id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20468 ChimeraX bug report submission chimerax-bug-report@… "{{{ The following bug report has been submitted: Platform: macOS-26.4-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description Last time you used ChimeraX it crashed. 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All rights reserved. > open ""/Volumes/bzmh01$/_Members/casano0002/For Chris A3 paper /Chimera > /Models_ATP13A3-AZ1_yeast_worm_fly.cxs"" Log from Mon Jun 8 08:35:03 2026UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/casano0002/Downloads/fold_catp6_oaz1_celegans_shortaz1/fold_catp6_oaz1_celegans_shortaz1_model_3.cif Chain information for fold_catp6_oaz1_celegans_shortaz1_model_3.cif #1 --- Chain | Description A | . B | . Computing secondary structure > select /B:1-121 976 atoms, 1004 bonds, 121 residues, 1 model selected > show sel cartoons > log metadata #1 The model has no metadata > log chains #1 Chain information for fold_catp6_oaz1_celegans_shortaz1_model_3.cif #1 --- Chain | Description A | . B | . > set bgColor white > ui tool show ""Color Actions"" > color sel bychain > color sel #ff8758ff > color sel #ff944eff > color sel #ff8d48ff > color sel #ff8e48ff > color sel #ff944eff > color sel #ff9751ff [Repeated 1 time(s)] > color sel #ff9953ff > color sel #ff9a54ff > color sel #ff9b54ff > color sel #ff9c54ff > color sel #ff9c53ff > color sel #ff9d53ff > color sel #ff9e52ff [Repeated 2 time(s)] > color sel #ff9f52ff > color sel #ffa150ff > color sel #ffa04fff > color sel #ffa14eff > color sel #ffa14dff > color sel #ffa14bff > color sel #ffa24bff > color sel #ffa24aff [Repeated 1 time(s)] > color sel #ffa148ff > color sel #ffa146ff > color sel #ffa044ff > color sel #ff9f44ff > color sel #ff9f43ff > color sel #ff9f42ff > color sel #f99c1c > select /B:1-121 976 atoms, 1004 bonds, 121 residues, 1 model selected > select /B:1-121 976 atoms, 1004 bonds, 121 residues, 1 model selected > select /B:1-121 976 atoms, 1004 bonds, 121 residues, 1 model selected > select/B Unknown command: select/B > select /B:1-121 976 atoms, 1004 bonds, 121 residues, 1 model selected > select/A Unknown command: select/A > select/A:1-1267 Unknown command: select/A:1-1267 > select /A:1-1267 9985 atoms, 10198 bonds, 1267 residues, 1 model selected > color #1 #3e8bf6ff > color #1 #5cc9f8ff > color #1 #3272f4ff > color #1 #2250f1ff > color #1 #316aedff > color #1 #336decff > color #1 #346beaff > color #1 #2532e6ff > color #1 #416ae3ff > color #1 #4a7ce3ff > select /B:1-121 color sel #f99c1c, Expected a keyword > select /B:1-121 976 atoms, 1004 bonds, 121 residues, 1 model selected > color sel #f99c1c > show sel cartoons > select /B:1-121, select /A:1-1267 10961 atoms, 11202 bonds, 1388 residues, 1 model selected > show sel cartoons > select /A:1-1267 9985 atoms, 10198 bonds, 1267 residues, 1 model selected > color #1 #5eb4e6ff > color #1 #60b0e4ff > color #1 #4884e5ff > color #1 #5487e3ff > select /B:1-121 976 atoms, 1004 bonds, 121 residues, 1 model selected > color sel #f99c1c > select /A:1-1267 select /B:1-121 Expected a keyword > select /A:1-1267, select /B:1-121 10961 atoms, 11202 bonds, 1388 residues, 1 model selected > cartoon style sel xsection oval modeHelix default > cartoon style (sel & coil) xsection oval > cartoon style sel xsection barbell modeHelix default > cartoon style sel xsection oval modeHelix default > cartoon > cartoon style width 1.5 thickness 0.5 > graphics silhouettes true > graphics silhouettes width 2 > graphics silhouettes color black > lighting flatck Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a keyword > lighting flat > lighting simple > cartoon > graphics silhouettes true width 3 color black > lighting flat > set bgColor white > graphics depthCue false Expected a keyword > graphics depthCue false Expected a keyword > select subtract #1 