For internal use
Sidebar
pymol
Table of Contents
Cheat Sheet
Cook Book
Startup file of pymol on windows
On Windows, use 'pymolrc', 'pymolrc.py' or 'pymolrc.pym'. For global defaults (all users), you can place a .pymolrc file in C:\Program Files\DeLano Scientific\PyMOL (or C:\Program Files\PyMOL\PyMOL). You can launch PyMOL from the applications menu or from the icon on your desktop (if you placed one there).
Change coordinates by mouse
- Click “Mouse Mode” until you see “3-Button Editing”, and then use mouse following the instruction Ref
- Shift + left click to rotate
- Shift + middle click to translate
- Ctrl + right click on a bond to show dihedral angle
- Ctrl + left click and drag to change dihedral angle
Electrostatic surface
Change number of threads
RNA/DNA representation
- Example:
set orthoscopic, on bg_color white set cartoon_ring_mode, 1 set cartoon_ring_transparency, 0.3 set cartoon_ring_color, green color green viewport 480, 480 ray
Make a movie
- Make a animation for rotating a molecule
cmd.movie.add_roll(2.0, axis='y', start=1) set ray_trace_frames, 1 mpng snapshot/mov # after that you can convert the snapshots into animation under Linux by # convert -delay 20 snapshot/*.png out.gif
Installation
From compiled package
- Unpack it and run ./setup.sh
- copy the created “pymol” to /home/usr/bin
From source
Tutorial
pymol.txt · Last modified: 2020/04/11 14:52 by 127.0.0.1
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