PyMOL SyntaxError: invalid syntax with 'JumpDefinition' - Correcting Jump Definitions

Fixing 'SyntaxError: invalid syntax' with 'JumpDefinition' in PyMOL

If you encounter the error message 'SyntaxError: invalid syntax' after entering 'JumpDefinition my_pose A 462 CA X 1 CA' in PyMOL, you're trying to use an incorrect command. PyMOL doesn't recognize 'JumpDefinition'.

The correct way to define jumps in PyMOL is by using the 'cmd.set_jump' command.

Here's how to properly define a jump between residues in PyMOL:

Example:

To create a jump between the CA atom of residue 462 and the CA atom of residue 1 in the object 'my_pose', use the following command:

cmd.set_jump('my_pose', 1, 'CA', 462, 'CA') 

Explanation:

• cmd.set_jump(): This is the correct PyMOL command for defining jumps.
• 'my_pose': This is the name of the object containing the residues you want to connect with a jump.
• 1: This is the residue number of the first atom (CA atom in this case).
• 'CA': This specifies that you are selecting the alpha-carbon (CA) atom of the residue.
• 462: This is the residue number of the second atom (CA atom).
• 'CA': This again specifies the alpha-carbon (CA) atom of the second residue.

This command effectively bridges residue 1 and residue 462 in the 'my_pose' object based on their CA atoms.