Nothing selected > select add #1 10961 atoms, 11202 bonds, 1388 residues, 1 model selected > select subtract #1 Nothing selected > graphics silhouettes false > graphics silhouettes color white > graphics silhouettes color grey > cartoon > graphics silhouettes true width 3 color black > lighting flat > set bgColor white > graphics depthCue false Expected a keyword > ~display > cartoon > cartoon style modeHelix tube > cartoon style width 2.0 thickness 0.3 > graphics silhouettes false > lighting soft > set bgColor white > cartoon style default Expected an atoms specifier or a keyword > cartoon style modeHelix ribbon Invalid ""modeHelix"" argument: Should be one of 'default', 'tube', or 'wrap' > cartoon > graphics silhouettes true width 3 color black > lighting flat > set bgColor white > graphics depthCue false Expected a keyword > ~display > cartoon > lighting soft > set bgColor white > graphics silhouettes false > ~display > cartoon > lighting soft > set bgColor white > graphics silhouettes false > ~display > cartoon > lighting soft > set bgColor white > graphics silhouettes false > cartoon style width 1.5 thickness 0.5 > lighting soft > lighting shadows true intensity 0.5 > graphics silhouettes true width 8 > set bgColor white > cartoon style modeHelix ribbon Invalid ""modeHelix"" argument: Should be one of 'default', 'tube', or 'wrap' > cartoon style modeHelix default > graphics silhouettes true width 5 > graphics silhouettes true width 4 > graphics silhouettes true width 3 > graphics silhouettes true width 2 > save /Users/casano0002/ATP13A3_canonicalOrganisms.cxs > graphics silhouettes true width 8 > save mystructure.png supersample 3 > save /Users/casano0002/ATP13A3_canonicalOrganisms.png supersample 3 > save /Users/casano0002/ATP13A3_canonicalOrganisms.png width 6000 height 6000 > supersample 3 > open > /Users/casano0002/Downloads/fold_catp5_oaz1_celegans_shortaz1/fold_catp5_oaz1_celegans_shortaz1_model_1.cif Chain information for fold_catp5_oaz1_celegans_shortaz1_model_1.cif #2 --- Chain | Description A | . B | . Computing secondary structure > hide #1 models > select add #2 10432 atoms, 10648 bonds, 1324 residues, 1 model selected > select /A:1-1327 19441 atoms, 19842 bonds, 2470 residues, 2 models selected > select add #1 20417 atoms, 20846 bonds, 2591 residues, 2 models selected > select subtract #1 9456 atoms, 9644 bonds, 1203 residues, 1 model selected > color #2 #6a91e0ff > select #2/B:1-121 976 atoms, 1004 bonds, 121 residues, 1 model selected > color #f99c1c > select /A:1-1327, color #2 #6a91e0ff Expected a keyword > select /A:1-1327, color #6a91e0ff Expected a keyword > select /A:1-1327, Expected an objects specifier or a keyword > select /A:1-1327 19441 atoms, 19842 bonds, 2470 residues, 2 models selected > color #2 #2c57e9ff > color #2 #0f1deeff > color #2 #5f81e0ff > select #2/B:1-121 976 atoms, 1004 bonds, 121 residues, 1 model selected > color sel #eeaa43ff > hide #2 models > show #1 models > select add #1 11937 atoms, 12206 bonds, 1509 residues, 2 models selected > select #2/A:1-1203 9456 atoms, 9644 bonds, 1203 residues, 1 model selected > select #2/A:1-1203 9456 atoms, 9644 bonds, 1203 residues, 1 model selected > select /A:1-1267 19441 atoms, 19842 bonds, 2470 residues, 2 models selected > color #1 #718bdeff > select #2/B:1-121 976 atoms, 1004 bonds, 121 residues, 1 model selected > select #2/B:1-121 976 atoms, 1004 bonds, 121 residues, 1 model selected > select #2/B:1-121 976 atoms, 1004 bonds, 121 residues, 1 model selected > select #2/B:1-121 976 atoms, 1004 bonds, 121 residues, 1 model selected > hide #1 models > show #2 models > hide #2 models > show #1 models > select #2/B:1-121 976 atoms, 1004 bonds, 121 residues, 1 model selected > select #2/B:1-121 976 atoms, 1004 bonds, 121 residues, 1 model selected > select #2/A:1-1203 9456 atoms, 9644 bonds, 1203 residues, 