chemistry, Computational Chemistry, pymol

Pymol for computational chemistry.

A picture is worth a thousand words.

So goes the saying, and it is true.

The pymol wiki has lots of ideas for styling atoms. Below are instructions for styling atoms, as in the image shown below, which I think produces an image that is particularly clear (and pretty) and suited to publication in journal articles.

hide everything
show sticks
show spheres
set stick_radius, .07
set sphere_scale, .18
set sphere_scale, .13, elem H
set bg_rgb=[1, 1, 1]
set stick_quality, 50
set sphere_quality, 4
color gray85, elem C
color red, elem O
color slate, elem N
color gray98, elem H
set stick_color, black
set ray_trace_mode, 1
set ray_texture, 2
set antialias, 3
set ambient, 0.5
set spec_count, 5
set shininess, 50
set specular, 1
set reflect, .1
set dash_gap, 0
set dash_color, black
set dash_gap, .15
set dash_length, .05
set dash_round_ends, 0
set dash_radius, .05

This can be copied directly into the pymol command line, followed by enter. If you have non-bonded atoms such as a central metal with attached ligands, for which pymol sometimes does not detect, you can use the measurement tool and then remove the labels and change dash_radius to a very small number; alternatively, use the bond command.

An image of xantphos rendered in PyMol
An image of xantphos rendered in PyMol and in stereo. Cross your eyes to see a three-dimensional image.

Another nice effect is to change the display types of certain atoms. For example, I have highlighted the  coordination of the oxygen atoms in the crown ether molecules by hiding the spheres:

 hide spheres, elem C

Also, shown below is a GIF animation an animation of an optimization of the crown ether complex.







One thought on “Pymol for computational chemistry.

  1. Very nice. Thanks for sharing your script! Do you know if PyMOL can draw quadrants on spheres? This will make it easier for the viewer to get a feel at what three-dimensional angles the bonds sprout out from each atom. I’ve searched around online in many places and haven’t found anything on drawing quadrants.

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