<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear UCSF Chimera Community,<div class=""><br class=""></div><div class=""><div class="">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.</div><div class="">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]</div><div class=""><br class=""></div><div class="">Please help me find out my mistake in the process as I am a beginner-level user of UCSF Chimera.</div></div><div class=""><br class=""></div><div class="">Thank you very much.</div><div class=""><br class=""></div><div class="">[1]</div><div class=""><a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html</a></div><div class=""><br class=""></div><div class="">[2]</div><div class=""><b class="">Assigning chain ID A to 306 residues, e.g. SER</b></div><div class=""><b class="">fillCoordSet: coordinates [arg 2] must be same length as atoms</b></div><div class=""><b class=""><br class=""></b></div><div class=""><b class="">TclError Exception in Tk callback</b></div><div class=""><b class=""> Function: <bound method ComboBox._resizeArrow of <_Pmw.Pmw_1_3_3.lib.PmwComboBox.ComboBox instance at 0x7fc164add170>> (type: <type 'instancemethod'>)</b></div><div class=""><b class=""> 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)</b></div><div class=""><b class=""> Args: (<Tkinter.Event instance at 0x7fc164ae65a8>,)</b></div><div class=""><b class=""> Event type: ConfigureNotify (type num: 22)</b></div><div class=""><b class="">Traceback (innermost last):</b></div><div class=""><b class=""> File "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py", line 1747, in __call__</b></div><div class=""><b class=""> return apply(self.func, args)</b></div><div class=""><b class=""> File "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwComboBox.py", line 351, in _resizeArrow</b></div><div class=""><b class=""> bw = (string.atoi(self._arrowBtn['borderwidth']) +</b></div><div class=""><b class=""> File "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1336, in cget</b></div><div class=""><b class=""> return self.tk.call(self._w, 'cget', '-' + key)</b></div><div class=""><b class="">TclError: invalid command name ".140468625963920.140468635650744.140468640420064.140468635457080.140468635625736.140468640714048.140468640714120.140468594528696.140468594529848"</b></div><div class=""><b class=""><br class=""></b></div><div class=""><b class="">================================================</b></div><div class=""><b class=""> Event contents:</b></div><div class=""><b class=""> char: ??</b></div><div class=""><b class=""> delta: 0</b></div><div class=""><b class=""> height: 24</b></div><div class=""><b class=""> keycode: ??</b></div><div class=""><b class=""> keysym: ??</b></div><div class=""><b class=""> keysym_num: ??</b></div><div class=""><b class=""> num: ??</b></div><div class=""><b class=""> send_event: False</b></div><div class=""><b class=""> serial: 79507</b></div><div class=""><b class=""> state: ??</b></div><div class=""><b class=""> time: ??</b></div><div class=""><b class=""> type: 22</b></div><div class=""><b class=""> widget: .140468625963920.140468635650744.140468640420064.140468635457080.140468635625736.140468640714048.140468640714120.140468594528696.140468594529344.140468594529488</b></div><div class=""><b class=""> width: 1194</b></div><div class=""><b class=""> x: 0</b></div><div class=""><b class=""> x_root: ??</b></div><div class=""><b class=""> y: 0</b></div><div class=""><b class=""> y_root: ??</b></div><div class=""><b class=""><br class=""></b></div><div class=""><b class="">TclError: invalid command name ".140468625963920.140468635650744.140468640420064.140468635457080.140468635625736.140468640714048.140468640714120.140468594528696.140468594529848"</b></div><div class=""><b class=""><br class=""></b></div><div class=""><b class=""> File "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1336, in cget</b></div><div class=""><b class=""> return self.tk.call(self._w, 'cget', '-' + key)</b></div><div class=""><b class=""><br class=""></b></div><div class=""><b class="">See reply log for Python traceback. </b></div><div class=""><br class=""><div class="">
<div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;">——<br class="">Jatin Kashyap <br class="">Ph.D. Student<br class="">Dr. Dibakar Datta Group</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;">Department of Mechanical and Industrial Engineering<br class="">New Jersey Institute of Technology (NJIT)</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;">University Heights<br class="">Newark, NJ 07102-1982<br class=""></div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;">Phone- (201)889-5783</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;">Email- <a href="mailto:jk435@njit.edu" class="">jk435@njit.edu</a></div></div></div></div></div></div></div></div></div></div></div></div></div>
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