ternviz 0.6.3

Render SMILES into 3D video

Tern Viz

Convert SMILES to a 3D rotating video. Check-out the Twitter bot @ternviz!

Install

You need to install both VMD and ffmpeg. After that:

pip install ternviz

Usage

It can be used to render stills, rotating videos, comparisons of molecules, and compilation videos of multiple proteins.

Render a molecule

To render a molecule:

ternviz CCCO

You may need to specify the path to VMD or ffmpeg:

ternviz CO --vmd /path/to/vmd/executable

You can modify a few things too:

ternviz CCCO --name "my molecule" --color white

try --low-quality to render quickly.

Render a protein

This will do a still frame

ternviz-pdb 1A1L

To do a rotating movie, specify number of frames (at 60 fps)

ternviz-pdb 1A1L --frames 60

You can pass in multiple PDBs

ternviz-pdb my.pdb other.pdb

You can specify how the structure is colored and other details

ternviz-pdb 1A1L --frames 60 --color white --scolor Chain

Aligning PDBs

You can align structures before rendering

ternviz-align ref.pdb *.pdb

by default it aligns on the protein. You can also change selection string, using MDAnalysis Selection String Syntax

ternviz-align ref.pdb --sel "chainid B" *.pdb

Example Render

https://user-images.githubusercontent.com/908389/147892964-c15ac0fd-44be-4473-b82a-799260e0f373.mp4