Hi,
The ‘set transparency’ command will set the transparency of a surface (e.g. the
interface between a protein and the surrounding water). I think the command
you’re after is ‘set cartoon_transparency’
(https://pymolwiki.org/index.php/Cartoon#Various_Transparency_Levels).
Depending on your ch
Hi Yeping,
To avoid this ‘breaking’ of your protein you will first need to create a copy
of the entire molecule, set the transparency of the copy to your desired value,
then hide the residues you want to make transparent on your original object.
So, you will do something like this:
# create a
