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

Hồ Phương Dung phuongdunghongoc at gmail.com
Thu Oct 3 16:30:27 PDT 2019

Dear Madam,
I am so grateful for your advice. I will give it a try. Once again, thank
you for your detail instruction.
Wish you all the best.
Yours sincerely,
Hồ Ngọc Phương Dung
International University - Vietnam National University
Email: phuongdunghongoc at gmail.com

Vào Th 6, 4 thg 10, 2019 vào lúc 00:53 Elaine Meng <meng at cgl.ucsf.edu> đã

> 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:
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#building
> >
> 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:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html>
> Deleting atoms:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html>
> Model Panel copy/combine:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#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
> -----
> 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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