[Chimera-users] 3D-visualization of protein chain and mutation

[Coci, Emanuele]

Dear Elaine,

many thanks for your detailed information and sorry for my delayed answer- I was out of duties.

Since I will need soon to use properly the software, I have looked in details the links you sent me; nevertheless I think I will come back to you for some specific question in the near future.

Best regards

Emanuele

________________________________
Von: Elaine Meng [mailto:meng at cgl.ucsf.edu]
Gesendet: Freitag, 2. Oktober 2015 19:00
An: Coci, Emanuele
Cc: chimera-users at cgl.ucsf.edu List
Betreff: 3D-visualization of protein chain and mutation


From: "Coci, Emanuele" <Emanuele.Coci at akh-celle.de<mailto:Emanuele.Coci at akh-celle.de><mailto:Emanuele.Coci at akh-celle.de>>
Date: Friday, October 2, 2015 at 8:54 AM
Subject: 3D-visualization of protein chain

Deat Chimera team,
my name is Emanuele Coci, MD PhD.

I would kindly ask you for help about Chimera software in solving the following technical issue. I want to visualize the 3D-structure of a mutated protein chain.

Which of the chimera tools is more indicated to visualize the 3D structure?
Is the toll open source?
Which software do I need to download the tool on my PC : JAVA, ...?

Best regards and many thanks in advance?
Emanuele Coci

Dear Emanuele Coci,
Chimera is a free download for any noncommercial use (research, education, ...) and is available for Windows, Mac, and Linux.  You should not have to download any other software to use it.  All you need is a reasonably modern computer. See Chimera homepage and download links:
<http://www.rbvi.ucsf.edu/chimera/index.html>
<http://www.rbvi.ucsf.edu/chimera/download.html>

I've CC'd chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu> - that is the proper address for user questions.

There are many possible styles of displaying a protein, and you have to use your own judgement and artistic taste to decide which style is best for what you want to see for yourself or show to others.  There are several step-by-step tutorials for learning how to use Chimera, including "getting started" for beginners and some example image tutorials:
<http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html>

For showing a mutation, the first thing you could do is just show the location of that amino acid on the structure (without mutating it), for example coloring it differently than the rest of the structure.  It may be helpful to show the sequence of the protein so that you can identify the correct position (Chimera menu: Favorites... Sequence).  You can choose a residue with the mouse in the sequence window, which will automatically select-highlight it in the structure.

Secondly, you could try "mutating" that residue computationally.  This could be done with the Rotamers tool (in menu under Tools... Structure Editing) or the "swapaa" command.  There is an example of using the Rotamers tool in the "Structure Analysis and Comparison" tutorial:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/rotamers.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>

However, Chimera will not predict any larger-scale changes in the structure from the mutation or calculate changes in stability or affinity. It will only change the sidechain and not move anything else.  You can use Rotamers to analyze the H-bonds and clashes (bad contacts) of different conformations of the sidechain, which may allow you to hypothesize whether the mutation would be disruptive to the stability or interactions of the protein.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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