The default view of cartoon presentation in PyMOL is provided below.
PyMOL provides commands “cartoon_oval_length“, “cartoon_oval_width“, “cartoon_rect_length” and “cartoon_rect_width” to customize the display of helices and strands.
PyMOL users should be aware that the 4 commands can’t be combined with “cartoon_fancy_helices” and “cartoon_fancy_strands”. Once the fancy mode is turned on, the manually customized width/length will be changed back to default number.
The first few examples will be related to the oval view
command: set cartoon_oval_length 0.2
command: set cartoon_oval_length 1
command: set cartoon_oval_length 1.7
We can also change the thickness of the helix in our target by using “cartoon_oval_width”
The figure below shows the default thickness of helix.
command: set cartoon_oval_width 0.8
command: set cartoon_oval_width 1.5
Now. let me show you some examples to change the width and thickness of strand by using PyMOL.
command: set cartoon_rect_length 0.3
command: set cartoon_rect_length 0.7
command: set cartoon_rect_length 2
command: set cartoon_rect_width 0.1
command: set cartoon_rect_width 0.9
command: set cartoon_rect_width 1.6