{"id":12018,"date":"2024-12-04T15:47:49","date_gmt":"2024-12-04T15:47:49","guid":{"rendered":"https:\/\/www.blopig.com\/blog\/?p=12018"},"modified":"2024-12-04T15:47:49","modified_gmt":"2024-12-04T15:47:49","slug":"making-pretty-pictures-in-pymol-v2","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2024\/12\/making-pretty-pictures-in-pymol-v2\/","title":{"rendered":"Making Pretty Pictures in PyMOL v2"},"content":{"rendered":"\n

Throughout my PhD I’ve needed nice PyMOL visualizations, but struggled to quickly and easily make the pictures I wanted. I’ve used Claire Marks<\/a>‘ blopig post, Making Pretty Pictures in PyMOL<\/a>, many<\/em> times and wanted to expand it with what I’ve learned to make satisfying visualizations quickly!<\/p>\n\n\n\n\n\n\n\n

Use scripts<\/h2>\n\n\n\n

The most helpful thing I’ve learned is to use a script to define functions that change settings to a preset you’re happy with. You can find my script here<\/a>.<\/p>\n\n\n\n

To load it into your current PyMOL session:<\/p>\n\n\n\n

run <path_to_pymol_style.py><\/pre>\n\n\n\n
Preset workspace setting<\/h2>\n\n\n\n
First thing I like to do in a new session is to first load my pymol_style.py<\/code> and then perform:<\/p>\n\n\n\n
setPretty<\/pre>\n\n\n\n
\n
\n
Default PyMOL style:<\/p>\n\n\n\n
\"\"<\/a><\/figure>\n<\/div>\n\n\n\n
\n
After setPretty:<\/p>\n\n\n\n
\"\"<\/a><\/figure>\n<\/div>\n<\/div>\n\n\n\n
def setPretty():\n    # Workspace settings\n    cmd.bg_color(\"white\")\n    cmd.set(\"ray_opaque_background\", \"off\")\n    cmd.set(\"orthoscopic\", 0)\n    cmd.set(\"transparency\", 0.5)\n    cmd.set(\"dash_gap\", 0)\n    cmd.set(\"ray_trace_mode\", 1) # normal color + black outline\n    cmd.set(\"antialias\", 3)\n    cmd.set(\"ambient\", 0.5)\n    cmd.set(\"spec_count\", 5)\n    cmd.set(\"shininess\", 50)\n    cmd.set(\"specular\", 1)\n    cmd.set(\"reflect\", 0.1)\n    cmd.space(\"cmyk\")<\/pre>\n\n\n\n
Transparency<\/h2>\n\n\n\n
Increasing the transparency of non-important features helps what you’d like the reader to focus on stand out. For example in this binding site, using a higher transparency of the cartoon versus the binding site residues helps them stick out.<\/p>\n\n\n\n
# define ligand, binding site residues, and chain\nselect\u00a0ligand,\u00a0resn\u00a0LIG\u00a0and\u00a0chain\u00a0B # change to whatever chain you are working in\nselect\u00a0binding,\u00a0br.\u00a0(ligand\u00a0around\u00a04) # bonds within 4 angstroms of ligand \nselect chainB, chain B\nhide everything, not binding\nshow sticks, binding\nshow sticks, ligand\nshow cartoon, chainB<\/pre>\n\n\n\n
\n
\n
set cartoon_transparency, 0.0<\/code><\/p>\n\n\n\n
\"\"<\/a><\/figure>\n<\/div>\n\n\n\n
\n
set cartoon_transparency, 0.6<\/code><\/p>\n\n\n\n
\"\"<\/a><\/figure>\n<\/div>\n<\/div>\n\n\n\n
Also use transparency to show binding site residues underneath a surface.<\/p>\n\n\n\n
hide (hydro and not (elem N+O+S) and binding) # hide non-polar hydrogens\nshow surface, chainB\ncolor gray80, chainB and not ligand<\/pre>\n\n\n\n
\n
\n
set transparency, 0.2<\/code><\/p>\n\n\n\n
\"\"<\/a><\/figure>\n<\/div>\n\n\n\n
\n
set transparency, 0.<\/code>4<\/p>\n\n\n\n
\"\"<\/a><\/figure>\n<\/div>\n<\/div>\n\n\n\n
Ball and stick<\/h2>\n\n\n\n
I personally like the ball and stick representation of small molecules, and I’ve defined it in my script going off of Rob Paton’s pymol_style.py<\/a>, where I use the same BallnStick<\/code> command! I’ve defined another BallnStickThick<\/code> command along with some other fun colors. <\/p>\n\n\n\n
\n
\n
BallnStick ligand<\/code><\/p>\n\n\n\n
\"\"<\/a><\/figure>\n<\/div>\n\n\n\n
\n
BallnStickThick ligand, marine<\/code><\/p>\n\n\n\n
\"\"<\/a><\/figure>\n<\/div>\n<\/div>\n\n\n\n
\n
\n
BallnStickThick ligand, purpleblue<\/code><\/p>\n\n\n\n
\"\"<\/a><\/figure>\n<\/div>\n\n\n\n
\n
BallnStickThick ligand, orangecream<\/code><\/p>\n\n\n\n
\"\"<\/a><\/figure>\n<\/div>\n<\/div>\n\n\n\n
Lighting<\/h2>\n\n\n\n
Another cool thing you can do is use preset Lighting Settings located in the Plugin bar.<\/p>\n\n\n\n
\n
\n
Rubber setting (and increased ambient value)<\/p>\n\n\n\n
\"\"<\/a><\/figure>\n<\/div>\n\n\n\n
\n
X-Ray setting with reflect = 1 and light_count = 1<\/p>\n\n\n\n
\"\"<\/a><\/figure>\n<\/div>\n<\/div>\n\n\n\n
Focal blur<\/h2>\n\n\n\n
The next thing I found was a focal blur script <\/a> which has a fun blurring effect.<\/p>\n\n\n\n
# https:\/\/pymolwiki.org\/index.php\/FocalBlur and get script!\nrun ~\/pymol_focal_blur.py\nFocalBlur<\/pre>\n\n\n\n
\n
\n
FocalBlur samples=20, aperture=2.0<\/code><\/p>\n\n\n\n
\"\"<\/a><\/figure>\n<\/div>\n\n\n\n
\n
FocalBlur samples=20, aperture=4.0<\/code><\/p>\n\n\n\n
\"\"<\/a><\/figure>\n<\/div>\n<\/div>\n\n\n\n
Resources<\/h2>\n\n\n\n