Coot for Cryo-EM: The Basics

By Ana Casañal & Paul Emsley
This tutorial is designed for 0.9-pre

1: Start

Get the files demo-box.tar.gz and put them in the directory from where you launch Coot. The tar file for the demo box can be found in the “Auxiliary Files” section of the Coot web page (

1.1 Load the Tutorial Data

1.2 Representation

Note: if you have a speedy computer, then you can make a copy of the map (Calculate → Map Tools → Copy Map Molecule…) and use Standard Lines for one and Solid/Transparent for the copied map - that looks quite good and can be helpful. It can be laggy though with a big radius, and that is the opposite of useful.

Now let’s try with a white background:

Moving around the molecule:

To change the “residue to residue” speed:

Add Here Dragged Map Off

You might like the residue reorienting mode:

3: Short-cuts and Interface

Go To Residue:

You can toggle spin and rock the view with:
- “I”, “Ctrl R”

3.1 Install a Few Buttons

3.2 Install Key-bindings

3.3 Install a Few Extensions

3.4 Try it out

Use the cursor to navigate using the map

To undo last navigation/screen recentre:


3.5 Quick Save-As

The new version of coot is a lot more advanced and a bit more crashy than the standard version. It’s a good idea to save every now and then - making it easier to recover.

Quick Save as will save all models that have not been saved and will save the session too.

4: Model-Building

4.1 Find and Fix a Bad Rotamer

Fix the Rotamer, First the Traditional usage

But let’s use the Key-bindings to speeds up, so undo the previous fit:

And to tidy up after that:

4.2 Let’s Find Something Else to Fix

ValidateRamachandran Plot

Note: Peptide Flags:
- Green: cis-peptide in front of a PRO
- Yellow: twisted trans-peptide
- Red: cis-peptide in front of a non-PRO

When it comes to fixing up model-building/validation problems,
often times “Neighbour Refine” is the first tool to try. If we try that, we see that it doesn’t work in this case. We have to look and think. We see that the one of the peptides is facing the wrong way and we need to flip it:

So, let’s fix this with Real Space Refine and flipping:

5: Now To the Demo Box!

For these refinements, it might be useful to use Coot Probe dots:


OK, let’s find the script and run it:

Now try that with a blurred map:

The point of this exercise is for you to see/learn how coot behaves with lower resolution data.