**UCSF Chimera**
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[Image Source][1]
[Learn More][2]
This page will help you get started with Chimera, a program used to visualize, edit, and compare 3D models of your molecules. It is a powerful tool with many features, but they are buried under menus and can take some time to feel comfortable with using. This tutorial was taken, and minimally modified, from a portion of Dr. Stephanie Lewis' tutorial "AutoDock 4.0 and AutoDockTools 1.5.2 Tutorial."
Things to know when working with UCSF Chimera
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Mouse options
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Items viewed in Chimera can be seen as three-dimensional objects. As such, there are options for the mouse that allow one to rotate, scale, and translate the item of interest. You can select which buttons and keys to use for specific actions.
1. Favorites -> Preferences...
2. Click and hold the button at the top beside “Category:”
3. Move the cursor down to the Mouse option and release.
A table will appear with selection dots for each mouse action. You can select options and adjust the location and/or position of your protein in the viewer without saving. If you would like to keep your options for future visualization, you can click Save at the bottom. When you have finished with the Preferences window, click Close to dismiss. There are other categories listed in the Preferences window. Take some time to look at what these other options are and make adjustments if you deem it necessary to aid in your visualization work.
Commands
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Chimera works primarily with a Graphical User Interface (GUI), but there are also command line options that may prove useful when visualizing a system. The command line should appear at the bottom of the viewer window (“Command:” followed by a box). If it does not, you can show the command line by clicking the following;
Favorites -> Command Line
**Some useful commands**
select :11,22,33
Select specifically numbered residues in a protein. This command will select all residues present in the session with the listed numbers. If you have multiple proteins present, such as when doing alignments are comparing structures, residues with these numbers will be selected for ALL proteins. The values “11,22,33” can be changed to any of the residue numbers for you protein. For example, you want to look at residues 474 and 323 of your protein. You would enter “select :323,474” or “select :474,323”, and then press ENTER. The order of the numbers does not matter.
display :11,22,33
Display listed residues if not already visible. Just as with select, all residues with the numbers listed will be displayed regardless to which protein the residues belong.
Free-floating lists
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Each menu and submenu can be opened as a separate widget. If you click the dashed line at the top of any menu or submenu, a new window will appear and stay open with the contents of that menu. This is useful when the same menu option will need to be selected multiple times, such as hiding or viewing selected atoms or selecting a single ligand chain from a long list of ligand chains.
A full list of commands can be found in the [User’s Guide][3] on the UCSF Chimera home page.
There are also many useful tutorials available for UCSF Chimera on the [developer site][4].
The “[Getting Started Tutorial – Menu Version][5]” has helpful tips on basic manipulations (e.g.hiding and showing atoms, selecting chains, molecular representations)
When in doubt, consult the User’s Guide.
[1]: https://dl2.macupdate.com/images/icons256/60881.png
[2]: https://docs.google.com/document/d/1yKpyQ0LjhuLSTqlU8qzyyhqxg-WYkvOFUsu38H0qRkM/edit
[3]: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/framecommand.html
[4]: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html
[5]: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html
