id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2729 Graphics error after switching users zlwatson@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-5.0.0-36-generic-x86_64-with-debian-buster-sid ChimeraX Version: 0.91 (2019-10-24) Description Switched user on computer, error was open when returning to original user Log: Startup Messages --- warnings | QXcbConnection: XCB error: 148 (Unknown), sequence: 213, resource id: 0, major code: 140 (Unknown), minor code: 20 QXcbConnection: XCB error: 148 (Unknown), sequence: 234, resource id: 0, major code: 140 (Unknown), minor code: 20 UCSF ChimeraX version: 0.91 (2019-10-24) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /media/RAIDA/zoe/19May15_MMAL/triple2.cxs format session opened ChimeraX session > show #!1 models > fitmap #1 inMap #4 Fit map combined-pp.mrc in map job081-CPmap.mrc using 951733 points correlation = 0.01503, correlation about mean = 0.01046, overlap = 13.93 steps = 212, shift = 3.43, angle = 2.42 degrees Position of combined-pp.mrc (#1) relative to job081-CPmap.mrc (#4) coordinates: Matrix rotation and translation -0.98065748 0.15709624 0.11675444 318.95320176 -0.15246799 -0.23906505 -0.95895847 411.31555185 -0.12273688 -0.95821115 0.25839308 341.45387201 Axis 0.00190941 0.61189837 -0.79093410 Axis point 186.25871072 317.81517615 0.00000000 Rotation angle (degrees) 168.71465347 Shift along axis -17.77518410 > select #1 4 models selected > ui mousemode rightMode ""translate selected models"" > select clear > fitmap #1 inMap #4 Fit map combined-pp.mrc in map job081-CPmap.mrc using 951733 points correlation = 0.01303, correlation about mean = 0.01115, overlap = 12.17 steps = 104, shift = 2.79, angle = 2.08 degrees Position of combined-pp.mrc (#1) relative to job081-CPmap.mrc (#4) coordinates: Matrix rotation and translation -0.97376483 0.17952206 0.13983493 300.70082557 -0.18249633 -0.24902065 -0.95114864 421.63294797 -0.13593039 -0.95171449 0.27524968 331.36314238 Axis -0.00124339 0.60596181 -0.79549276 Axis point 181.01546299 315.23520473 0.00000000 Rotation angle (degrees) 166.84751047 Shift along axis -8.47740301 > select #1 4 models selected > view all > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > select clear > fitmap #1 inMap #4 Fit map combined-pp.mrc in map job081-CPmap.mrc using 951733 points correlation = 0.5112, correlation about mean = 0.3594, overlap = 708.6 steps = 260, shift = 2.98, angle = 13.6 degrees Position of combined-pp.mrc (#1) relative to job081-CPmap.mrc (#4) coordinates: Matrix rotation and translation -0.97381729 0.20470735 -0.09886720 335.24605566 0.09306682 -0.03779581 -0.99494220 349.20419328 -0.20740876 -0.97809320 0.01775475 389.38821546 Axis 0.10758117 0.69303982 -0.71282684 Axis point 206.60215848 354.67194330 0.00000000 Rotation angle (degrees) 175.50866592 Shift along axis 0.51220471 > toolshed show ""Side View"" > fitmap #1 inMap #4 Fit map combined-pp.mrc in map job081-CPmap.mrc using 951733 points correlation = 0.5112, correlation about mean = 0.3594, overlap = 708.6 steps = 40, shift = 0.0151, angle = 0.00716 degrees Position of combined-pp.mrc (#1) relative to job081-CPmap.mrc (#4) coordinates: Matrix rotation and translation -0.97382680 0.20465378 -0.09888440 335.25662348 0.09310764 -0.03769077 -0.99494237 349.19188782 -0.20734576 -0.97810846 0.01764945 389.40741488 Axis 0.10757027 0.69307869 -0.71279069 Axis point 206.59984610 354.70194056 -0.00000000 Rotation angle (degrees) 175.51224307 Shift along axis 0.51512016 > show #2 models > hide #!4 models > hide #3 models > view all > fitmap #2 inMap #1 Fit molecule input-50S-jc95.pdb (#2) to map combined-pp.mrc (#1) using 86113 atoms average map value = 0.006754, steps = 128 shifted from previous position = 3.09 rotated from previous position = 1.84 degrees atoms outside contour = 78669, contour level = 0.034998 Position of input-50S-jc95.pdb (#2) relative to combined-pp.mrc (#1) coordinates: Matrix rotation and translation 0.97748973 0.04576037 -0.20596074 22.90652579 -0.08104260 0.98274220 -0.16628248 38.43504194 0.19479716 0.17923101 0.96432894 -48.13359155 Axis 0.63499622 -0.73652623 -0.23304273 Axis point 266.60891633 -0.00000000 89.92772486 Rotation angle (degrees) 15.78685514 Shift along axis -2.54567590 > select #2 86113 atoms, 93813 bonds, 1 model selected > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > fitmap #2 inMap #1 Fit molecule input-50S-jc95.pdb (#2) to map combined-pp.mrc (#1) using 86113 atoms average map value = 0.00743, steps = 92 shifted from previous position = 3.22 rotated from previous position = 2.48 degrees atoms outside contour = 77913, contour level = 0.034998 Position of input-50S-jc95.pdb (#2) relative to combined-pp.mrc (#1) coordinates: Matrix rotation and translation 0.99932738 0.02913605 -0.02226830 -3.91825319 -0.03276313 0.98214445 -0.18525352 35.81662598 0.01647313 0.18585850 0.98243842 -27.11723048 Axis 0.98118559 -0.10242874 -0.16365568 Axis point 0.00000000 165.21351949 175.71405821 Rotation angle (degrees) 10.90108730 Shift along axis -3.07529671 > ~select #2 Nothing selected > hide #2 models > show #2 models > hide #!1 models > show #3 models > show #!1 models > hide #!1 models > hide #2 models Expected an objects specifier or a view name or a keyword > view sel No displayed objects specified. > select clear > select clear > view sel No displayed objects specified. > view sel No displayed objects