Chimera

Chimera is a molecular visualization program developed at UCSF (https://www.cgl.ucsf.edu/chimera/). It can be obtained for free for non-commercial use and can also be easily installed on your own computer. Chimera is a Python-based program.

General tips for usage

Most Chimera operations can be performed with commands via the commandline, by clicking and/or by using the toolbar in the top. I would recommend following the Tutorials in the Help section for first-time users (Header | Help | Tutorials). In general the program functions by making a selection of particular set of atoms (for instance a ligand) and then performing some action on them. If the action is more advanced than colouring or representation of the atoms, you can generally find it in Header | Tools. Each file you load in will be loaded as a separate model (shown at the bottom of the screen). The file you load in first will be #0, the second file #1 etc. Keep in mind that if a file contains multiple molecules (for instance a combined .mol2 file), the molecules are referenced individually as #0.1 #0.2 etc.

It is also important to realize a PDB-file can contain multiple molecules. When these are multiple protein molecules, these are stored in separate so-called chains. If you are in doubt what is stored in what chain, use the info on the PDB's page on the RCSB.

Here are my general use-cases for Chimera (illustrated with the PDB-file 5ceh). If the command line is used no '|' character is used. The commandline can be enabled Header | Favorites | Command Line, which would indicate in the screen's header click Favorites and then Command Line.

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Showing the protein-ligand interactions

open 5ceh, loads 5ceh.pdb from the RCSB.‎
sel ligand, selects all atoms recognized as the ligand in the pdb-file.‎
col cyan sel, colors the selected atoms cyan.‎
col byhet sel, colors the selected atoms by heteroatom (the carbons will retain the original color; these steps could have been done at once with col cyan sel & C which is a conditional).‎
~disp, hide all default displayed atoms.‎
disp #0 & sel z < 6, shows all residues within 6 Ångstrom of the selection.‎
~ribbon, hides the cartoon representation of helices and sheets.‎
focus sel, set the selection at the center of the screen and hide far-away atoms.‎
Header | Tools | Surface/Binding Analysis | Find Clashes/Contacts.‎
In the pop-up window 'Find Clashes/Contacts' with the ligand still selected click 'Designate selection as second set'.‎
Sel ~sel, select everything that wasn't selected.‎
Click in the same window 'Designate' currently selected atoms for checking.‎
Click the 'Contact' button.‎
Click apply.‎
This will give you something like this:

Tips for cluster usage

Chimera should generally only be used on the cluster if you want to run a large-scale experiment (for instance downloading 500 PDB files and superposing them). In such cases it can be useful to either:

• Run Chimera without a graphical user interface (GUI) with chimera --nogui
• Use X11 forwarding to forward the cluster screen. This requires upon each execution of the ssh command that you add the -X -Y flags which would result in ssh -X -Y user@cn142.science.ru.nl. In the case of Windows Powershell users, this may not function correctly due to antivirus scanners/firewalls. In such case, using the windows subsystem linux (WSL) can offer a solution.