id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2721 Index out of bounds showing interface contact residues leygkn@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 0.91 (2019-12-23) Description (Describe the actions that caused this problem to occur here) I tried Interfaces -> select contact residue~~ or Residue plot ... and this error occured Log: UCSF ChimeraX version: 0.91 (2019-12-23) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:/Users/leygk/OneDrive/구조 모델링 관련 자료/VHL mutation (4wqo).cxs"" opened ChimeraX session > graphics silhouettes false > lighting full > toolshed show ""Side View"" > select clear > graphics silhouettes true > rainbow Unknown command: clor /a red > color /a red > color /c green > color bychain > color byhetero > color byhetero > color bychain > interfaces ~solvent 3 buried areas: A C 1001, D C 965, A D 340 > show sel atoms > color sel byatom > label sel > label sel size 100 > label sel size 200 > label sel size 30 > label sel size 50 > help help:user > label sel height 100 size 50 > label sel height 10 size 50 > label sel height 1 size 50 > label sel height 0.5 size 100 > toolshed show ""Command Line Interface"" > toolshed show ""Basic Actions"" > label sel height 0.5 size 200 > label sel height 0.5 > label sel height 0.5 color purple > label sel height 0.5 color red > select clear > show sel atoms > label sel height 0.5 color red > label sel height 0.5 color yellow > label sel height 0.5 color blue > color sel byatom > select clear > hide /D target c Alignment identifier is 1.A Alignment identifier is 1.C Alignment identifier is 1.D > select clear > delete sel > select clear Alignment identifier is 1.A Alignment identifier is 1.C Alignment identifier is 1.D > select clear > interfaces ~solvent 3 buried areas: D C 965, C A 902, D A 340 > color red > color sel red > undo > color sel red > undo > select /C:89 9 atoms, 8 bonds, 1 model selected > hide sel atoms > label > save session ""C:/Users/leygk/OneDrive/구조 모델링 관련 자료/VHL - Cul2.cxs"" > select clear > select /A:191 10 atoms, 10 bonds, 1 model selected > select /A:190 8 atoms, 7 bonds, 1 model selected > select /A:189 9 atoms, 8 bonds, 1 model selected > select /A:188 8 atoms, 7 bonds, 1 model selected > select /A:184 8 atoms, 7 bonds, 1 model selected > select /a 470 atoms, 476 bonds, 1 model selected > show sel surfaces > undo > hide sel surfaces > select /A:184 8 atoms, 7 bonds, 1 model selected > show sel surfaces > hide sel surfaces > select /A:187 8 atoms, 7 bonds, 1 model selected > show sel surfaces > hide sel surfaces > select /A:191 10 atoms, 10 bonds, 1 model selected > show sel surfaces > delete sel > select /c 739 atoms, 755 bonds, 1 model selected > show sel surfaces > hide sel surfaces > select /C:68 10 atoms, 10 bonds, 1 model selected > show sel surfaces > hide sel surfaces > select /C:64 9 atoms, 8 bonds, 1 model selected > show sel surfaces > hide sel surfaces > select /C:65 8 atoms, 7 bonds, 1 model selected > show sel surfaces > show sel surfaces > select /C:65 8 atoms, 7 bonds, 1 model selected > select /C:66 7 atoms, 7 bonds, 1 model selected > select /C:66 7 atoms, 7 bonds, 1 model selected > select /C:74 6 atoms, 5 bonds, 1 model selected > select clear > select /C:64 9 atoms, 8 bonds, 1 model selected > show sel surfaces > select /C:38@O 1 atom, 1 model selected > select /C:38@CG2 1 atom, 1 model selected > select /c 739 atoms, 755 bonds, 1 model selected > hide sel surfaces > select /C:38 7 atoms, 6 bonds, 1 model selected > show sel surfaces > select /C:64 9 atoms, 8 bonds, 1 model selected > select /C:65 8 atoms, 7 bonds, 1 model selected > show sel surfaces > color sel red > select /c 739 atoms, 755 bonds, 1 model selected > show sel surfaces > select clear > delete sel > undo Undo failed, probably because structures have been modified. > select /c 368 atoms, 377 bonds, 1 model selected > hide sel surfaces > select clear > save session ""C:/Users/leygk/OneDrive/구조 모델링 관련 자료/VHL - Cul2 (Core).cxs"" > toolshed show ""Command Line Interface"" > ui favorite true ""Command Line Interface"" > help help:user > help help:user/tools/cli.html > ui dockable false ""Command Line Interface"" > ui dockable true ""Command Line Interface"" > ui dockable false ""Command Line Interface"" > select /c 368 atoms, 377 bonds, 1 model selected > show sel surfaces > hide sel surfaces Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\interfaces\graph.py"", line 416, in a.triggered.connect(lambda checked, cb=callback, args=args: cb(*args)) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\interfaces\tool.py"", line 240, in _show_residue_plot self._show_interface_residues(c, g) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\interfaces\tool.py"", line 218, in _show_interface_residues af = c.contact_residue_atoms(gf, min_area) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\interfaces\cmd.py"", line 264, in contact_residue_atoms res = self.contact_residues(group, min_area) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\interfaces\cmd.py"", line 274, in contact_residues res, rareas = group.atoms[i].residue_sums(areas) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\molarray.py"", line 158, in __getitem__ ptrs = self._pointers[i].copy() IndexError: index 428 is out of bounds for axis 0 with size 368 IndexError: index 428 is out of bounds for axis 0 with size 368 File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\molarray.py"", line 158, in __getitem__ ptrs = self._pointers[i].copy() See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\interfaces\graph.py"", line 416, in a.triggered.connect(lambda checked, cb=callback, args=args: cb(*args)) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\interfaces\tool.py"", line 240, in _show_residue_plot self._show_interface_residues(c, g) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\interfaces\tool.py"", line 218, in _show_interface_residues af = c.contact_residue_atoms(gf, min_area) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\interfaces\cmd.py"", line 264, in contact_residue_atoms res = self.contact_residues(group, min_area) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\interfaces\cmd.py"", line 274, in contact_residues res, rareas = group.atoms[i].residue_sums(areas) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\molarray.py"", line 158, in __getitem__ ptrs = self._pointers[i].copy() IndexError: index 428 is out of bounds for axis 0 with size 368 IndexError: index 428 is out of bounds for axis 0 with size 368 File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\molarray.py"", line 158, in __getitem__ ptrs = self._pointers[i].copy() See log for complete Python traceback. Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\drawing.py"", line 1113, in __del__ self.delete() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\drawing.py"", line 1122, in delete c.make_current() # Make OpenGL context current for deleting OpenGL resources. File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 128, in make_current qc = self._initialize_context() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 157, in _initialize_context window.setFormat(fmt) RuntimeError: wrapped C/C++ object of type QWindow has been deleted Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2483, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""position"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2483, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""normal"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2483, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""vcolor"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2483, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""tex_coord"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\drawing.py"", line 1577, in __del__ self.delete() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\drawing.py"", line 1586, in delete self.element_buffer.delete_buffer() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2488, in delete_buffer self.release_buffer() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2497, in release_buffer GL.glDeleteBuffers(1, [self.opengl_buffer]) File ""src\latebind.pyx"", line 32, in OpenGL_accelerate.latebind.LateBind.__call__ File ""src\wrapper.pyx"", line 318, in OpenGL_accelerate.wrapper.Wrapper.__call__ File ""src\wrapper.pyx"", line 311, in OpenGL_accelerate.wrapper.Wrapper.__call__ File ""src\errorchecker.pyx"", line 53, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glDeleteBuffers, pyArgs = ( 1, , ), cArgs = ( 1, , ), cArguments = ( 1, , ) ) Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2483, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""instance_shift_and_scale"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2483, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""instance_placement"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2483, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""vcolor"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2319, in __del__ raise OpenGLError('OpenGL vertex array object was not deleted before core.graphics.Bindings destroyed') chimerax.core.graphics.opengl.OpenGLError: OpenGL vertex array object was not deleted before core.graphics.Bindings destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\drawing.py"", line 1113, in __del__ self.delete() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\drawing.py"", line 1122, in delete c.make_current() # Make OpenGL context current for deleting OpenGL resources. File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 128, in make_current qc = self._initialize_context() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 157, in _initialize_context window.setFormat(fmt) RuntimeError: wrapped C/C++ object of type QWindow has been deleted Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2483, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""position"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2483, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""normal"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2483, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""vcolor"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2483, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""tex_coord"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\drawing.py"", line 1577, in __del__ self.delete() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\drawing.py"", line 1586, in delete self.element_buffer.delete_buffer() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2488, in delete_buffer self.release_buffer() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2497, in release_buffer GL.glDeleteBuffers(1, [self.opengl_buffer]) File ""src\latebind.pyx"", line 32, in OpenGL_accelerate.latebind.LateBind.__call__ File ""src\wrapper.pyx"", line 318, in OpenGL_accelerate.wrapper.Wrapper.__call__ File ""src\wrapper.pyx"", line 311, in OpenGL_accelerate.wrapper.Wrapper.