Hi, Paul,
Thank you for your reply. I think the ‘set transparency’ command is on the
correct direction, but there is another problem. In order to apply the ‘set
transparency’, we should use "create" or "extract" command to make a new
objective for the selected atoms. However, after I select th
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
