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Visualize geometry optimization trajectory and torsion scans #374
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Yup, this is something that we have been looking at doing for some time. The major issue is that our 3dMol.js pick for molecular visualization is not DOM-wrapped which means that its widget integration is limited. I think we will have to switch over to nglview for this kind of tech, but nglview doesn't have the volumetric rending for orbitals... this will be fun. This is something I will get back to early September unless someone else tackles it first. |
@dgasmith does orbital's volume data have its own format? |
Do you have sample file? Thanks.
…On Wed, Aug 21, 2019 at 1:19 PM Daniel Smith ***@***.***> wrote:
@hainm <https://github.com/hainm> We could give you any of those formats.
Looking through your docs I see this
<https://github.com/arose/nglview/blob/master/examples/images/display_ccp4_file.md>
which I missed before (sorry!). Could you provide orbital rendering similar
to what you see in the bottom left here <https://3dmol.csb.pitt.edu>?
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nevermind, it's in 3dmol repo. |
Ok, I'm sold :). I will look into integration when I get from a few trips. PS: Will you happen to be at ACS? Might be a good time to hack a few things out. |
No I won't. Do feel free do open any issue in nglview. |
Is your feature request related to a problem? Please describe.
When exploring a geometry optimization trajectory or a torsion scan, each molecule needs to be loaded separately which can become cumbersome.
Describe the solution you'd like
Something like NGLViewer to scroll through conformations in a torsion scan or geometry optimization.
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