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 ?
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
>> _______________________________________________
>> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 17 2021 - 14:30:02 PDT
