My software notes

October 5, 2011

[PyMOL] customized display of helices and strands

Filed under: pymol/ molmol — kpwu @ 11:43 am
Tags: , ,

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


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