[Chimera-users] [EXTERNAL] Re: Morphing PDB

Reza Khayat rkhayat at ccny.cuny.edu
Mon Oct 26 13:56:18 PDT 2020

Thanks Elaine.


Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031

From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Monday, October 26, 2020 3:34 PM
To: Reza Khayat
Cc: chimera-users at cgl.ucsf.edu
Subject: [EXTERNAL] Re: [Chimera-users] Morphing PDB

Hi Reza,
Yes, but since you can't say to morph only part of a model and ignore the rest, I believe you would have to prepare pairs of input structures where only the morphing part changes.  One way would be to make whole complexes, e.g. ABC in conf 1, another with A in conf 2 and BC in conf 1,  another with AB in conf 2 and C in conf 1, etc. However, that would be a lot work.  Another, probably easier way is:

(1) open structure of ABC in conf 1 (say it is model #0)
(2) open structure of ABC in conf 2  (say it is model #1)
(3) split both models by chain with command "split"
<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_midas_split.html&d=DwIFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=V5OlZUyWYZU8l29kILD05nc2HrwLgl42spvxxnQGvR0&s=5vOKfi6BFBaH55clUgB9hj-2tVK8wDjfGDAVqskhfXQ&e= >
....so that you now have six models: #0.1, 0.2, 0.3 and #1.1, 1.2., 1.3
(4) morph chain A #0.1 -> #1.1
(5) morph chain B #0.2 -> #1.2
(6) morph chain C #0.3 -> #1.3

So you will have 3 morph trajectories (which I recommend then saving as a session so you don't have to re-make them over and over).  You can play them back one after the other, e.g. with the "coordset" command.
<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_midas_coordset.html&d=DwIFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=V5OlZUyWYZU8l29kILD05nc2HrwLgl42spvxxnQGvR0&s=HgN9rowSAGjDSTiyFoW8ZYApTTUD2QLEiFsngZPaGmk&e= >

Depending on your whole workflow, you might want to consider using ChimeraX instead of Chimera for this morphing.  The "morph" command in ChimeraX is much easier to use and has more options.  ChimeraX also has "coordset" "split" "movie" and many others, as well as more robust molecular surface calculations and some fancier lighting options.  ChimeraX User Guide with command index:
<https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_docs_user_index.html&d=DwIFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=V5OlZUyWYZU8l29kILD05nc2HrwLgl42spvxxnQGvR0&s=2SsGq-eqq5HV0dGcWoT2_p8QLBXfX6yMn879MM_H56A&e= >

ChimeraX advantages:
<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chimerax_docs_user_advantages.html&d=DwIFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=V5OlZUyWYZU8l29kILD05nc2HrwLgl42spvxxnQGvR0&s=WLBr5Q1enx7u3NMgG6750Jyh6Le9n7zL19m13qNO9Bo&e= >

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

> On Oct 26, 2020, at 12:14 PM, Reza Khayat <rkhayat at ccny.cuny.edu> wrote:
> Hi,
> Is it possible to morph multiple chains serially? I have a trimer in two different conformations, I would like to morph Chain A in conformation 1 to Chain A in conformation 2. Then, I'd like to do this with chain B and finally chain C.
> Best wishes,
> Reza

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