1 model selected > hide #1 models > show #2 models > hide #2 models > show #1 models > select add #2 10432 atoms, 10648 bonds, 1324 residues, 1 model selected > select subtract #2 Nothing selected > select add #1 10961 atoms, 11202 bonds, 1388 residues, 1 model selected > select /B:1-121 1952 atoms, 2008 bonds, 242 residues, 2 models selected > select #2/B:1-121, color #f99c1c Expected a keyword > select #2/B:1-121, color #2 #f99c1c Expected a keyword > color (#1 & sel) #deaa4cff > color (#1 & sel) #deb03fff > color (#1 & sel) #deab3cff [Repeated 1 time(s)] > color (#1 & sel) #deaa3cff > color (#1 & sel) #dea93cff > color (#1 & sel) #dea73eff > color (#1 & sel) #dea53fff > color (#1 & sel) #dea440ff > color (#1 & sel) #dea341ff > color (#1 & sel) #dea242ff > color (#1 & sel) #de9f46ff > color (#1 & sel) #de9e47ff > color (#1 & sel) #de9d48ff > color (#1 & sel) #de9e4bff > color (#1 & sel) #dea051ff > color (#1 & sel) #dea357ff > color (#1 & sel) #dea459ff > color (#1 & sel) #dea45aff [Repeated 1 time(s)] > color (#1 & sel) #dea55bff > color (#1 & sel) #dea65dff > color (#1 & sel) #dea75eff > color (#1 & sel) #dea862ff > color (#1 & sel) #dea963ff > color (#1 & sel) #deaa64ff > color (#1 & sel) #deaa66ff > color (#1 & sel) #deaa67ff > color (#1 & sel) #deac69ff [Repeated 1 time(s)] > color (#1 & sel) #dead6bff > color (#1 & sel) #dead6cff [Repeated 1 time(s)] > color (#1 & sel) #deae6dff > color (#1 & sel) #deae6eff > color (#1 & sel) #deaf6fff > color (#1 & sel) #deaf70ff > color (#1 & sel) #deb071ff > color (#1 & sel) #deb173ff > color (#1 & sel) #deb276ff > color (#1 & sel) #deb378ff > color (#1 & sel) #deb47aff > color (#1 & sel) #deb67cff > color (#1 & sel) #deb77eff > color (#1 & sel) #deb880ff > color (#1 & sel) #deb981ff > color (#1 & sel) #debc85ff > color (#1 & sel) #debe88ff > color (#1 & sel) #debe89ff > color (#1 & sel) #debe8aff > color (#1 & sel) #debf8aff > color (#1 & sel) #dec08cff > color (#1 & sel) #dec08dff > color (#1 & sel) #dec18fff > color (#1 & sel) #dec190ff > color (#1 & sel) #dec291ff > color (#1 & sel) #dec293ff > color (#1 & sel) #dec394ff > color (#1 & sel) #dec395ff > color (#1 & sel) #dec396ff > color (#1 & sel) #dec498ff > color (#1 & sel) #debd82ff > color (#1 & sel) #deba7fff > color (#1 & sel) #deb77bff > color (#1 & sel) #deb376ff > color (#1 & sel) #deb374ff > color (#1 & sel) #deb172ff > color (#1 & sel) #deb070ff > color (#1 & sel) #deaf6eff > color (#1 & sel) #dead6bff > color (#1 & sel) #deab68ff > color (#1 & sel) #deab66ff > color (#1 & sel) #deab62ff > color (#1 & sel) #deaa61ff > color (#1 & sel) #deaa60ff > color #2 #f99c1c > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #1 models > select #2/A:1-1203 9456 atoms, 9644 bonds, 1203 residues, 1 model selected > color #2 #8195ddff > select #2/B:1-121 976 atoms, 1004 bonds, 121 residues, 1 model selected > color #2 #f99c1c > select #2/A:1-1203 9456 atoms, 9644 bonds, 1203 residues, 1 model selected > color #2 #8195ddff > select #2/B:1-1211203 976 atoms, 1004 bonds, 121 residues, 1 model selected > select #2/B:1-1211203 color #2 #f99c1c Expected a keyword > select #2/B:1-1211203, color #2 #f99c1c Expected a keyword > color #2 #f99c1c > select #2/A:1-1203 9456 atoms, 9644 bonds, 1203 residues, 1 model selected > select #2/A:1-1203, color #2 #8195ddff Expected a keyword > select #2/A:1-1203, color #2 #8195ddf Expected a keyword > select #2/A:1-1203, color #2 #8195dd Expected a keyword > select #2/A:1-1203, color #2 #8195d Expected a keyword > color #2 #8195ddff > select #2/B:1-121, color #2 #f99c1c Expected a keyword > select #2/B:1-121 976 atoms, 1004 bonds, 121 residues, 1 model selected > select #2/B:1-121 976 atoms, 1004 bonds, 121 residues, 1 model selected > select #2/B:1-121 976 atoms, 1004 bonds, 121 residues, 1 model selected > select #2/B:1-121 976 atoms, 1004 bonds, 121 residues, 