Adaptation of Paul Emsley's distributed Tutorial (Sept '08) by Michael Chapman, Oct '09

1 Mousing

The following is for quick reference, once you have some objects on the display to view.

Left-mouse Drag Rotate view
Ctrl Left-Mouse Drag Translates view
Shift Left-Mouse Label Atom
Right-Mouse Drag Zoom in and out
Middle-mouse Centre on atom
Scroll-wheel Forward Increase map contour level
Scroll-wheel Backward Decrease map contour level

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

2.1 Get the files

Hopefully, we will be making the files available to you in a convenient location.  If so, skip the rest of the section 2.1.

If not and you are doing this tutorial independently, then the coordinates and data files are available from several locations.

The easiest might be from the examples sub-directory of the Coot installation, such as:  C:\Programs\WinCoot_0.6\examples.

Failing that, they are available from Paul Emsley's web site.  You can open your web browser to the http: address below, or use the Unix command wget, as below:

$ wget˜emsley/coot/tutorial/tutorialmodern.pdb
$ wget˜emsley/coot/tutorial/rnasa-1.8all refmac1.mtz

2.2 StartCoot

To use coot,in a terminal window, type:

Unix (MacOS)

$ coot


This is a little more complicated.  The default installation will provide a desktop icon which you can use considering the caveats below.  You should only do this if it is a single-user computer, and probably only if you use Coot only for a single project.  The problem is that the started from a Desktop icon, Coot will store "state" and backup files in the installation directories, and will not differentiate those of different people / projects.  You really want to run Coot in a specific directory for each directory.  The documented way to do this is to copy the link to the directory and edit the "run in" setting in the properties.  An easier approach is just to copy the run_wincoot.bat file from the installation directory to each user directory where you want to run coot.  Then double-click this run_wincoot.bat.

Unix, MacOS & Windows

From here on, the running will be mostly the same, independent of operating system.  When started you should get a blank window like that shown below.  In future illustrations, this documentation will use a white background, but yours will continue to be dark.


2.3 Display Coordinates

[Coot displays a Coordinates File Selection window]

– Select tutorial-modern.pdb from the “Files” list

("Recenter?" should be set to "Recenter on Molecule" for this, your first set of coordinates, but for subsequent coordinate sets, "Don't recenter" keeps the same view which is usually more convenient.)

Figure2: Coot After Loading Coordinates

2.5 Display maps

We are at the stage where we are looking at the results of the refinement. The refinement programs stores its data (labeled lists of structure factor amplitudes and phases) in an “MTZ” file.  Let’s take a look...

2.6 Zoom in and out

To zoom in, click Right-mouse and drag it left-to-right or up-to-down. To zoom out again, move the mouse the opposite way.


Figure4:Coot after reading an MTZ file and zoomed in.

2.7 Recentre on Different Atoms


  1. Click Middle-mouse over an atom in the graphics window [Coot recenters on that atom]

  2. Ctrl Left-mouse & Drag moves the view around. If this is a too slow and jerky:


Using dialog:

Figure5: Coot’s Go To Atom Window.

[You can’t change the color of the Environment distances]

You can turn off the Environment distances if you like.

Figure6: Coot showing Atom Label and environment distances.

2.8 Change the Clipping (Slab)

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).

2.9 Recontour the Map

  1. Scroll your scroll-wheel forwards one click5 [Coot recontours the map using a 0.05 electron/A higher contour level]

  2. Scroll your scroll-wheel forwards and backwards more notches and seethe contour level changing.

  3. If you don’t have a wheel on your mouse you can use “+” and “-” on the keyboard.

  4. Note that the “Scroll” button in the Display Manager allows you to select which map is affected by this.

2.10 Change the Map Colour (skip if short of time...)

2.11 Select a Map

For much of what follows, you will need access to modeling widgets.  In new versions of Coot, there is a tool-bar which is (by default) placed at (by default) the right edge of the display area.  By default, it displays only icons, but for the novice user it is helpful to have the text names of the commands as well.  These can be obtained by clicking on the bottom triangular icon.  The toolbar properties are set through "Edit --> Preferences --> Refinement Toolbar tab".  If you still can't find a toolbar, an equivalent dialog can be displayed with "Calculate --> Model/Fit/Refine"

Click on "Map". If you were displaying more than one, it would allow you to select which is to be used for commands such as "Real Space Refine Zone".

3 Model Building

“So what’s wrong with this structure?” you might ask. There are several ways to analyze structural problems and some of them are available in Coot.

