Coot Tutorial
Coot Tutorial
Coot Tutorial
Contents
1 Mousing 2
2 Introductory Tutorial 2
2.1 Get the files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
2.2 Start Coot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
2.3 Display Coordinates . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
2.4 Adjust Virtual Trackball . . . . . . . . . . . . . . . . . . . . . . . . . . 3
2.5 Display maps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
2.6 Zoom in and out . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
2.7 Recentre on Different Atoms . . . . . . . . . . . . . . . . . . . . . . . . 4
2.8 Change the Clipping (Slab) . . . . . . . . . . . . . . . . . . . . . . . . 6
2.9 Recontour the Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.10 Change the Map Colour . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.11 Select a Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
3 Model Building 8
3.1 Rotamers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3.2 More Real Space Refinement . . . . . . . . . . . . . . . . . . . . . . . . 10
4 Blobology - Optional 11
4.1 Find Blobs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
4.1.1 Blob 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
4.1.2 Blobs 2 and 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
6 Extra Fun 12
1
1 Mousing
First, how do we move around and select things?
2 Introductory Tutorial
In this tutorial, we will learn how to do the following:
1. Start Coot
2. Display coordinates
3. Display a map
4. Zoom in and out
5. Recentre on Different Atoms
6. Change the Clipping (Slab)
7. Recontour the Map
8. Change the Map Colour
9. Display rotamers and refine residue
2
Figure 1: Coot at Startup
Not much to see at present... Actually, after this, coot screenshots will be
displayed with a white background, whereas you will see a black one
• Either
– Select tutorial-modern.pdb from the “Files” list
or
– Type tutorial-modern.pdb in the Selection: entry
• Click “OK” in the Coordinates File Selection window
[Coot displays the coordinates in the Graphics Window]
3
Figure 2: Coot After Loading Coordinates
If you choose instead “Open MTZ, cif or phs...” you will see:
• [Coot displays a Dataset File Selection window]
• Select the filename rnasa-1.8-all refmac1.mtz
[Coot displays a Dataset Column Label Selection window]
Notice that you have a selection of different column labels for the “Ampli-
tudes” and “Phases”, however, let’s use the defaults: “FWT” and “PHWT”.
• Press “OK” in the Column Label Window
Now open the MTZ file and select column labels “DELFWT” and “PHDELWT”.
So now we have 2 maps (whether auto-opened or not).
4
Figure 3: Coot MTZ Column Label Selection Window
5
• Expand the tree for the “A” chain
• Select 1 ASP in the residue list
• Click “Apply” in the Go To Atom window
• At your leisure, use “Next Residue” and “Previous Residue” (or “Space” and
“Shift” “Space”in the graphics window) to move along the chain.
• Click Middle-mouse over an atom in the graphics window
[Coot recentres on that atom]
• Ctrl Left-mouse & Drag moves the view around. If this is a too slow and
jerky:
– Select Edit → Preferences. . . from Coot’s menu-bar
– Select the “Maps” toolbutton on the left
– Select the “Dragged Map” notebook tab.
– Select “No” in the “Active Map on Dragging” window
– Click “OK” in the “Preferences” window
Now the map is recontoured at the end of the drag, not at each step3 .
Another, additional way to make the movements faster is to change the num-
ber of steps for the “Smooth Recentering”. Again you find this in the “Prefer-
ences” (Preferences → General → Smooth Recentering). Change the “Num-
ber of Steps” from the default 80 to something smaller, e.g. 20.
• You can display the contacts too, as you do this:
Alternatively, you can use “D” and “F” 4 on the keyboard, or Control Right-
mouse up/down (Control Right-mouse left/right does z-translation).
3 which looks less good on faster computers.
4 think: Depth of Field.
6
Figure 5: Coot’s Go To Atom Window (it doesn’t look exactly like this any more).
7
2.9 Recontour the Map
• Scroll your scroll-wheel forwards one click5
[Coot recontours the map using a 0.05electron/Å3 higher contour level]
• Scroll your scroll-wheel forwards and backwards more notches and see the
contour level changing.
• If you don’t have a wheel on your mouse you can use “+” and “-” on the
keyboard.
• Note that the “Scroll” button in the Display Manager allows you to select
which map is affected by this6 .
