Visualize geometry optimization trajectory and torsion scans

[ChayaSt]

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.

[dgasmith]

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.

[hainm]

but nglview doesn't have the volumetric rending for orbitals.

@dgasmith does orbital's volume data have its own format?
Those are supported ones in NGL: MRC/MAP/CCP4, DX/DXBIN, CUBE, BRIX/DSN6, XPLOR/CNS

[dgasmith]

@hainm We could give you any of those formats. Looking through your docs I see this which I missed before (sorry!). Could you provide orbital rendering similar to what you see in the bottom left here?

[hainm]

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>? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#374?email_source=notifications&email_token=ABB645MCHEYATISDHXDFOG3QFV2LDA5CNFSM4INFQNAKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD42OQ2I#issuecomment-523561065>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABB645KUISGXQPLHG3FB5IDQFV2LDANCNFSM4INFQNAA> .

[hainm]

Do you have sample file? Thanks.

nevermind, it's in 3dmol repo.

[hainm]

Could you provide orbital rendering similar to what you see in the bottom left here?

I think so, close enough, please see below:

[dgasmith]

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.

[hainm]

PS: Will you happen to be at ACS?

No I won't. Do feel free do open any issue in nglview.