On Wed, Mar 17, 2021 at 5:13 PM aishen.free.fr <aishen.free.fr> wrote:
> There is although py3dmol in jupyter notebook compatible with pymol
> through biotite/ammolite, by the way I use to work with nglview but now
> it doesn't display anything ?
>
> I got message error
>
> Enabling notebook extension widgetsnbextension...
> - Validating: problems found:
> - require? X widgetsnbextension
>
> but
>
> Enabling notebook extension jupyter-js-widgets/extension...
> - Validating: OK
> I don't understand ?
>
>
Please report the issue in nglview's github:
https://github.com/nglviewer/nglview/issues/new
Hai
>
> Le 17/03/2021 à 17:47, Hai Nguyen a écrit :
> > On Tue, Mar 16, 2021 at 9:21 PM Jatin Kashyap <jk435.njit.edu> wrote:
> >
> >> Hi Gustaf,
> >>
> >> You got it right! I am sorry for not providing additional information in
> >> the first place.
> >> I am using macOS, and it is mentioned in the VMD’s docs that NetCDF
> >> functionality is not supported on macOS Catalina.
> >> I am working through UCSF Chimera, but there is no Amber param file
> format
> >> available to load the file as I try to load the parameter file.
> >> Is there any tutorial that I can follow for analyzing the Amber
> trajectory
> >> with UCSF Chimera?
> >>
> >>
> > If you are familiar with jupyter notebook and don't mind learning new
> > software, you can give nglview a try. (
> > https://github.com/nglviewer/nglview/blob/master/README.md)
> >
> > nglview is not as powerful as VMD or Chimera but it's quite convenient
> for
> > visualization.
> >
> > PS: See Lily's talk mentioning about the usage of nglview:
> > https://youtu.be/X5umNQDqfqQ?t=616
> > Cheers
> > Hai
> >
> >
> >> Thank you.
> >>
> >>
> >> ——
> >> Jatin Kashyap
> >> Ph.D. Student
> >> Dr. Dibakar Datta Group
> >> Department of Mechanical and Industrial Engineering
> >> New Jersey Institute of Technology (NJIT)
> >> University Heights
> >> Newark, NJ 07102-1982
> >> Phone- (201)889-5783
> >> Email- jk435.njit.edu
> >>
> >>> On Mar 16, 2021, at 4:00 AM, Gustaf Olsson <gustaf.olsson.lnu.se>
> wrote:
> >>>
> >>> Without additional information, helping identifying potential problems
> >> will be hard.
> >>> If you, like me, are using a mac, there is still no support for NetCDF
> >> format in VMD in version vmd 1.9.4a48-Catalina-Rev7. I do not know if
> this
> >> support has been dropped in windows/linux versions as well or if this
> only
> >> affects macOS. If this is the case then one recommendation would be to
> use
> >> some other software, like UCSF Chimera, which supports NetCDF on macOS.
> >>> If not, then check the content of the “out” file for errors. There are
> >> also likely some useful tools available to check the integrity of
> >> trajectory files as well, cpptraj may have some tools, parmed maybe.
> >>> Best regards
> >>> // Gustaf
> >>>
> >>>> On 16 Mar 2021, at 05:23, Jatin Kashyap <jk435.njit.edu> wrote:
> >>>>
> >>>> Dear AMBER Community,
> >>>>
> >>>> I am trying to visualize a .nc file in VMD by following a tutorial[1].
> >> The tutorial visualization works fine but when I try the same steps
> with my
> >> own files [2], it throws following error:
> >>>> Problem reading CRD file
> >>>> Info) Finished with coordinate file .../short_traj.nc
> >>>>
> >>>> Can anybody please help to understand what is wrong with my approach.
> >>>>
> >>>> Thank you.
> >>>>
> >>>> [1]
> >>>> https://ambermd.org/tutorials/basic/tutorial2/section6.htm <
> >> https://ambermd.org/tutorials/basic/tutorial2/section6.htm>
> >>>>
> >>>> ——
> >>>> Jatin Kashyap
> >>>> Ph.D. Student
> >>>> Dr. Dibakar Datta Group
> >>>> Department of Mechanical and Industrial Engineering
> >>>> New Jersey Institute of Technology (NJIT)
> >>>> University Heights
> >>>> Newark, NJ 07102-1982
> >>>> Phone- (201)889-5783
> >>>> Email- jk435.njit.edu
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
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> >>
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Received on Wed Mar 17 2021 - 21:00:02 PDT
