id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2351 volume eraser: output array is read-only yazan.abbas@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-4.15.0-58-generic-x86_64-with-debian-stretch-sid ChimeraX Version: 0.91 (2019-08-20) Description Was trying to erase small regions of density from a volume that was generated by the volume zone command Log: UCSF ChimeraX version: 0.91 (2019-08-20) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/yazan/Dropbox/Abbas_etal_2019_brainV- ATPase/Figures/Figure2/figure2_6.cxs opened ChimeraX session > windowsize 1800 1800 > view list Named views: ABpairs, ADP1, ADP1234, ADP2, ADP3, ADPcloseup3, ADPcloseup4, EGcloseup1, EGcloseup2, EGcloseup2_2, EGcloseup2_3, mutsSIDE, mutsSIDE2, mutstop, overall1, overall2, slice1 > view ADPcloseup4 > hide #!10 models > hide #!9 models > surface dust #12,16-18 size 10 > show #!1 models > hide #!16 models > hide #!1 models > show #!1 models > show adp target abp > set silhouetteDepthJump 0.03 > show #!16 models > hide #!16 models > surface dust #12,16-18 size 10 > hide #!11 models > show #!10 models > hide #!10 models > show #!9 models > hide #!18 models > hide #!9 models > show #!10 models > show #!17 models > hide #!10 models > show #!11 models > hide #!17 models > toolshed show ""Side View"" > clip off > save session /home/yazan/Dropbox/Abbas_etal_2019_brainV- ATPase/Figures/Figure2/figure2_6.cxs QXcbConnection: XCB error: 3 (BadWindow), sequence: 36755, resource id: 29519822, major code: 18 (ChangeProperty), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 36756, resource id: 29519822, major code: 25 (SendEvent), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 36760, resource id: 29519829, major code: 18 (ChangeProperty), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 36761, resource id: 29519829, major code: 25 (SendEvent), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 36765, resource id: 29519836, major code: 18 (ChangeProperty), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 36766, resource id: 29519836, major code: 25 (SendEvent), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 36769, resource id: 29519843, major code: 18 (ChangeProperty), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 36770, resource id: 29519843, major code: 25 (SendEvent), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 36774, resource id: 29519850, major code: 18 (ChangeProperty), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 36775, resource id: 29519850, major code: 25 (SendEvent), minor code: 0 > hide #!16 models > show #!16 models > hide #!16 models > show #!16 models > ui mousemode rightMode ""map eraser"" > volume erase #16 center 205.27,149.99,145.23 radius 4.411 Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map_eraser/eraser.py"", line 308, in _erase_in_sphere self._erase() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map_eraser/eraser.py"", line 327, in _erase run(self.session, cmd) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2688, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map_eraser/eraser.py"", line 24, in volume_erase _zero_data_in_sphere(v.data, cvol, radius) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map_eraser/eraser.py"", line 41, in _zero_data_in_sphere subtract(dmatrix, mdmatrix, dmatrix) ValueError: output array is read-only ValueError: output array is read-only File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map_eraser/eraser.py"", line 41, in _zero_data_in_sphere subtract(dmatrix, mdmatrix, dmatrix) See log for complete Python traceback. > volume erase #16 center 205.27,149.99,145.23 radius 4.411 Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map_eraser/eraser.py"", line 308, in _erase_in_sphere self._erase() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map_eraser/eraser.py"", line 327, in _erase run(self.session, cmd) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2688, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map_eraser/eraser.py"", line 24, in volume_erase _zero_data_in_sphere(v.data, cvol, radius) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map_eraser/eraser.py"", line 41, in _zero_data_in_sphere subtract(dmatrix, mdmatrix, dmatrix) ValueError: output array is read-only ValueError: output array is read-only File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map_eraser/eraser.py"", line 41, in _zero_data_in_sphere subtract(dmatrix, mdmatrix, dmatrix) See log for complete Python traceback. > volume erase #16 center 204.46,149.93,144.85 radius 4.411 Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map_eraser/eraser.py"", line 308, in _erase_in_sphere self._erase() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map_eraser/eraser.py"", line 327, in _erase run(self.session, cmd) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2688, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map_eraser/eraser.py"", line 24, in volume_erase _zero_data_in_sphere(v.data, cvol, radius) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map_eraser/eraser.py"", line 41, in _zero_data_in_sphere subtract(dmatrix, mdmatrix, dmatrix) ValueError: output array is read-only ValueError: output array is read-only File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map_eraser/eraser.py"", line 41, in _zero_data_in_sphere subtract(dmatrix, mdmatrix, dmatrix) See log for complete Python traceback. > volume erase #16 center 204.46,149.93,144.85 radius 4.411 Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map_eraser/eraser.py"", line 308, in _erase_in_sphere self._erase() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map_eraser/eraser.py"", line 327, in _erase run(self.session, cmd) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2688, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map_eraser/eraser.py"", line 24, in volume_erase _zero_data_in_sphere(v.data, cvol, radius) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map_eraser/eraser.py"", line 41, in _zero_data_in_sphere subtract(dmatrix, mdmatrix, dmatrix) ValueError: output array is read-only ValueError: output array is read-only File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map_eraser/eraser.py"", line 41, in _zero_data_in_sphere subtract(dmatrix, mdmatrix, dmatrix) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 418.56 OpenGL renderer: GeForce RTX 2070/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Volume Data fixed all ChimeraX