Re: [PyMOL] Replace main/side chain with a H atom in a script

Hi Qianyi, The command to replace an atom is "replace". It replaces the currently picked atom, the command for picking is "edit". Example: edit first (resn ALA & name CB) replace H, 1, 1 See also: https://pymolwiki.org/index.php/Replace Cheers, Thomas > On May 2, 2017, at 5:49 PM, Qianyi C

[PyMOL] Replace main/side chain with a H atom in a script

I want to run QM calculation on reaction center of a large protein. So I need to chop off many parts of the protein. I want to replace some side/main chains with H atoms (for example replace the CB atom by a H atom and also modify the C-H bond to the correct length). I know how to make it work by