1 model selected > color #2 #f99c1c > select #2/A:1-1203 9456 atoms, 9644 bonds, 1203 residues, 1 model selected > select #2/A:1-1203, color #2A:1-1203 #8195d Expected a keyword > select #2/A:1-1203, color #2/A:1-1203 #8195d Expected a keyword > select #2/A:1-1203, color #2/A:1-1203 #8195d Expected a keyword > color #2 #8195ddff > elect #2/B:1-121, color #2/B:1-121, #f99c1c Unknown command: elect #2/B:1-121, color #2/B:1-121, #f99c1c > elect #2/B:1-121, color #2/B:1-121 #f99c1c Unknown command: elect #2/B:1-121, color #2/B:1-121 #f99c1c > select #2/B:1-121, color #2/B:1-121 #f99c1c Expected a keyword > color #2/B:1-121 #f99c1c > select add #2 10432 atoms, 10648 bonds, 1324 residues, 1 model selected > select subtract #2 Nothing selected > show #1 models > sequence chain #1/A Alignment identifier is 1/A > sequence chain #1/B#2/B Alignment identifier is 1 > sequence chain #2/A Alignment identifier is 2/A > matchmaker #1 to #2 alwaysAlign true Expected a keyword > matchmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2) with fold_catp6_oaz1_celegans_shortaz1_model_3.cif, chain A (#1), sequence alignment score = 3396.8 RMSD between 948 pruned atom pairs is 0.860 angstroms; (across all 1124 pairs: 4.359) > alwaysAlign true Unknown command: alwaysAlign true > always Align true Unknown command: always Align true > hide #1 models > save /Users/casano0002/ATP13A3_canonicalOrganismsCATP6.png width 6000 height > 6000 supersample 3 [Repeated 1 time(s)] > hide #2 models > show #1 models > show #2 models > hide #2 models > hide #1 models > show #1 models > show #2 models > save /Users/casano0002/catp5_catp6_alphafoldmodels.cxs Unsupported scale factor (0.000000) detected on Display0 [Repeated 3 time(s)]Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. > open > /Users/casano0002/Downloads/fold_oaz1_ypk9_yeast_shortyeast/fold_oaz1_ypk9_yeast_shortyeast_model_2.cif Chain information for fold_oaz1_ypk9_yeast_shortyeast_model_2.cif #3 --- Chain | Description A | . B | . Computing secondary structure > matchmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2) with fold_catp6_oaz1_celegans_shortaz1_model_3.cif, chain A (#1), sequence alignment score = 3396.8 RMSD between 948 pruned atom pairs is 0.860 angstroms; (across all 1124 pairs: 4.359) > matchmaker #1 to #2 #3 Specify a single 'to' model only > matchmaker #1 to #3 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_oaz1_ypk9_yeast_shortyeast_model_2.cif, chain B (#3) with fold_catp6_oaz1_celegans_shortaz1_model_3.cif, chain A (#1), sequence alignment score = 2515 RMSD between 398 pruned atom pairs is 1.011 angstroms; (across all 1115 pairs: 9.507) > matchmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2) with fold_catp6_oaz1_celegans_shortaz1_model_3.cif, chain A (#1), sequence alignment score = 3396.8 RMSD between 948 pruned atom pairs is 0.860 angstroms; (across all 1124 pairs: 4.359) > matchmaker #1 to #3 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_oaz1_ypk9_yeast_shortyeast_model_2.cif, chain B (#3) with fold_catp6_oaz1_celegans_shortaz1_model_3.cif, chain A (#1), sequence alignment score = 2515 RMSD between 398 pruned atom pairs is 1.011 angstroms; (across all 1115 pairs: 9.507) > matchmaker #2 to #3 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_oaz1_ypk9_yeast_shortyeast_model_2.cif, chain B (#3) with fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2), sequence alignment score = 2454.1 RMSD between 387 pruned atom pairs is 1.137 angstroms; (across all 1130 pairs: 19.908) > hide #1 models > hide #2 models > open > /Users/casano0002/Downloads/fold_fly_oaz1_atp13a3_shorteraz1_shortera3-2/fold_fly_oaz1_atp13a3_shorteraz1_shortera3_model_2.cif Chain information for fold_fly_oaz1_atp13a3_shorteraz1_shortera3_model_2.cif #4 --- Chain | Description A | . B | . Computing secondary structure > matchmaker #2 to #4 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_fly_oaz1_atp13a3_shorteraz1_shortera3_model_2.cif, chain A (#4) with fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2), sequence alignment score = 2596.7 RMSD between 727 pruned atom pairs is 1.203 angstroms; (across all 1146 pairs: 18.869) > show #2 models > matchmaker #2 to #4 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_fly_oaz1_atp13a3_shorteraz1_shortera3_model_2.cif, chain A (#4) with fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2), sequence alignment score = 2596.7 RMSD between 727 pruned atom pairs is 1.203 angstroms; (across all 1146 pairs: 18.869) > matchmaker #2 to #3 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_oaz1_ypk9_yeast_shortyeast_model_2.cif, chain B (#3) with fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2), sequence alignment score = 2454.1 RMSD between 387 pruned atom pairs is 1.137 angstroms; (across all 1130 pairs: 19.908) > matchmaker #3 ro #4 Expected a keyword > matchmaker #3 to #4 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_fly_oaz1_atp13a3_shorteraz1_shortera3_model_2.cif, chain A (#4) with fold_oaz1_ypk9_yeast_shortyeast_model_2.cif, chain B (#3), sequence alignment score = 2553.6 RMSD between 395 pruned atom pairs is 0.973 angstroms; (across all 1215 pairs: 19.189) > matchmaker #1 to #4 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_fly_oaz1_atp13a3_shorteraz1_shortera3_model_2.cif, chain A (#4) with fold_catp6_oaz1_celegans_shortaz1_model_3.cif, chain A (#1), sequence alignment score = 2967.9 RMSD between 737 pruned atom pairs is 1.072 angstroms; (across all 1169 pairs: 16.160) > matchmaker #2 to #4 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_fly_oaz1_atp13a3_shorteraz1_shortera3_model_2.cif, chain A (#4) with fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2), sequence alignment score = 2596.7 RMSD between 727 pruned atom pairs is 1.203 angstroms; (across all 1146 pairs: 18.869) > hide #2 models > hide #4 models > hide #3 models > show #4 models > select #4/B:1-212 1671 atoms, 1710 bonds, 212 residues, 1 model selected > color #4/B:1-212 #f99c1c > select #4/A:1-1416 11277 atoms, 11554 bonds, 1416 residues, 1 model selected > select #4/A:1-1416 11277 atoms, 11554 bonds, 1416 residues, 1 model selected > select #4/A:1-1416, color #8195d Expected a keyword > select #4/A:1-1416, color #8195ddff Expected a keyword > hide #4 models > show #2 models > hide #2 models > show #4 models > select #4/A:1-1416, color #8195d Expected a keyword > show target m > hide target m > show #4 models > color sel #718bdeff > hide #4 models > show #2 models > select add #4 12948 atoms, 13264 bonds, 1628 residues, 1 model selected > select subtract #4 Nothing selected > select #2/A 9456 atoms, 9644 bonds, 1203 residues, 1 model selected > color sel #718bdeff > hide #2 models > show #3 models > hide #3 models > show #4 models > show #3 models > hide #4 models > select #3A Expected an objects specifier or a keyword > select #3/A 2399 atoms, 2451 bonds, 292 residues, 1 model selected > show #4 models > color sel #ffa81eff > hide #4 models > select #3/A, color#3/A #f99c1c Expected a keyword > select #3/A, color sel #f99c1c Expected a keyword > show #4 models > hide #4 models > show #2 models > color sel #f0961bff > color sel #d38418ff > color sel #d18318ff > select #3/A, color sel #f99c1c Expected a keyword > select #3/A, color #f99c1c Expected a keyword > color sel #f99c1c > hide #2 models > select #3/B, color sel #f99c1c Expected a keyword > select #3/B 11504 atoms, 11782 bonds, 1440 residues, 1 model selected > color sel #718bdeff > hide #3 models > show #3 models > show #4 models > show #2 models > show #1 models > hide #1 models > hide #2 models > hide #3 models > select add #3 13903 atoms, 14233 bonds, 1732 residues, 1 model selected > select subtract #3 Nothing selected > show #3 models > cartoon style width 1.5 thickness 0.5 > lighting soft > lighting shadows true intensity 0.5 > graphics silhouettes true width 8 > set bgColor white > show #1 models > show #2 models > hide #2 models > hide #3 models > hide #4 models > save /Users/casano0002/ATP13A3_canonicalOrganismsCATP5.png width 6000 height > 6000 supersample 3 > hide #1 models > show #2 models > save /Users/casano0002/ATP13A3_canonicalOrganismsCATP5.png width 6000 height > 6000 supersample 3 > show #1 models > hide #2 models > hide #1 models > show #3 models > hide #3 models > show #1 models > save /Users/casano0002/ATP13A3_canonicalOrganismsCATP6.png width 6000 height > 6000 supersample 3 > hide #1 models > show #3 models > save /Users/casano0002/ATP13A3_canonicalOrganismsYEAST.png width 6000 height > 6000 supersample 3 > hide #3 models > show #4 models > show #3 models > show #2 models > show #1 models > hide #1 models > hide #2 models > hide #3 models > save /Users/casano0002/ATP13A3_canonicalOrganismsfly.png width 6000 height > 6000 supersample 3 > hide #4 models > show #1 models > select /B:1-121 3829 atoms, 3927 bonds, 484 residues, 4 models selected > color sel #f99c1c > select add #1 13814 atoms, 14125 bonds, 1751 residues, 4 models selected > select subtract #1 2853 atoms, 2923 bonds, 363 residues, 3 models selected > show #2 models > show #3 models > hide #3 models > hide #2 models > save /Users/casano0002/ATP13A3_canonicalOrganismsCATP6.png width 6000 height > 6000 supersample 3 > open /Users/casano0002/Downloads/A3_full-OAZ1_N-trunc_0009_best.pdb Summary of feedback from opening /Users/casano0002/Downloads/A3_full-OAZ1_N- trunc_0009_best.pdb --- warnings | Ignored bad PDB record found on line 21726 # All scores below are weighted scores, not raw scores. Ignored bad PDB record found on line 21727 #BEGIN_POSE_ENERGIES_TABLE A3_full-OAZ1_N-trunc_0009.pdb Ignored bad PDB record found on line 21728 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd fa_elec hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega fa_dun p_aa_pp yhh_planarity ref rama_prepro cart_bonded total Ignored bad PDB record found on line 21729 weights 1 0.55 1 0.005 1 1 1 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 0.5 NA Ignored bad PDB record found on line 21730 pose -8342.82 835.552 4700.04 18.9827 228.62 -212.212 -2635.55 -623.123 -300.969 -262.172 -242.384 -0.93833 19.7511 1352.03 -288.768 1.81732 655.338 -99.8253 675.911 -4520.72 1367 messages similar to the above omitted Chain information for A3_full-OAZ1_N-trunc_0009_best.pdb #5 --- Chain | Description A | No description available B | No description available Computing secondary structure > matchmakee #1 #5 Unknown command: matchmakee #1 #5 > matchmakee #1, #5 Unknown command: matchmakee #1, #5 > matchmakee #1 and #5 Unknown command: matchmakee #1 and #5 > matchmaker #1 and #5 Expected a keyword > matchmaker #1 #5 Missing required ""to"" argument > matchmaker #1, #5 Missing or invalid ""matchAtoms"" argument: only initial part ""#1"" of atom specifier valid > matchmaker #2 to #5 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker A3_full-OAZ1_N-trunc_0009_best.pdb, chain A (#5) with fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2), sequence alignment score = 2693.2 RMSD between 699 pruned atom pairs is 1.229 angstroms; (across all 1113 pairs: 5.931) > matchmaker #2 to #5 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker A3_full-OAZ1_N-trunc_0009_best.pdb, chain A (#5) with fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2), sequence alignment score = 2693.2 RMSD between 699 pruned atom pairs is 1.229 angstroms; (across all 1113 pairs: 5.931) > matchmaker #2 to #4 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_fly_oaz1_atp13a3_shorteraz1_shortera3_model_2.cif, chain A (#4) with fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2), sequence alignment score = 2596.7 RMSD between 727 pruned atom pairs is 1.203 angstroms; (across all 1146 pairs: 18.869) > matchmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_catp6_oaz1_celegans_shortaz1_model_3.cif, chain A (#1) with fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2), sequence alignment score = 3396.8 RMSD between 948 pruned atom pairs is 0.860 angstroms; (across all 1124 pairs: 4.359) > show #2 models > show #3 models > show #4 models > hide #1 models > hide #2 models > hide #3 models > hide #4 models > show #4 models > matchmaker #4 to #5 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker A3_full-OAZ1_N-trunc_0009_best.pdb, chain A (#5) with fold_fly_oaz1_atp13a3_shorteraz1_shortera3_model_2.cif, chain A (#4), sequence alignment score = 3007.7 RMSD between 547 pruned atom pairs is 1.077 angstroms; (across all 1173 pairs: 10.910) > show #3 models > show #1 models > show #2 models > matchmaker #4 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2) with fold_fly_oaz1_atp13a3_shorteraz1_shortera3_model_2.cif, chain A (#4), sequence alignment score = 2596.7 RMSD between 727 pruned atom pairs is 1.203 angstroms; (across all 1146 pairs: 18.869) > matchmaker #5 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2) with A3_full-OAZ1_N-trunc_0009_best.pdb, chain A (#5), sequence alignment score = 2693.2 RMSD between 699 pruned atom pairs is 1.229 angstroms; (across all 1113 pairs: 5.931) > hide #5 models > hide #4 models > hide #3 models > hide #2 models > hide #1 models > select add #2 12309 atoms, 12567 bonds, 1566 residues, 3 models selected > select add #3 25280 atoms, 25845 bonds, 3177 residues, 3 models selected > select add #4 37283 atoms, 38145 bonds, 4684 residues, 3 models selected > select subtract #4 24335 atoms, 24881 bonds, 3056 residues, 2 models selected > select subtract #3 10432 atoms, 10648 bonds, 1324 residues, 1 model selected > select subtract #2 Nothing selected > show #1 models > show #2 models > show #3 models > show #4 models > show #5 models > hide #1 models > show #1 models > hide #4 models > hide #3 models > hide #2 models > hide #1 models > select #5/A:1-1226 19526 atoms, 19751 bonds, 1226 residues, 1 model selected > color #5 #718bdeff > select add #5 21713 atoms, 21961 bonds, 1364 residues, 1 model selected > select subtract #5 Nothing selected > select #5/B:1-138 2187 atoms, 2210 bonds, 138 residues, 1 model selected > color sel #f99c1c > select add #5 21713 atoms, 21961 bonds, 1364 residues, 1 model selected > select subtract #5 Nothing selected > cartoon style width 1.5 thickness 0.5 > lighting soft > lighting shadows true intensity 0.5 > graphics silhouettes true width 8 > set bgColor white > save /Users/casano0002/ATP13A3_canonicalOrganismshuman.png width 6000 height > 6000 supersample 3 Unsupported scale factor (0.000000) detected on Display0 [Repeated 5 time(s)] Unsupported scale factor (0.000000) detected on Display1 [Repeated 5 time(s)]Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. > save /Users/casano0002/Models_ATP13A3-AZ1_yeast_worm_fly.cxs ——— End of log from Mon Jun 8 08:35:03 2026 ——— > view name session-start opened ChimeraX session OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,7 Model Number: Z1AF001PSSM/A Chip: Apple M3 Pro Total Number of Cores: 12 (6 Performance and 6 Efficiency) Memory: 18 GB System Firmware Version: 18000.101.7 OS Loader Version: 18000.101.7 Software: System Software Overview: System Version: macOS 26.4 (25E246) Kernel Version: Darwin 25.4.0 Time since boot: 28 days, 1 hour, 32 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 18 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal P27q-30: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 70.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect new normal Unassigned