[Chimera-users] [ Asking how to combine loops of models after refinement ]

Elaine Meng meng at cgl.ucsf.edu
Thu Oct 3 10:53:33 PDT 2019

Dear Dung,
The Model Loops/Refine Structure dialog only allows adding all missing segments in the same step (not one missing loop at a time), so I guess you first added them all, but then after they were added, refined the different loops in different Modeller runs.

Model Loops/Refine Structure:

We created this interface for fairly simple uses of Modeller, not more complicated things like multiple separate refinements.  So there is no automatic (easy) way to combine the results from the separate runs.  Instead you would have to do it manually by first choosing the model of each loop that you like the best, and then by saving and text-editing PDB files, or possibly even in Chimera by carefully deleting the overlapping parts of those models and then combining what is left of them into a single model befire writing it out as PDB.  It can be tricky, however, and would still probably require some text-editing of the resulting file.

For example, if I refined one loop and the output models are #1.1,#1.2,#1.3 and refined a different loop and the output models are #2.1,#2.2,#2.3,  I first need to decide which model is best for each loop.  It would also be a good idea to save the session so you can always go back if you make mistakes in later steps. Pretend the best models are #1.3 and #2.1 — next I’d probably close all the other models to avoid confusion (e.g. use Model Panel, open from Favorites menu).  Then save those 2 models as PDB files (menu: File… Save PDB) and then do a lot of manual editing and combining to make 1 PDB file of your final model.  Or you could (very carefully) in Chimera delete parts of #1.3 and #2.1 so that together they do not include any duplicate residues, then use “copy/combine” function in the Model Panel to combine them into one model, then save as PDB.  

Modifying and saving data in Chimera:

Deleting atoms:

Model Panel copy/combine:

However, it would really be best to do the refinement in a single step, especially if those two loops might be interacting with each other.  You can use the mouse to choose two separate segments in the Sequence window at the same time (click-drag and then Shift-click-drag to add separate segments) to use with the “active region” option in Model Loops/Refine Structure.

Finally, realize that if the missing segments are large, the models may not be very reliable anyway, so you may also want to try other modeling programs (not just Chimera/Modeller). 

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

> On Oct 2, 2019, at 9:11 PM, Hồ Phương Dung <phuongdunghongoc at gmail.com> wrote:
> Dear Sir/Madam,
> I am Dung. I am currently using Chimera to do the refinement for my protein because it has some large missing residues segments. I use Tools/ Loops- Model refinement of Chimera software to do that task. As it was failed to generate models if I performed refinements for all missing residues segments. Thus, I decided to refine them not at once. The problem is that I could not find how to combine the  separated loops from models after refinement. I am new to Chimera so I hope that my description can be useful for you to imagine my problem. 
> I hope that you could support me to solve this problem. I really appreciate it. 
> Thank you for spending your valuable time. 
> Yours sincerely, 
> Dung 
> Hồ Ngọc Phương Dung
> International University - Vietnam National University
> Email: phuongdunghongoc at gmail.com

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