Comments (3)
I'm glad you find Uni-Dock helpful!
For visualizing the input and results in 3D, there are several tools and Python packages available. Here are a few popular ones:
- PyMOL: PyMOL is a widely used molecular visualization tool that can be extended with Python scripting. You can find tutorials and documentation on their official website: https://pymol.org/2/
PyMOL can be installed using conda:
conda install -c conda-forge pymol
- NGLview: NGLview is a Python package that allows you to visualize molecular structures and trajectories in Jupyter notebooks. It is an IPython widget that uses the NGL WebGL-based molecular viewer. You can find more information and examples in their GitHub repository: https://github.com/nglviewer/nglview
NGLview can be installed using conda:
conda install -c conda-forge nglview
Happy visualizing!
from uni-dock.
Thank you so much! This is super helpful. BTW, if not limited to python, is there any other tool you would suggest as a better choice? Or you would think PyMOL would be the go-to option?
from uni-dock.
PyMOL is indeed a popular and powerful tool for working with molecular structures, and it's widely used in the scientific community. However, there are also other tools that you might consider like VMD (https://www.ks.uiuc.edu/Research/vmd/).
Especially, I would like to recommend Mol* Viewer (https://molstar.org/viewer/), a web-based Software-as-a-Service (SaaS) tool for molecular visualization. As a web-based tool, Mol* Viewer requires no installation and can be accessed from any device with an internet connection, providing a convenient and flexible solution for your molecular visualization needs.
from uni-dock.
Related Issues (20)
- 1.1.1 source release contains version string 1.1.0 HOT 1
- Error in vina score HOT 2
- typo in examples HOT 1
- missing installation instruction in unidock_tools
- How to dock
- WARNING: Could not find any conformations
- run unidock, report segmentation fault while using file index
- OOM using ad4 scoring function
- CUDA Runtime Error when using ad4 maps HOT 4
- Fail on screening test case mmp13 on version v1.1.x HOT 2
- Unidock pipeline fails to read ligand index HOT 1
- target_compile_features no known features for CXX compiler HOT 6
- Unknown order of ligands in the output HOT 2
- in ligand index, unable to find mol file, only first without others. HOT 1
- Seed doesn't seem to be working properly. HOT 3
- Potential array index out of range. HOT 1
- MCDock Run Rigid Docking with Incorrect Input SDF Files
- How to get score when run unidock tooks? HOT 4
- cmake -B build -D FETCH_BOOST=ON does not fetch boost HOT 6
- Compiling error on CUDA 11
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from uni-dock.