Validate --> Density Fit Analysis --> tutorial-modern.pdb.  [Coot displays a bar graph]

Look at the graph. The bigger and redder the bar the worse the geometry. There are 2 areas 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 that89ACAis at the centre of the screen]

3.1 Rotamers

Figure7:89A now fits the density nicely.

3.2 More Real Space Refinement

Now let’s have a look at the other region of outstanding badness:

[As the backbone is far from the correct location, you will likely have to drag the residue into approximately the right place for refinement to converge properly.  This is an example of non-linear refinement being local.  It finds a local optimum, not necessarily a global optimum.  Move residue 41A by dragging the white intermediate atoms with the left mouse button.  When you release the button, refinement will start automatically.]

At this point you would normally accept the structure if you think it is an improvement.  However, let's reject it, so that you can see an alternative approach.

[When you let go, you may be surprised how well refinement takes care of not just the carbonyl, but it now places the entire side chain in the density.]

[Before you now click "Accept", compare the backbone structures of the intermediate atoms to the old ones.  Perhaps you can recognize why the model was no originally built in the correct configuration.  Look for something unusual (but valid) in the new intermediate structure.  Click accept.]

[Near the end of the side chain of residue 41 you will see a large blob of density.  It is seen in both the blue (regular) map and green (a difference map).  The difference map shows regions where model is missing (green) or is present where there is no data (red).  This large blob suggest that there might be a ligand that needs to be modeled.  What? - not an easy answer.]

4 Blobology

4.1 Find Blobs

To be found under Validate (called “Unmodelled Blobs”). You can use the defaults in the subsequent pop-up. Press “Find Blobs” and wait a short while. You will get a new window that tell you that it has found unexplained blobs. Time to find out what they are.

4.1.1 Blob3 - in the interests of time, skip to 4.1.2 Blob2 (or 4.1.3 Blob 1)

Let’s start from Blob3 (the blobs are ordered biggest to smallest -Blobs3 and 4 (if you have it) are the smallest).

4.1.2 Blob2

Click on the button “Blob 2” and examine the density. Something is missing from the model. What? This protein has been co-crystallized with its ligand substrate. That’s what missing: 3’GMP.  So let’s add it. . .

On a Mac or Unix computer with RefMac and CCP4 software installed

[If you don't have RefMac and CCP4 available, a non-fatal error message should appear by now.  Proceed with the WinCoot directions.  If no error message occurs, skip to "All computers".]

WinCoot on a PC (RefMac / CCP4 generally not available):

Open the file  monomer-3GP.pdb.

All computers...

4.1.3 Blob1

[Looks to me (Michael) that this auto-building has done a great job of residues 94 & 95, but a lousy one for 96.  There is density extending to Cys 7 A, and I suspect that residue 96 should be part of a disulfide with its side chain pointing in the opposite direction.  If you are ahead of everyone else at this point, you might want to use the skills you have used to model the Cysteine to point in the other direction.]

Ending Coot

This is where we will leave the distributed tutorial.  Before exiting, one would normally save coordinates and the state.  Decide whether you want to do this (using menu File) or whether you would want the files to be ready to start the tutorial from scratch.  Then File --> Exit.

More Challenging Maps

The examples used for the Coot tutorial are chosen to put Coot in its best light, and to be easy on the student learning Coot.  i.e. they are examples where the density is clear and at high resolution making it relatively easy to see where the model atoms should be placed.  Here is an example from the other end of the spectrum, one of the poorer parts of a structure determined at 2.4 A resolution.  While these regions might represent only a few percent of the structure, they take a big proportion of the time remodeling.  The files will only be available locally in tutorials mentored by Michael Chapman.  In the future they might be available from the PDB database, but not now.

Start up Coot again, rejecting the option to use a previously saved state.  See if you can use the skills that you have learned to examine the differences between the original model (1M80.pdb) and one (1M80-coot-10.pdb) that was remodeled using an improved map (calculated from  ak_apo_091022d_002_map_coeffs.mtz).  The region near chain A residue 294 is the most illustrative.  A few residues to each side, the density is reasonably good.  However, here it may appear missing, until you lower the contor level.  Perhaps you can see that one of the models is a better fit, but the density through both models is weak, and it is not difficult to see how the worse model might have been built into an inferior map.  If you look carefully, you can see that the error created a frame-shift of one residue.  Thus everything is off in terms of sequence until there is another error a few residues away.  If you have a bunch of time, you could hide the corrected structure, and try to remodel 1M80.pdb into the new path of the density.  When you are done, compare to 1M80-coot-10.pdb to see how well you have done.


This document was originall written using XEmacs 21.5 in LATEX using AUCTEX and is distributed with theCoot source code.   It was converted to html and edited in SharePoint Designer.