How to Add a Symmetry Related Molecule using Coot
You can do this by using Coot and a simple text editor. This can be helpful in preparing figures that discuss biological function. The steps are as follows:
1) Display the symmetry related molecules:
Draw -> Cell & Symmetry…
Note: I changed the master switch to ‘Yes’, adjusted the radius to 50, and then hit ‘Apply’
Below is an overview of the crystal packing:
2) Attain a perspective that will allow you to easily click on your desired symmetry molecule. Below is a zoomed in view of that same packing.
3) File -> Save Symmetry Coordinates
Your pointer will become a small cross shape. Now, click on your desired symmetry molecule.
4) Give the file a name you can remember for at least 15 seconds:
5) Open your original pdb file and then newly generated symmetry pdb files in a simple text editor. I am using gedit on a linux machine in this example.
6) Rename the newly created pdb file from ‘chain A’ to ‘chain B’.
Note: If you do not rename the chains, the atoms may create strange connectivity such as long distance disulphide bonds in cysteines.
Important: I have an ” A ” (there is a space on either side of the A). I always scroll through the pdb file to make sure I’m not replacing the letter A in an undesired place. For example, if you simply replace “A” you will mess up all your CA (carbon alphas) and residues abbreviations such as VAL.
7) Copy and paste ‘chain B’ into your original pdb file. You should copy/paste the ‘ATOM’ section and leave out the header (everything above the ATOM section) and the END (it is at the bottom of your pdb file).
Rename the file and save using ‘Save As’. This way you will have the original monomer available should you need it in the future. If you accidentally overwrite the original, you can always just delete the second chain and re-save the file.
9) Display your newly created pdb file and make sure that your new pdb file is correct.