[Chimera-users] superimposing structures with Chimera

[Kaina Quintero Chavez]

Thanks, and correct I am making a schematic. 2o03 is a known protein and
“map” is a hypothetical protein. I want to compare both by overlapping and
read the difference in the zinc distance. For this I would be hiding chain
A of “map” and overlapping chain B to 2o03.
In the case of rotating the backbone, in this case “map” since it’s the
hypothetical protein, I would have to know what residues are not
superimposed select those, rotate and this would adjust to the 2o03 ? Or
would I have to make the rotation similar  to 2o03 and redo the matchmaker?

Again thanks for the helpful insight, I did try and read through the manual
but didn’t get nowhere.


On Fri 11 Feb 2022 at 1:30 p.m. Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Kaina,
> The problem is not how to superimpose the structures, which you are
> already doing correctly.  The problem is that the structures are in a
> totally different conformation from each other.  Also, your "map" PDB is a
> dimer of two copies of the protein as chains A and B, whereas 2o03 is a
> monomer with just chain A.  Even if I hide or delete one of the chains in
> the "map" PDB, however, it is clearly a very different conformation than
> the 2o03 monomer, so that is the main problem.
>
> However, you can't just start changing torsions in a 3D structure and
> expect that structure to be valid... and it would be very difficult to do
> by hand, perhaps impossible.  In my opinion, the only way (without fairly
> advanced modeling) to get something that looks like your first image is to
> already have another monomer structure that is in a similar conformation to
> 2o03.
>
> This image shows 2o03 (tan color) in similar orientation to your first
> image, superimposed with your "map" PDB chain A in transparent blue. The
> other monomer of the "map" PDB is in transparent pink. About half of the
> blue chain matches well, but then a difference in conformation in the
> middle of the blue chain sends the rest of that chain in a different
> direction to what is in 2o03.
>
>
>
>
> If you're just making a schematic and you don't care if the protein
> structure is really valid, you could delete one chain of your "map"
> structure and try rotating the backbone phi,psi angles in the middle of the
> other chain.  You'd probably want to hide ribbon and show backbone atoms
> first. However, I would not want to try that myself, because it is usually
> much harder than you think to make the structure look the way you want.
>
> I hope this makes sense,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Feb 11, 2022, at 11:50 AM, Kaina Quintero Chavez via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
>
> Hi, thank you very much for the information, and I apologize for not being
> so detailed about my question/problem. With the information provided I was
> able to superimpose my two proteins but still not in the way I want to. I
> was given a photo of how it should look and my structure just does not seem
> to orientate the same way using the default method. I hope it is not too
> much trouble and are able to help me out. I attached my two proteins and a
> copy of the picture I was given to replicate. this with the objective to be
> able to duplicate the work with more complex proteins.
> <image.png>
> ps. I am sorry for the quality of the photo, this was the best I could
> sharpen since they only have this one copy and are unable to duplicate the
> work.
>
> <image.png>
> As you can see I am still left with some part of the protein not
> overlapped and my question and inquiry is how can I modify the structure so
> both proteins overlap or if the program can make the torshions or necessary
> turns so they fit.
> <map3773c.pdb><2o03.pdb>_______________________________________________
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>
> --
Kaina
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