Pymol Command Scripts

preRender.pymolcom

cartoon automatic
set cartoon_loop_radius, 0.3
set cartoon_side_chain_helper, 1
set cartoon_discrete_colors, 1
bg_color white
set ray_opaque_background, off
set ray_texture, 5
set ray_shadows, 0
set antialias, 2
set ray_trace_mode, 1

ray.properties

set max_threads, 4
set specular, 0
set hash_max, 600
draw 2000, 1500, 2

standardColorBySecondaryStructure.pymolcom

color blue, ss h
color red, ss s
color forest, ss l+''
util.cnc *

Mimic Low Resolution Structures

Represent alpha helices as cylinders:

set cartoon_cylindrical_helices, 1

Represent helix as low-res (no arrow)

set cartoon_fancy_sheets, 0

Go back to normal helix representation with:

set cartoon_cylindrical_helices, 0
set cartoon_fancy_sheets, 1

Hide Hydrogents

hide (hydro)

Cartoon Trace in CA structures

set cartoon_trace, 1

Align multiple states to a selection (in a given state)

intra_fit (selection),state

Change the width of the distance lines

set dash_width, 4

Take out dashed lines in chain breaks

set cartoon_gap_cutoff, 0

https://pymolwiki.org/index.php/Cartoon_gap_cutoff

Alter line thickness in ray trace mode 1

set ray_trace_gain, 0.0

https://pymolwiki.org/index.php/Ray_Trace_Gain

Remove light highlights

set spec_reflect, 0

https://pymolwiki.org/index.php/Spec_reflect

check also
https://pymolwiki.org/index.php/Spec_power

Change the size of a sphere

with 1 being the default value...

set sphere_scale, 0.3

https://pymolwiki.org/index.php/Sphere_scale

Play with cartoon representations?

http://pymol.sourceforge.net/newman/user/S0260cartoons.html