[Chimera-users] Visualizing Amber Trajectory in MD Movie

[Elaine Meng]

Hi Jatin,
You cannot use the same .top file after you removed some atoms.  The .top file has to match the number of atoms.

In the original system, maybe some of the waters are just hidden and you need to display them, e.g. command "display" will show all atoms.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 16, 2021, at 11:11 PM, Jatin Kashyap <jk435 at njit.edu> wrote:
> 
> Dear UCSF Chimera Community,
> 
> I am trying to visualize an Amber NetCDF(.nc) trajectory in UCSF Chimera using a tutorial.[1] I have two trajectory files of the same system: first, the solvated system, and second I stripped the water molecules in the CPPTRAJ utility of AMBER.
> I am using the same .top file for both visualizations; however first one showing me the system, although the water molecules are missing. But the second one is throwing me an error, and nothing appears in GUI window.[2]
> 
> Please help me find out my mistake in the process as I am a beginner-level user of UCSF Chimera.
> 
> Thank you very much.
> 
> [1]
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html
> 
> [2]
> Assigning chain ID A to 306 residues, e.g. SER
> fillCoordSet: coordinates [arg 2] must be same length as atoms
> 
> TclError Exception in Tk callback
>   Function: <bound method ComboBox._resizeArrow of <_Pmw.Pmw_1_3_3.lib.PmwComboBox.ComboBox instance at 0x7fc164add170>> (type: <type 'instancemethod'>)
>   Module: <module '_Pmw.Pmw_1_3_3.lib.PmwComboBox' from '/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwComboBox.py'> (line: 350)
>   Args: (<Tkinter.Event instance at 0x7fc164ae65a8>,)
>   Event type: ConfigureNotify (type num: 22)
> Traceback (innermost last):
>   File "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py", line 1747, in __call__
>     return apply(self.func, args)
>   File "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwComboBox.py", line 351, in _resizeArrow
>     bw = (string.atoi(self._arrowBtn['borderwidth']) +
>   File "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1336, in cget
>     return self.tk.call(self._w, 'cget', '-' + key)
> TclError: invalid command name ".140468625963920.140468635650744.140468640420064.140468635457080.140468635625736.140468640714048.140468640714120.140468594528696.140468594529848"
> 
> ================================================
>   Event contents:
>     char: ??
>     delta: 0
>     height: 24
>     keycode: ??
>     keysym: ??
>     keysym_num: ??
>     num: ??
>     send_event: False
>     serial: 79507
>     state: ??
>     time: ??
>     type: 22
>     widget: .140468625963920.140468635650744.140468640420064.140468635457080.140468635625736.140468640714048.140468640714120.140468594528696.140468594529344.140468594529488
>     width: 1194
>     x: 0
>     x_root: ??
>     y: 0
>     y_root: ??
> 
> TclError: invalid command name ".140468625963920.140468635650744.140468640420064.140468635457080.140468635625736.140468640714048.140468640714120.140468594528696.140468594529848"
> 
>   File "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1336, in cget
>     return self.tk.call(self._w, 'cget', '-' + key)
> 
> See reply log for Python traceback. 
> 
> ——
> 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 at njit.edu
> 
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