB in which i want to transfer propionaldehyde coordinates from one active site to another
> is there any way that we can transfer the docked confirmation coordinates into another chain.
> Kindly, help me to solve this issue. It will be helpful if you suggest the process. 
> Thank you
> Regards 
> Chittari Jaya Shree
> <1qgd_48.pdb>

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