Molecular Visualization with Chimera
In this session, you will utilize USCF Chimera to view and interrogate two biomolecular structures. This program is freely available for Microsoft Windows, Mac OSX, Linux, and UNIX-based computer operating systems such as IRIX. From home (or your home lab), you may download the Chimera structure viewer from the UCSF website: http://www.cgl.ucsf.edu/chimera/download.html
Chimera menu commands will be designated as: Button -> button -> button .
Chimera command line commands are indicated after: command>
In addition to this handout, you should receive a copy of The Chimera Quick Reference Guide (UCSF).
In a terminal window, type chimera. This is a newer, larger program than e.g. RasMol, and will take much longer to start running. You can drag the bottom right corner of the Chimera window to expand the window size to something comfortable for you.
Now, automatically fetch the structure of hemoglobin from the Protein Data Bank.
File -> Fetch by ID -> Type 1GZX -> Fetch
Rotate the structure with the left mouse button (button 1)
Translate (move) the structure with the middle mouse button (button 2)
Zoom in on the structure with the right mouse (button 3)
Here, we start with a PDB code we already know. Usually, we don't know that beforehand, so you would go to rcsb.org and search for your protein of interest. If you haven't done this before, go there and examine the "Molecule of the Month" entry for hemoglobin.
Tools -> Depiction -> Rainbow -> Chain
(if the command line is not visible at the bottom of the window, choose Favorites -> Command Line)
command> color purple #0:HEM
command> color orange #0:HEM@FE
You'll want to learn the syntax used for specifying selections:
#[model number]:[residue name or number]@[atom name]
Further details can be found under atom specification on this page (it's not a bad idea to keep this page open while working in Chimera):
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecore.html
Select -> Residue-> HEM
Shift+Ctrl+click on Fe atoms to deselect just the iron atoms.
(A Ctrl+click on the background will deselect everything.)
Actions -> Atoms/Bonds -> ball and stick
Ctrl+click on any atom of the heme to select it (Hover over different hemes to determine which is chain B)
Shift+Ctrl+up-arrow to expand selection to include entire heme
Actions-> Focus
Select -> Zone -> <5.0 angstroms from currently selected atoms
Click button for ‘Select all atoms/bonds of any residue in selection zone’
Actions -> Atoms/Bonds -> show
Select -> Invert (all models)
Actions -> Atoms/Bonds -> hide
Actions -> Ribbon -> hide
Invert the selection again (or re-select the heme and the zone of nearby residues).
Actions -> Color -> by heteroatom
You should now see Nitrogen atoms in blue, Oxygen atoms in red, and Sulfur atoms in yellow.
command> select #0:235.B
Actions -> Atoms/Bonds -> ball & stick
Actions -> Color -> all options
Select "Coloring applies to: atoms/bonds".
Click the "red" button.
Select -> Structure -> sidechain/base -> without CA/C1'
command> ~select #0:235.B
(That command begins with a "tilde" character meaning de-select.)
Action -> Color -> yellow
Select -> Clear selection
Select -> Structure -> solvent
Actions -> Atoms/Bonds -> ball & stick
Actions -> Color -> by element
File -> Save Session As -> hg_session.py
File -> Close Session
Exploration of the high resolution X-ray structure for bovine rhodopsin should provide an opportunity for us to combine many of the visualization techniques covered up to this point – plus an opportunity to see a few more. Here, the ligand, 11-cis-retinal (RET), is a covalently bound inverse agonist that locks the protein into an inactive (dark state) conformation. Our annotation of this structure will illustrate in atomic detail the chemical and physical composition of the ligand-binding site of this G-protein coupled receptor, an integral membrane protein that has seven membrane-spanning segments.
A pre-edited version of the rhodopsin PDB file exists locally to load into Chimera.
Display the protein backbone trace.
File -> Open -> Filename: /home/momokurs/rosetta_workshop/tutorials/day02/sample_files/rho.pdb
Actions -> Atoms/Bonds -> backbone only -> chain trace
Display the protein secondary structure.
