[Chimera-users] superimposing structures with Chimera

[Elaine Meng]

Also keep in mind that usually the reason to make a figure showing a superposition is to demonstrate real similarities and differences between structures.  If you manually alter one structure to make it look like the other one, it seems like that would defeat the purpose of making such a figure.

Elaine

> On Feb 11, 2022, at 1:30 PM, Elaine Meng via Chimera-users <chimera-users 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.
> 
> <kaina.png>
> 
> 
> 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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