Coot 1.1 - Tutorial 1

Lucrezia Catapano & Paul Emsley - March 2025



Let’s do the Coot Tutorial using modern methods!

Before we start, familiarise yourself with the basic navigation and keyboard shortcuts in Coot 1.1:

Basic Navigation - Mouse & Keyboard Shortcuts.


1. Load the data

Load the tutorial:

The map is quite nice looking - the resolution of the data is 1.8 Å.

Let’s turn on Updating Maps (so that the maps track the current model):

2. Check the problems

Let’s view the structure anomalies:

A dialog is presented with Outliers listed by chain-id and residue number

Note: This structure is old, at which time the criteria for chiral volumes outliers was less strict than today standards. So, let’s ignore the chiral volume outliers for now.

Click on the first button (for A 2). Take a look at what is interacting with this VAL. See that it’s actually the PHE at A 89 that’s wrong. Recentre on that residue (middle-mouse click on the CB).

3. Fix and Refine

The figure shows the new types of geometry validation markups


Fix the rotamer:

The sidechain will jump into the density, the maps will update and the difference maps will disappear in this region.

A new overlay with Coot Points, and R factors, will appear. You will collect Coot points as the model improves.

Note: The R factors are calculated by a clipper function, not REFMAC5.

Next problem in the dialog is at A 32. The density here is not very good and there may be a number of different conformers/rotamers. Let’s, for now, just choose one of them that has higher probability than the current model.

Notice that the number of Outliers/Problems has decreased.

Now look at the rest of the labels in that dialog. Many of them are around the same residues, 40, 41 and 42.

Let’s look at the Ramachandran Plot for this chain.

Let’s click on the first red spot on the left.

In the refinement dialog:

The Rama balls go green. The 2 outliers (red spots) in the Ramachandran plot are now gone.

Let’s fix the other rotamer outliers, ignoring the chiral volumes outliers.

Finally, click on Refine - RSR Chain to refine the entire chain. If you reopen the validation dialog, you will see that all the chiral volume issues are resolved.

Let’s have a look at some missing atoms:

Here we have missing main-chain atoms and missing side-chain atoms

4. Unmodelled blobs

Let’s find parts of the map that are as yet not modelled, i.e. find unmodelled blobs:

Blobs are sorted by size.

What are we looking at?

Blob 4 (if present in the dialog) and Blob 3 are the same thing. Let’s do Blob 3 first because the density is better. Notice the shape of the blobs and the environment. The precipitant for this structure was ammonium sulfate. So let’s add a SO4 here:

Coot adds a sulfate ion using “Jiggle Fit”

Now you can do the same thing for Blob 4 if you wish.

5. Fitting the ligand

Blob 2 is the ligand. Let’s build a ligand into that:

Check the chemistry (yes the phosphate is on the 3’ end).

Go to the Display Manager, and there will be Fitted-ligand in the molecule window.

When the ligand is corrected placed, let’s merge it into the main molecule:

6 . Missing Residues

Blob 1 is a piece of missing protein.

You can see on the right hand side of the sequence view that the A chain is missing the residues “QTC”

Coot builds the loop!

Is there still work to be done?

Maybe. You can use Ctrl Shift Arrow keys to reorient the CYS A 96 if needed (Use Ctrl Arrow keys to rotate the residue (about an axis that’s into the screen))