Select -> Structure -> secondary structure-> helix
Actions -> Ribbon -> show; Actions -> Ribbon -> edged
Actions -> Color -> all options; ribbons; green
Select -> Structure -> secondary structure -> strand
Actions -> Ribbon -> show; Actions -> Ribbon -> edged
Actions -> Color -> orange
Display and color the conserved disulfide bond in rhodopsin.
command> select #0:110.A,187.A
Actions -> Atoms/Bonds -> show
Actions -> Focus
Actions -> Atoms/Bonds -> stick
Actions -> Color -> all options; atoms/bonds; by element
Position the camera looking into the helix bundle from just above the beta strands.
Highlight the ligand, 11-cis retinal (RET)
Select -> Residue -> RET
Actions -> Atoms/Bonds -> stick
Actions -> Color -> all options; atoms/bonds; medium blue
Display any water molecules bound near the ligand.
Select -> Structure -> solvent
Actions -> Atoms/Bonds -> ball & stick
Actions -> Color -> red
Try adjusting the clipping planes to hide some detail and focus on the ligand binding site.
Tools -> Viewing Controls -> Side View <or> Favorites -> Side View
Drag front (left) and back (right) yellow clipping planes to adjust the molecular detail in your view.
Chimera starts in mono viewing mode by default. You can enable stereo viewing mode.
Tools -> Viewing Controls -> Camera -> camera mode: cross-eye or wall-eye stereo
You can continue in stereo or mono.
Focus on the 11-cis retinal ligand-binding site.
Select -> Residue -> RET
Actions -> Focus
Show amino acid side chains within 5.0 Angstrom of the ligand.
Select -> Zone -> <= 5.0 angstrom from currently selected atoms
Click 'Select all atoms/bonds of any residue in selection zone'
Actions -> Atoms/Bonds -> show
Actions -> Atoms/Bonds -> stick
command> ~select #0:RET.A (with a tilde to negate the select command)
Actions -> Color -> all options; atoms/bonds; by element
Render a semi-transparent surface for the ligand.
Select -> Residue -> RET
Actions -> Surface -> show
Actions -> Color -> all options; surfaces; gray
Actions -> Surface -> transparency -> 50%
Save the image in a file
Actions -> Color -> all options; background; white
File -> Save Image -> adjust Image width to 1024 pixels
File name -> rhodopsin.png
Save
Two additional points. You can see that the repetive use of menus gets tiresome. As you use chimera more, you will get faster if you learn the commands listed on the quick reference sheet, and type them into the commandline.
Secondly, writing and modifying scripts can be very useful for creating figures. The script can also be customized by editing it as a text file. This is a very powerful method for accelerating your visualization work, so an example script has been provided here for you to experiment with and customize.
~/rosetta_workshop/tutorials/day02/sample_files/startup.cmd
Copy it to your home directory. Load a new structure and run the script. (Run scripts by opening them with File -> Open) View it in a text editor. Try making changes to suit your protein of interest.
Duplicate the DNA-duocarmycin representation you already made with pymol. If you can, try to do it without reading the steps below. Then read through them to find any things you might have missed.
File -> Fetch by ID -> 1DSM
command> select
command> ~select #0.1
(That line begins with a "tilde" character)
command> delete sel
Tools -> Depiction -> Rainbow (Change color every chain; apply)
Actions -> Atoms/Bonds -> nucleotide objects -> off
select (Ctrl-click) the covalent bond between Adenosine 5 and the DSA
Actions -> Atoms/Bonds -> delete (so that the surfacing command can be limited)
Select -> Residue -> DSA
Actions -> Color -> by heteroatom
Actions -> Surface -> show
Actions -> Surface -> transparency -> 80%
Favorites -> Model Panel -> double-click on MSMS surface to see attributes, set vertex density=10
Select -> Chemistry -> Element -> H
Actions -> Atoms/Bonds -> hide
Tools -> Depictions -> Nucleotides (start with defaults. Vary the options according to taste.)
Save a .png image in your working directory. Save the session for later.