__call__ File ""src\errorchecker.pyx"", line 53, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glDeleteBuffers, pyArgs = ( 1, , ), cArgs = ( 1, , ), cArguments = ( 1, , ) ) Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2483, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""instance_shift_and_scale"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2483, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""instance_placement"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2483, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""vcolor"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2319, in __del__ raise OpenGLError('OpenGL vertex array object was not deleted before core.graphics.Bindings destroyed') chimerax.core.graphics.opengl.OpenGLError: OpenGL vertex array object was not deleted before core.graphics.Bindings destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\drawing.py"", line 1113, in __del__ self.delete() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\drawing.py"", line 1122, in delete c.make_current() # Make OpenGL context current for deleting OpenGL resources. File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 128, in make_current qc = self._initialize_context() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 157, in _initialize_context window.setFormat(fmt) RuntimeError: wrapped C/C++ object of type QWindow has been deleted Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2483, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""position"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2483, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""normal"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2483, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""vcolor"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2483, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""tex_coord"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\drawing.py"", line 1577, in __del__ self.delete() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\drawing.py"", line 1586, in delete self.element_buffer.delete_buffer() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2488, in delete_buffer self.release_buffer() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2497, in release_buffer GL.glDeleteBuffers(1, [self.opengl_buffer]) File ""src\latebind.pyx"", line 32, in OpenGL_accelerate.latebind.LateBind.__call__ File ""src\wrapper.pyx"", line 318, in OpenGL_accelerate.wrapper.Wrapper.__call__ File ""src\wrapper.pyx"", line 311, in OpenGL_accelerate.wrapper.Wrapper.__call__ File ""src\errorchecker.pyx"", line 53, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glDeleteBuffers, pyArgs = ( 1, , ), cArgs = ( 1, , ), cArguments = ( 1, , ) ) Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2483, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""instance_shift_and_scale"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2483, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""instance_placement"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2483, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""vcolor"" was not deleted before core.graphics.Buffer destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2319, in __del__ raise OpenGLError('OpenGL vertex array object was not deleted before core.graphics.Bindings destroyed') chimerax.core.graphics.opengl.OpenGLError: OpenGL vertex array object was not deleted before core.graphics.Bindings destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2861, in __del__ raise OpenGLError('OpenGL texture was not deleted before core.graphics.Texture destroyed') chimerax.core.graphics.opengl.OpenGLError: OpenGL texture was not deleted before core.graphics.Texture destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2861, in __del__ raise OpenGLError('OpenGL texture was not deleted before core.graphics.Texture destroyed') chimerax.core.graphics.opengl.OpenGLError: OpenGL texture was not deleted before core.graphics.Texture destroyed Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\graphics\opengl.py"", line 2861, in __del__ raise OpenGLError('OpenGL texture was not deleted before core.graphics.Texture destroyed') chimerax.core.graphics.opengl.OpenGLError: OpenGL texture was not deleted before core.graphics.Texture destroyed Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\interfaces\graph.py"", line 416, in a.triggered.connect(lambda checked, cb=callback, args=args: cb(*args)) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\interfaces\tool.py"", line 219, in _show_interface_residues ab = c.contact_residue_atoms(gb, min_area) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\interfaces\cmd.py"", line 264, in contact_residue_atoms res = self.contact_residues(group, min_area) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\interfaces\cmd.py"", line 274, in contact_residues res, rareas = group.atoms[i].residue_sums(areas) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\molarray.py"", line 158, in __getitem__ ptrs = self._pointers[i].copy() IndexError: index 428 is out of bounds for axis 0 with size 368 IndexError: index 428 is out of bounds for axis 0 with size 368 File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\molarray.py"", line 158, in __getitem__ ptrs = self._pointers[i].copy() See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\interfaces\graph.py"", line 416, in a.triggered.connect(lambda checked, cb=callback, args=args: cb(*args)) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\interfaces\tool.py"", line 167, in _select_contact_residues atoms = c.contact_residue_atoms(g, min_area) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\interfaces\cmd.py"", line 264, in contact_residue_atoms res = self.contact_residues(group, min_area) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\interfaces\cmd.py"", line 274, in contact_residues res, rareas = group.atoms[i].residue_sums(areas) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\molarray.py"", line 158, in __getitem__ ptrs = self._pointers[i].copy() IndexError: index 428 is out of bounds for axis 0 with size 368 IndexError: index 428 is out of bounds for axis 0 with size 368 File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\molarray.py"", line 158, in __getitem__ ptrs = self._pointers[i].copy() See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 440.97 OpenGL renderer: GeForce GTX 1070 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation File attachment: VHL - Cul2 (Core).cxs }}} [attachment:""VHL - Cul2 (Core).cxs""] " defect closed normal Surface/Binding Analysis fixed all ChimeraX