PDB animations?

[thomashrabe]

Looking into 3DMol to replace our JSMol visualization.
Does 3DMol display animations as we do here?

http://pdbflex.org/cluster.html#!/4hn4A/20981/1a50A

If yes, I would switch immediately.

[dkoes]

Sure, if you have multiple frames you can animate like this:
http://3dmol.csb.pitt.edu/tests/auto/generate_test.cgi?test=test39
or if you have vibration vectors you can animate like this:
http://3dmol.csb.pitt.edu/tests/auto/generate_test.cgi?test=test36
(view source to see the implementation).

[Jack-XHP]

Hello, want to ask some additional question about animations. I have a look at the source code and find the multiple frames are from a single downloaded file. Right now I have a list of mol2 files. How can I add them manually as each frame? I try to use addModelsAsFrames call for each file. Yet it only results in overlapping all molecules together into one frame instead of an animation. BTW I use py3Dmol.

for i in range(10):
    if os.path.isfile('{}.mol2'.format(i)):
        with open('{}.mol2'.format(i), 'r') as content_file:
            mol = content_file.read()
        view.addModelsAsFrames(mol, 'mol2')
view.animate({'loop': 'forward'})
view.setStyle({'stick':{}})
view.setStyle({'model':0},{'stick':{'colorscheme':'cyanCarbon'}})
view.zoomTo()
view.show()```

[dkoes]

I would put all your data into a single string and addModelsAsFrames with that. You'll probably have to pass multimodel:true as an option (can't test it right now - let me know if it works).

[Jack-XHP]

Thanks for you help, It works perfectly by simply concat all mol2 file together and put them in one addModelsAsFrames