Hi Grace,
You may want to use a protein homology modeling software for more advanced 
structure building, such as Modeller.
https://salilab.org/modeller/

Nese

________________________________
From: Grace Ciabattoni <[email protected]>
Sent: Thursday, May 21, 2020 12:49 PM
To: [email protected] <[email protected]>
Subject: [PyMOL] tertiary structure/protein folding

Hello,
I am trying to model my protein of interest using the builder function in 
version 2.3. Is there a way to induce protein folding to properly mimic 
tertiary structure, or is secondary structure the highest manipulatable level 
of protein order in PyMol?
Thank you,
Grace
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