Coot Cryo-EM Practical

This is out of date. We have a better tutorial now

Aim: we will fit a domain of the human respiratory complex I matrix arm starting from an empty (part of the) map.

WARNING::This is non-trivial, a familiarity with Coot is assumed. This is not like the basic tutorial. This is approximately how I use coot. It is tricky because fitting cryo-EM maps is tricky.

Put the scripting files in $HOME/.coot-preferences (make the directory if needed)

Using Coot:

Hint 1: Density Fit analysis is a good tool to start off.

Hint 2: Use the sequence file J-chain.seq for alignment

End: You may notice that theres a ligand in the middle of the protein - it's NDP. Get an instance of NDP and fit it to the map using Calculate → Other Modelling Tools → Ligand Fitting