3 Model Building
“So what’s wrong with this structure?” you might ask.
There are several ways to analyse structural problems and some of them are
available in Coot.
8
Look at the graph. The bigger and redder the bar the worse the geometry. There
are 2 area of outstanding badness in the A chain, around 41A and 89A.
Let’s look at 89A first - click on the block for 89A.
[Coot moves the view so that 89A CA is at the centre of the screen ]
3.1 Rotamers
• Examine the situation. . . [ The sidechain is pointing the wrong way. Let’s Fix it...]
7
• Menubar: Calculate → Model/Fit/Refine...
[Coot displays the Model/Fit/Refine window]
• Select “Rotamers” from the Model/Fit/Refine window 8 .
• In the graphics window, (left-mouse) click on an atom of residue 89A (the
Cγ, say)
[Coot displays the “Select Rotamer” window]
• Choose the Rotamer that most closely puts the atoms into the side-chain den-
sity
• Click “Accept” in the “Select Rotamer” window
[Coot updates the coordinates to the selected rotamer]
• Click “Real Space Refine Zone” in the Model/Fit/Refine window9 .
• In the graphics window, click on an atom of residue 89A. Click it again.
[Coot displays the refined coordinates in white in the graphics and a new
“Accept Refinement” window]
• Click “Accept” in the “Accept Refinement” window.
[Coot updates the coordinates to the refined coordinates. 89A now fits the
density nicely.]
OK. That’s good.
Now, how about if we just use Real Space Refinement only?
• Click “Undo” twice
[Coot puts the sidechain back to the original position]
• Click “Real Space Refine Zone” in the Model/Fit/Refine window10 .
• In the graphics window, click on an atom of residue 89A. Click it again.
[Coot displays the refined coordinates in white in the graphics and a new
“Accept Refinement” window]
• Now using left-mouse, click and drag on the intermediate (white) CZ atom
of the PHE (if you mis-click the atom, the view will rotate).
• Can you pull the atom around so that the side-chain fits the density?
[Yes, you can]
7 or use the modelling toolbar on the right of the Coot window, i.e. you don’t need to open the
Model/Fit/Refine window
8 Or click on the “Rotamers” button of the modelling toolbar
9 . . . or use the modelling toolbar button
10 . . . or modelling toolbar button
9
Figure 7: 89A now fits the density nicely.
10
4 Blobology - Optional
This is an optional section11 - generally you are expected to skip this and move on
to “Use the EDS”. However, if you have time and are feeling adventurous (this is
not expected) you can explore more density fitting tools:
4.1.1 Blob 3
Let’s start from Blob 3 (the blobs are ordered biggest to smallest - Blobs 3 and 4 (if
you have it) are the smallest).
• Click on “Blob 3”
[Coot centres the screen on a blob]
• Examine the situation. . .
[We need something tetrahedral there. . . ]
• “Place Atom At Pointer” on the Model/Fit/Refine window12
[Coot shows a Pointer Atom Type window]
• “SO4” in the new window. . .
• In the “Pointer Atom Added to Molecule:” frame, change “New Molecule”
to ‘‘tutorial-modern.pdb”
• Click OK.
• Examine the situation. . .
• the orientation is not quite right.
• Let’s Real Space Refine it (you should know what to do by now. . . )
• (“Real Space Refine Zone” then click an atom in the SO4 twice. Accept)
[The SO4 fits better now].
These are the blobs due to missing loops and the enzyme substrate.
Can you find the right tools to fit these parts of the map?
[No. Well, not easily. I am going to move on to the next section. . . ]
11 for the speedy.
12 also available in the modelling toolbar
11
5 Use the EDS
OK, so now you have some basics under your belt. We now want you to assess the
quality of models given an electron density map generated from the experimental
data. There are many thousands are structures with maps in the database, here are
a few examples:
• 2bf6
• 2aeq
• 3gvl
For each of these structures, consider how difficult it is to place the atoms given
the electron density map. For the structures 2aeq and 3gvl consider the ligands
in particular13 . Are the models consistent with the data and prior knowledge of
carboydrate chemistry or might the depositors have made a model-building error?
6 Extra Fun
Coot is Free Software. Google for it and you can download it and play with it at
home.
13 use the “Go To Ligand” toolbutton in the toolbar for rapid navigation
12