what's the final goal?

[albumns]

Hello:

I am playing around NGL these days. It is a really amazing tool for online 3D visualization of molecules. I am just wondering what's the ultimate goal for NGL? Have the developers consider to introduce more sophisticated GUI for NGL like what we see in PyMol or UCSF Chimer?

If yes, that's would be really amazing.

Thank you very much

[hainm]

one of the goals is here: https://github.com/arose/nglview :D

[albumns]

Aha. ^^_

I noticed that before. Actually I first saw the NGLView in Amber, then I found NGL.....

That's really fantastic work!!! I enjoy it a lot.

If we can have more menu for the normal operations like that in most offline tool, that's would be perfect.....

On 08/11/2016 04:32 PM, Hai Nguyen wrote:

one of the goal is here: https://github.com/arose/nglview :D

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[hainm]

You can also try mdsrv: https://github.com/Amber-MD/mdsrv/

I made a fork from original repo to work with pytraj in amber.

Also the nglview dev branch does have menu for Jupyter notebook version.

What kind of specific menu feature you are looking for?

(The one in NGL website is quite good:

http://arose.github.io/ngl/)

Hai

On Aug 11, 2016, at 10:35 AM, albumns notifications@github.com wrote:

Aha. ^^_

I noticed that before. Actually I first saw the NGLView in Amber, then I found NGL.....

That's really fantastic work!!! I enjoy it a lot.

If we can have more menu for the normal operations like that in most offline tool, that's would be perfect.....

On 08/11/2016 04:32 PM, Hai Nguyen wrote:

one of the goal is here: https://github.com/arose/nglview :D

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[albumns]

Hi Hai:

Indeed the NGL has very powerful function and we can do many things by the current menu.

However. there are still something one could be expected. For instance: there are plenty of good things in the example, and we probably need to build a .html file based on related .js file. There are not available in the menu operations.

For a specific case: I imported a local pdb into NGL and I would like to measure the distance/angle between atoms. I cannot find any menu in NGL could do this.

I saw NGL could support reading electron density map and creating surface for a ligand or protein. That's very useful function. However, all those good stuff cannot be done from the current available menu in a web browser.....

Another aspect one could expect is the implement of a command line window. That's would be extremely helpful if the menu is missing, but we can still obtain what we want from a command line.

I hope this would be helpful for improving NGL....

kind regards

Albert

On 08/11/2016 04:56 PM, Hai Nguyen wrote:

You can also try mdsrv: https://github.com/Amber-MD/mdsrv/

I made a fork from original repo to work with pytraj in amber.

Also the nglview dev branch does have menu for Jupyter notebook version.

What kind of specific menu feature you are looking for?

(The one in NGL website is quite good:

http://arose.github.io/ngl/)

Hai

[arose]

For a specific case: I imported a local pdb into NGL and I would like to measure the distance/angle between atoms. I cannot find any menu in NGL could do this.

Yeah, much needed, an open issue, see https://github.com/arose/ngl/issues/46

I saw NGL could support reading electron density map and creating surface for a ligand or protein. That's very useful function. However, all those good stuff cannot be done from the current available menu in a web browser.....

Reading electron density map can be done through Menu > File > Open or just by drag'n'droping the file onto the canvas.

A molecular surface for a ligand or protein can be created by loading a structure file and then adding "surface" representation to it (using the three-lines-icon) and then changing the selection (text field to the right of the funnel-icon) to "protein" or "hetero and not(water or ion)".

The NGL webapp certainly lacks documentation. Any contributions are most welcome!

Another aspect one could expect is the implement of a command line window. That's would be extremely helpful if the menu is missing, but we can still obtain what we want from a command line.

One way would be is to make the stage instance available to the browser console. Not super user-friendly, but a start.

[albumns]

I see.

Glad to learn more things about NGL.

Is it also possible to export movie for the MD simulation trajectory? At least I found that NGL could support playing the trajectory in a browser.

On 08/11/2016 05:37 PM, Alexander Rose wrote:

For a specific case: I imported a local pdb into NGL and I would
like to
measure the distance/angle between atoms. I cannot find any menu
in NGL
could do this.

Yeah, much needed, an open issue, see #46 https://github.com/arose/ngl/issues/46

I saw NGL could support reading electron density map and creating
surface for a ligand or protein. That's very useful function. However,
all those good stuff cannot be done from the current available
menu in a
web browser.....

Reading electron density map can be done through Menu > File > Open or just by drag'n'droping the file onto the canvas.

A molecular surface for a ligand or protein can be created by loading a structure file and then adding "surface" representation to it (using the three-lines-icon) and then changing the selection (text field to the right of the funnel-icon) to "protein" or "hetero and not(water or ion)".

The NGL webapp certainly lacks documentation. Any contributions are most welcome!

Another aspect one could expect is the implement of a command line
window. That's would be extremely helpful if the menu is missing,
but we
can still obtain what we want from a command line.

One way would be is to make the |stage| instance available to the browser console. Not super user-friendly, but a start.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/arose/ngl/issues/182#issuecomment-239199375, or mute the thread https://github.com/notifications/unsubscribe-auth/AF3KOOaT7ZtK9_1whDY_SkPOuRsrFRaSks5qe0GhgaJpZM4JiLos.

[hainm]

At current moment, I don't think there's an easy way to export a movie for MD (with either ngl or nglview).

But I wrote a tutorial with nglview here (with Jupyter notebook): http://ambermd.org/tutorials/analysis/tutorial_notebooks/nglview_movie/

[albumns]

I see. Probably it is even more easier just record the screen of my Linux for the movie. ^_^

On 08/11/2016 09:00 PM, Hai Nguyen wrote:

At current moment, I don't think there's an easy way to export a movie for MD (with either |ngl| or |nglview|).

But I wrote a tutorial with |nglview| here (with Jupyter notebook): http://ambermd.org/tutorials/analysis/tutorial_notebooks/nglview_movie/

[hainm]

Probably it is even more easier just record the screen of my Linux for the movie.

absolutely true.

[hainm]

The only difference I can think of is that you can generate high quality images from NGL to show on big screen.

[albumns]

Another foreseeing good thing is editing structure from NGL. Would it be good if we can do something like: mutate the amino acid for a protein or add an additional functional group for a small molecule? This would be particularly helpful for modellers' daily work.....

regards

On 08/11/2016 09:02 PM, Hai Nguyen wrote:

Probably it is even more easier just record the screen of my Linux
for the movie.

absolutely true.

—

[hainm]

I think there are many good programs out there for that task (e.g pymol, ...), NGL should focus mainly on visualization.

[arose]

Another foreseeing good thing is editing structure from NGL. Would it be good if we can do something like: mutate the amino acid for a protein or add an additional functional group for a small molecule? This would be particularly helpful for modellers' daily work.....

For the time being I focus on optimising display of static structures, static in the sense that the topology/composition does not change (coordinates can change).

[hainm]

FWIW, Autodesk team has very nice progress with 3Dmol in Jupyter notebook https://github.com/Autodesk/molecular-design-toolkit/pull/95