Dear developers,

I am trying to automatize a task using the chimera python interface.

In the graphical user interface, I can get the result I want by performing the following actions:

1) Select a carbon atom (ctrl+left button)

2) Tools --> Structure Editing --> Build Structure

3) In the "Build Structure" window, select "Modify Structure"

4) Change selected atom to...: "Element C", "Bonds 4", "Geometry Tetrahedral" (basically the default)

5) Apply

6) Save as pdb

Is it possible to create a python script to do 1-6 (repeating 1-5 for several carbon atoms identified by residue id and name)?

I could then very easily prepare a bash script to apply these changes to hundreds of pdb files.

I tried asking chatGPT for a quick answer, but most probably it is using python classes and methods that actually do not exist. Looking at the online documentation was also unsuccesful, but maybe you could point me to the right place.

Thanks a lot!

Best,

Davide