id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2484 Tile command: 'Volume' object has no attribute 'atomspec' jaremko@… Conrad Huang "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 0.91 (2019-09-28) Description I am trying to use the command 'tile' to positions my structures as described here: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/tile.html But I get an error (see in log). Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' > ui mousemode rightMode zoom > lighting soft > graphics silhouettes true > hide atoms > show cartoons UCSF ChimeraX version: 0.91 (2019-09-28) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:\Users\mattj\Documents\cryoem_chimera\2018-12-27_x108\relionnew\Refine3D\job080-162\vop- max_084-218_postprocess.mrc Opened vop-max_084-218_postprocess.mrc, grid size 320,320,320, pixel 1.07, shown at level 0.01, step 2, values float32 > surface dust #1 > transparency 50 > volume style surface > transparency 0 > select up Nothing selected > select up Nothing selected > select down Nothing selected > select down Nothing selected > volume #1 transparency 0.3 > volume #1 transparency 0.4 > volume #1 transparency 0.5 > volume #1 transparency 0.9 > volume #1 transparency 0.5 > open C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job080-162/HsORC- coot-78.pdb Summary of feedback from opening C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job080-162/HsORC- coot-78.pdb --- warning | Ignored bad PDB record found on line 16332 END Chain information for HsORC-coot-78.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > hide atoms > show cartoons > close session > open C:/Users/mattj/Documents/cryoem_chimera/2019-09-30_x124-Nuc207/P10/J57/cryosparc_P10_J57_class_00_final_volume.mrc C:/Users/mattj/Documents/cryoem_chimera/2019-09-30_x124-Nuc207/P10/J57/cryosparc_P10_J57_class_01_final_volume.mrc C:/Users/mattj/Documents/cryoem_chimera/2019-09-30_x124-Nuc207/P10/J57/cryosparc_P10_J57_class_02_final_volume.mrc Opened cryosparc_P10_J57_class_00_final_volume.mrc, grid size 128,128,128, pixel 2.81, shown at level 1.34, step 1, values float32 > tile Traceback (most recent call last): File ""C:\Program Files\ChimeraX_20190928\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 254, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX_20190928\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX_20190928\bin\lib\site- packages\chimerax\std_commands\tile.py"", line 51, in tile view_dist, anchor_spec, m.atomspec)) AttributeError: 'Volume' object has no attribute 'atomspec' AttributeError: 'Volume' object has no attribute 'atomspec' File ""C:\Program Files\ChimeraX_20190928\bin\lib\site- packages\chimerax\std_commands\tile.py"", line 51, in tile view_dist, anchor_spec, m.atomspec)) See log for complete Python traceback. > tile #1 Traceback (most recent call last): File ""C:\Program Files\ChimeraX_20190928\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 254, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX_20190928\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX_20190928\bin\lib\site- packages\chimerax\std_commands\tile.py"", line 51, in tile view_dist, anchor_spec, m.atomspec)) AttributeError: 'Volume' object has no attribute 'atomspec' AttributeError: 'Volume' object has no attribute 'atomspec' File ""C:\Program Files\ChimeraX_20190928\bin\lib\site- packages\chimerax\std_commands\tile.py"", line 51, in tile view_dist, anchor_spec, m.atomspec)) See log for complete Python traceback. Missing or invalid ""volumes"" argument: empty atom specifier > volume tile #1 > volume #!2-4#!1.1,3 style surface > close #2-4 > select up Nothing selected > tile viewAll true Traceback (most recent call last): File ""C:\Program Files\ChimeraX_20190928\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 254, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX_20190928\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX_20190928\bin\lib\site- packages\chimerax\std_commands\tile.py"", line 51, in tile view_dist, anchor_spec, m.atomspec)) AttributeError: 'Volume' object has no attribute 'atomspec' AttributeError: 'Volume' object has no attribute 'atomspec' File ""C:\Program Files\ChimeraX_20190928\bin\lib\site- packages\chimerax\std_commands\tile.py"", line 51, in tile view_dist, anchor_spec, m.atomspec)) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 430.86 OpenGL renderer: GeForce GTX 1050 Ti with Max-Q Design/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal General Controls fixed all ChimeraX