An IPython interface for embedding iCn3D viewer
The 3D view of icn3dpy in Jupyter Notebook is interactive, just like in any browser. The popup windows will appear under the 3D view. If you have a predefined cutom view, you can use the predefined commands in icn3dpy as shown below.
If you experience problems, please file an issue.
pip install icn3dpy
Install node if node is unavailable. One way in Mac is to use "brew":
brew update brew install node
Install Jupyter Lab and the extension "jupyterlab_3dmol":
pip install jupyterlab jupyter labextension install jupyterlab_3dmol or jupyterhub labextension install jupyterlab_3dmol
Open a notebook:
and issue Python script as follows:
"mmdbid" as input:
view = icn3dpy.view(q='mmdbid=6hjr') view
You can also try other input besides "mmdbid". "cid" as input:
view = icn3dpy.view(q='cid=2244') view
"url" as input for local PDB files, e.g., "./1TOP.pdb":
view = icn3dpy.view(q='url=pdb|./1TOP.pdb') view
"url" as input for remote PDB files:
view = icn3dpy.view(q='url=pdb|https://storage.googleapis.com/membranome-assets/pdb_files/proteins/FCG2A_HUMAN.pdb') view
"url" as input for iCn3D PNG Image files:
view = icn3dpy.view(q='url=icn3dpng|https://api.figshare.com/v2/file/download/39125801') view
Use predefined commands (The Jupyter Notebook commands can be copied from the "Copy Commands" button in the "File > Share Link" menu of interactive iCn3D viewers in Jupyter Notebook or in a web browser):
view = icn3dpy.view(q='mmdbid=6m0j',command='scatterplot interaction pairs | !A !E | hbonds,salt bridge,interactions,halogen,pi-cation,pi-stacking | false | threshold 3.8 6 4 3.8 6 6; show selection; add residue number labels') view
Embed a static image instead of an interactive 3D view to improve the performace of a page with multiple structures. The image is clickable to launch an interactive 3D view. The parameters are separated with the symbol "&" (e.g., "imageonly=1&showanno=1"). All parameters are described in the "URL parameters" section:
view = icn3dpy.view(q='mmdbid=6hjr', para='imageonly=1') view
You can use iCn3D interactive interface to generate a custom view, then click "File > Share Link" to get the commands in the "Original URL". All iCn3D commands are listed here.
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