![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 years ago
Closed 6 years ago
#2716 closed defect (not a bug)
User confused about how to show trajectories
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | MD/Ensemble Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Darwin-18.7.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-09-26) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.91 (2019-09-26) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open "/Users/anais/Dropbox/anais & tomek/SMOG/modeller/70S_coot_model(cryo)_USE/67A3A3RNC/67A3A3_CG_new.pdb" Chain information for 67A3A3_CG_new.pdb #1 --- Chain | Description $ | No description available 0 | No description available 1 | No description available 2 | No description available 3 | No description available 6 7 8 9 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available v | No description available w | No description available x | No description available y | No description available z | No description available > open "/Users/anais/Dropbox/anais & tomek/SMOG/modeller/70S_coot_model(cryo)_USE/70S_notRNA_coot.pdb" Summary of feedback from opening /Users/anais/Dropbox/anais & tomek/SMOG/modeller/70S_coot_model(cryo)_USE/70S_notRNA_coot.pdb --- warnings | Duplicate atom serial number found: 186 Duplicate atom serial number found: 186 Duplicate atom serial number found: 186 Duplicate atom serial number found: 186 Duplicate atom serial number found: 186 48500 messages similar to the above omitted Chain information for 70S_notRNA_coot.pdb #2 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 6 7 8 9 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available v | No description available w | No description available x | No description available y | No description available z | No description available > hide #!1.1 models > hide #!1.2 models > show #!1.2 models > hide #!1 models > show #!1 models > hide #!2 models > hide #!1.2 models > show #!2 models > close #1 > open "/Users/anais/Dropbox/anais & tomek/SMOG/modeller/70S_coot_model(cryo)_USE/31A3A3RNC/31A3A3_CG_new.pdb" Chain information for 31A3A3_CG_new.pdb #1 --- Chain | Description $ | No description available 0 | No description available 1 | No description available 2 | No description available 3 | No description available 6 7 8 9 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available v | No description available w | No description available x | No description available y | No description available z | No description available > close #1 > open "/Users/anais/Dropbox/anais & tomek/SMOG/modeller/70S_coot_model(cryo)_USE/26A3A3RNC/26A3A3_CG_new.pdb" Chain information for 26A3A3_CG_new.pdb #1 --- Chain | Description $ | No description available 0 | No description available 1 | No description available 2 | No description available 3 | No description available 6 7 8 9 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available v | No description available w | No description available x | No description available y | No description available z | No description available > open "/Users/anais/Dropbox/anais & tomek/SMOG/modeller/70S_coot_model(cryo)_USE/Results from Grace/26A3A3RNC_nocontacts/Sim1/traj1_comp.xtc" Must specify a structure model to read the coordinates into > open "/Users/anais/Dropbox/anais & tomek/SMOG/modeller/70S_coot_model(cryo)_USE/Results from Grace/26A3A3RNC_nocontacts/Sim1/traj1_comp.xtc" Must specify a structure model to read the coordinates into > open 1qfh 1qfh title: Dimerization of gelation factor from dictyostelium discoideum: crystal structure of rod domains 5 and 6 [more info...] Chain information for 1qfh #3 --- Chain | Description A B | protein (gelation factor) > close #3 > select #1 20741 atoms, 2 bonds, 11552 pseudobonds, 3 models selected > open "/Users/anais/Dropbox/anais & tomek/SMOG/modeller/70S_coot_model(cryo)_USE/Results from Grace/26A3A3RNC_nocontacts/Sim1/traj1_comp.xtc" Must specify a structure model to read the coordinates into Downloading bundle MolecularDynamicsViewer-1.1-py3-none-any.whl Successfully installed MolecularDynamicsViewer-1.1 Installed MolecularDynamicsViewer (1.1) > toolshed show "Molecular Dynamics Viewer" Please register the custom scheme 'kmd' via QWebEngineUrlScheme::registerScheme() before installing the custom scheme handler. Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py", line 571, in customEvent func(*args, **kw) File "/Users/anais/Library/Application Support/ChimeraX/0.91/site- packages/com/kdiller/dynamics/viewer/gui.py", line 57, in handle_scheme self.openFile() File "/Users/anais/Library/Application Support/ChimeraX/0.91/site- packages/com/kdiller/dynamics/viewer/gui.py", line 227, in openFile self.atomStruct.atoms.coords = self.atomLocation[0] IndexError: list index out of range IndexError: list index out of range File "/Users/anais/Library/Application Support/ChimeraX/0.91/site- packages/com/kdiller/dynamics/viewer/gui.py", line 227, in openFile self.atomStruct.atoms.coords = self.atomLocation[0] See log for complete Python traceback. Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py", line 571, in customEvent func(*args, **kw) File "/Users/anais/Library/Application Support/ChimeraX/0.91/site- packages/com/kdiller/dynamics/viewer/gui.py", line 57, in handle_scheme self.openFile() File "/Users/anais/Library/Application Support/ChimeraX/0.91/site- packages/com/kdiller/dynamics/viewer/gui.py", line 227, in openFile self.atomStruct.atoms.coords = self.atomLocation[0] IndexError: list index out of range IndexError: list index out of range File "/Users/anais/Library/Application Support/ChimeraX/0.91/site- packages/com/kdiller/dynamics/viewer/gui.py", line 227, in openFile self.atomStruct.atoms.coords = self.atomLocation[0] See log for complete Python traceback. Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py", line 571, in customEvent func(*args, **kw) File "/Users/anais/Library/Application Support/ChimeraX/0.91/site- packages/com/kdiller/dynamics/viewer/gui.py", line 57, in handle_scheme self.openFile() File "/Users/anais/Library/Application Support/ChimeraX/0.91/site- packages/com/kdiller/dynamics/viewer/gui.py", line 227, in openFile self.atomStruct.atoms.coords = self.atomLocation[0] IndexError: list index out of range IndexError: list index out of range File "/Users/anais/Library/Application Support/ChimeraX/0.91/site- packages/com/kdiller/dynamics/viewer/gui.py", line 227, in openFile self.atomStruct.atoms.coords = self.atomLocation[0] See log for complete Python traceback. > toolshed show "Molecular Dynamics Viewer" Please register the custom scheme 'kmd' via QWebEngineUrlScheme::registerScheme() before installing the custom scheme handler. Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py", line 571, in customEvent func(*args, **kw) File "/Users/anais/Library/Application Support/ChimeraX/0.91/site- packages/com/kdiller/dynamics/viewer/gui.py", line 57, in handle_scheme self.openFile() File "/Users/anais/Library/Application Support/ChimeraX/0.91/site- packages/com/kdiller/dynamics/viewer/gui.py", line 227, in openFile self.atomStruct.atoms.coords = self.atomLocation[0] IndexError: list index out of range IndexError: list index out of range File "/Users/anais/Library/Application Support/ChimeraX/0.91/site- packages/com/kdiller/dynamics/viewer/gui.py", line 227, in openFile self.atomStruct.atoms.coords = self.atomLocation[0] See log for complete Python traceback. > open "/Users/anais/Dropbox/anais & tomek/SMOG/modeller/70S_coot_model(cryo)_USE/Results from Grace/26A3A3_starting_models/Frame3.pdb" Summary of feedback from opening /Users/anais/Dropbox/anais & tomek/SMOG/modeller/70S_coot_model(cryo)_USE/Results from Grace/26A3A3_starting_models/Frame3.pdb --- warnings | Ignored bad PDB record found on line 3 Ignored bad PDB record found on line 5 Ignored bad PDB record found on line 7 Ignored bad PDB record found on line 9 Ignored bad PDB record found on line 11 20736 messages similar to the above omitted Chain information for Frame3.pdb #3 --- Chain | Description $ | No description available 0 | No description available 1 | No description available 2 | No description available 3 | No description available 6 7 8 9 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available v | No description available w | No description available x | No description available y | No description available z | No description available > close #1 > toolshed show "Molecular Dynamics Viewer" Please register the custom scheme 'kmd' via QWebEngineUrlScheme::registerScheme() before installing the custom scheme handler. Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py", line 571, in customEvent func(*args, **kw) File "/Users/anais/Library/Application Support/ChimeraX/0.91/site- packages/com/kdiller/dynamics/viewer/gui.py", line 57, in handle_scheme self.openFile() File "/Users/anais/Library/Application Support/ChimeraX/0.91/site- packages/com/kdiller/dynamics/viewer/gui.py", line 227, in openFile self.atomStruct.atoms.coords = self.atomLocation[0] IndexError: list index out of range IndexError: list index out of range File "/Users/anais/Library/Application Support/ChimeraX/0.91/site- packages/com/kdiller/dynamics/viewer/gui.py", line 227, in openFile self.atomStruct.atoms.coords = self.atomLocation[0] See log for complete Python traceback. OpenGL version: 4.1 INTEL-12.10.14 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640 OpenGL vendor: Intel Inc.
Change History (2)
comment:1 by , 6 years ago
| Component: | Unassigned → MD/Ensemble Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → User confused about how to show trajectories |
comment:2 by , 6 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