specified. > view sel No displayed objects specified. > select #3/A:432@C3' 1 atom, 1 model selected > select up 22 atoms, 24 bonds, 1 model selected > select up 62209 atoms, 69672 bonds, 1 model selected > select down 22 atoms, 24 bonds, 1 model selected > view sel > show #!1 models > show #2 models > select #3 92450 atoms, 100754 bonds, 1 model selected > select #2 86113 atoms, 93813 bonds, 1 model selected > ui mousemode rightMode ""translate selected models"" > fitmap #2 inMap #1 Fit molecule input-50S-jc95.pdb (#2) to map combined-pp.mrc (#1) using 86113 atoms average map value = 0.06231, steps = 204 shifted from previous position = 11.9 rotated from previous position = 10.7 degrees atoms outside contour = 20478, contour level = 0.034998 Position of input-50S-jc95.pdb (#2) relative to combined-pp.mrc (#1) coordinates: Matrix rotation and translation 0.99999578 0.00056821 -0.00285071 0.30639739 -0.00057584 0.99999625 -0.00267596 0.29964488 0.00284918 0.00267759 0.99999236 -1.07758995 Axis 0.67740365 -0.72122739 -0.14475963 Axis point 370.91227208 0.00000000 71.89705510 Rotation angle (degrees) 0.22640635 Shift along axis 0.14743413 > select clear > save session /media/RAIDA/zoe/19May15_MMAL/triple3.cxs > hide #!1 models > hide #2 models > view all > select #3/X:77@C19 1 atom, 1 model selected > select up 7 atoms, 6 bonds, 1 model selected > view sel > show #!1 models > show #!4 models > surface dust #1 size 5 > transparency 50 > hide #!1 models > transparency 50 > volume #4 toggle > volume #1 toggle > volume #4 toggle > volume #1 toggle > volume #4 toggle > volume #1 toggle > show #2 models > volume #4 toggle > volume #1 toggle > volume #4 toggle > volume #1 toggle > volume #4 toggle > volume #1 toggle > volume #4 toggle > volume #1 toggle > volume #4 toggle > volume #1 toggle > volume #4 toggle > volume #1 toggle > volume #4 toggle > volume #1 toggle > save session /media/RAIDA/zoe/19May15_MMAL/triple3.cxs > show #!1 models > hide #!4 models Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/sideview/tool.py"", line 116, in exposeEvent self.render() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/sideview/tool.py"", line 276, in render self.view.draw() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 166, in draw self._draw_scene(camera, drawings) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 248, in _draw_scene pixel_width = self._highlight_width) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1479, in draw_highlight_outline r.outline.finish_rendering_outline(color=color, pixel_width=pixel_width) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 1752, in finish_rendering_outline r.pop_framebuffer() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 638, in pop_framebuffer fb.activate() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2128, in activate GL.glDrawBuffer(self._draw_buffer) File ""src/errorchecker.pyx"", line 53, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_BACK,) ) OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_BACK,) ) File ""src/errorchecker.pyx"", line 53, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command ""graphics restart"" after changing the settings that caused the error. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 73, in draw_new_frame view.draw(check_for_changes = False) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 166, in draw self._draw_scene(camera, drawings) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 248, in _draw_scene pixel_width = self._highlight_width) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1479, in draw_highlight_outline r.outline.finish_rendering_outline(color=color, pixel_width=pixel_width) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 1752, in finish_rendering_outline r.pop_framebuffer() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 638, in pop_framebuffer fb.activate() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2128, in activate GL.glDrawBuffer(self._draw_buffer) File ""src/errorchecker.pyx"", line 53, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_BACK,) ) Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/sideview/tool.py"", line 112, in _redraw self.render() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/sideview/tool.py"", line 276, in render self.view.draw() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 166, in draw self._draw_scene(camera, drawings) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 248, in _draw_scene pixel_width = self._highlight_width) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1479, in draw_highlight_outline r.outline.finish_rendering_outline(color=color, pixel_width=pixel_width) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 1752, in finish_rendering_outline r.pop_framebuffer() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 638, in pop_framebuffer fb.activate() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2128, in activate GL.glDrawBuffer(self._draw_buffer) File ""src/errorchecker.pyx"", line 53, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_BACK,) ) Error processing trigger ""frame drawn"": OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_BACK,) ) File ""src/errorchecker.pyx"", line 53, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 430.50 OpenGL renderer: GeForce RTX 2080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect assigned normal Graphics all ChimeraX