[Chimera-users] Question on aligning one molecule to two other molecules

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 18 08:54:16 PST 2020

Hi Adèle,
There is a separate mailing list chimerax-users at cgl.ucsf.edu, so in the future you could mail that address instead of the Chimera one if it is a ChimeraX question. The two programs are different and we don't want to confuse everybody!

That description was pretty long, but if I understand correctly, you want to move one part of your DNA while leaving the other part where it is now.  If I were doing this, I would have the two parts of the DNA as two separate models.  For example, if the DNA that you are moving now has parts 1 and 2, and you want to leave part 1 in the same place but move 2, you can select part 1 and then use ChimeraX command "split" specifying that DNA model and also using the option "atoms sel"

Then your modeled DNA is in two separate models and you can put each model where you want it. If it's good enough for your modeling, you could leave it like that, but if you want it together in one model: ChimeraX does not have "combine" command yet, so you would have to save PDB files of both of those "relative to" your protein model, and then using text-editing, manually combine the mutually exclusive parts back into one PDB file.  Chimera has a "combine" command that you could use if you had deleted any overlapping parts beforehand (e.g. so there would not be duplicates of the same atoms).

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

> On Nov 18, 2020, at 4:45 AM, Doc Deldou <docdeldou at gmail.com> wrote:
> Dear Chimera team,
> I am trying to perform a "manual" docking of a DNA molecule in a protein structure using homology with proteins structures resolved with DNA. I know that the first part of my protein (the recognition domain) is similar to one structure and the other part (the cleavage domain) is similar to another one. So I built a dsDNA with the recognition sequence of my target protein and I first aligned it with the DNA of the similar recognition structure using the phoshore groups, then I matched aligned my protein structure to the protein part of the similar recognition structure. After that I matched aligned my protein to the similar protein cleavage domain bringing the DNA molecule with it. And now ideally I would like to align the DNA part with the DNA of the similar cleavage domain but keep the first recognition part of my DNA more or less at the same position. So I tried to align another copy of my DNA to both DNA molecules but I don't think it is possible. Do you have a trick or a command I could use to reach my goal?
> I'm using Chimera X. Below is what I obtained, in green my target protein, in purple the DNA I first aligned relatively to the DNA of my similar recognition structure, in "pink" the DNA strand of the similar cleavage structure with the bond to be cleaved in yellow, and the dsDNA with all the colored nucleotides is the one I am trying to position in between the two site with also the bond to be cleaved in yellow. I tried to rotate it and translate it manually to have something in between but some DNA parts are clashing with the protein part and I would like to have something the more accurate possible.
> <manualdocking.jpg>
> Best regards,
> -- 
> Adèle Dramé-Maigné

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