[Chimera-users] Visualizing Amber Trajectory in MD Movie

[Jatin Kashyap]

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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