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https://github.com/whitead/ternviz
https://github.com/whitead/ternviz
Last synced: about 2 months ago
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- Host: GitHub
- URL: https://github.com/whitead/ternviz
- Owner: whitead
- License: mit
- Created: 2022-01-01T16:00:58.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2024-05-07T23:36:01.000Z (8 months ago)
- Last Synced: 2024-09-14T01:55:01.880Z (4 months ago)
- Language: Python
- Size: 1.78 MB
- Stars: 11
- Watchers: 3
- Forks: 5
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Tern Viz
[](https://colab.research.google.com/github/whitead/ternviz/blob/main/colab/ternviz.ipynb)
Convert SMILES to a 3D rotating video. Check-out the Twitter bot [@ternviz](https://twitter.com/ternviz)!
## Install
You need to install both [VMD](https://www.ks.uiuc.edu/Research/vmd/) and ffmpeg. After that:
```py
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:
```sh
ternviz CCCO
```
You may need to specify the path to VMD or ffmpeg:
```sh
ternviz CO --vmd /path/to/vmd/executable
```
You can modify a few things too:
```sh
ternviz CCCO --name "my molecule" --color white
```
try `--low-quality` to render quickly.
### Render a protein
This will do a still frame
```sh
ternviz-pdb 1A1L
```
To do a rotating movie, specify number of frames (at 60 fps)
```sh
ternviz-pdb 1A1L --frames 60
```
You can pass in multiple PDBs
```sh
ternviz-pdb my.pdb other.pdb
```
You can specify how the structure is colored and other details
```sh
ternviz-pdb 1A1L --frames 60 --color white --scolor Chain
```
### Aligning PDBs
You can align structures before rendering
```sh
ternviz-align ref.pdb *.pdb
```
by default it aligns on the protein. You can also change selection string, using [MDAnalysis Selection String Syntax](https://docs.mdanalysis.org/stable/documentation_pages/selections.html)
```sh
ternviz-align ref.pdb --sel "chainid B" *.pdb
```
## Example Render
https://user-images.githubusercontent.com/908389/147892964-c15ac0fd-44be-4473-b82a-799260e0f373.mp4