gchemol-view is a simple molecule viewer based on gchemol and bevy.
- Lightweight molecule viewer: fast to load molecule with thousands of atoms
- Load molecules by drag-and-drop for files or directories.
- Input files generator for VASP, ORCA, Gaussian and more.
- Remote view: view molecules locally sent from a remote client in the terminal without an X environment
Download prebuilt binary for Linux/Windows/MacOS on the release page.
- follow bevy setup guide
Linux GTK is required for using native file dialog: On Ubuntu:
sudo apt-get install libgtk-3-dev
Visualization of molecules from common file formats supported by gchemol
gchemol-view foo.xyz
gchemol-view POSCAR
gchemol-view foo.cif
You can view a molecule in gchemol-view on your local machine that was sent from a remote HPC server in command line using spdkit-python.
from spdkit import *
mol = Molecule.from_file("foo.mol2", remote=True)
view(mol, remote=True)
To achieve this, you need a working reverse SSH channel.
Setup reverse port forwarding from desktop to remote SSH server:
ssh -N -R remote-port:localhost:3039 remote-ssh-server
To automatically set up a reverse channel when logging into a remote SSH server, you can create an entry in your ~/.ssh/config file.
host Khpcserver01
hostname remote-ssh-server
ExitOnForwardFailure yes
RemoteForward {{remote-port}} localhost:3039
If you are using XShell, you can refer to the image below:
- measure distance, angle, torsion angle
- visuailize volume data: orbital, DOS, etc.
- select atoms by atom serial numbers
- better animation system
- set atom freezing codes for optimization
Codes that inspired me: