Unknown C++ exception deleting atoms

[Tom Goddard]

On Windows 10 with current daily build deleting atoms causes a C++ exception

open 4v7s
del /ca-dz

This is reproducible on Windows (tried 3 times), but no error occurs on Mac.

UCSF ChimeraX version: 0.1 (2017-12-14)
OpenGL version: 3.3.0 NVIDIA 388.13
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
open 4v7s
Summary of feedback from opening 4v7s fetched from pdb
notes Used PDBx fixed column width tables to speed up reading mmCIF file
Used PDBx keywords to speed up reading mmCIF file
Chain information for 4v7s #1
Chain Description
AA 16S rRNA
AB CB 30S ribosomal protein S2
AC CC 30S ribosomal protein S3
AD CD 30S ribosomal protein S4
AE CE 30S ribosomal protein S5
AF CF 30S ribosomal protein S6
AG 30S ribosomal protein S7
AH CH 30S ribosomal protein S8
AI CI 30S ribosomal protein S9
AJ CJ 30S ribosomal protein S10
AK CK 30S ribosomal protein S11
AL CL 30S ribosomal protein S12
AM 30S ribosomal protein S13
AN CN 30S ribosomal protein S14
AO CO 30S ribosomal protein S15
AP 30S ribosomal protein S16
AQ CQ 30S ribosomal protein S17
AR CR 30S ribosomal protein S18
AS CS 30S ribosomal protein S19
AT CT 30S ribosomal protein S20
AU CU 30S ribosomal protein S21
B0 D0 50S ribosomal protein L32
B1 D1 50S ribosomal protein L33
B2 D2 50S ribosomal protein L34
B3 D3 50S ribosomal protein L35
B4 D4 50S ribosomal protein L36
BA DA 23S rRNA
BB 5S rRNA
BC DC 50S ribosomal protein L2
BD DD 50S ribosomal protein L3
BE DE 50S ribosomal protein L4
BF 50S ribosomal protein L5
BG DG 50S ribosomal protein L6
BH DH 50S ribosomal protein L9
BI DI 50S ribosomal protein L11
BJ DJ 50S ribosomal protein L13
BK DK 50S ribosomal protein L14
BL DL 50S ribosomal protein L15
BM DM 50S ribosomal protein L16
BN DN 50S ribosomal protein L17
BO DO 50S ribosomal protein L18
BP DP 50S ribosomal protein L19
BQ DQ 50S ribosomal protein L20
BR DR 50S ribosomal protein L21
BS DS 50S ribosomal protein L22
BT DT 50S ribosomal protein L23
BU DU 50S ribosomal protein L24
BV DV 50S ribosomal protein L25
BW DW 50S ribosomal protein L27
BX DX 50S ribosomal protein L28
BY DY 50S ribosomal protein L29
BZ DZ 50S ribosomal protein L30
CA 16S rRNA
CG 30S ribosomal protein S7
CM 30S ribosomal protein S13
CP 30S ribosomal protein S16
DB 5S rRNA
DF 50S ribosomal protein L5
4v7s mmCIF Assemblies
1 author_defined_assembly
2 author_defined_assembly

Opened mmCIF data containing 284525 atoms and 306836 bonds
delete /ca-dz
Traceback (most recent call last):

File "C:\Program Files\ChimeraX-Dec-14-2017\bin\lib\site-packages\chimerax\cmd_line\tool.py", line 201, in execute

cmd.run(cmd_text)

File "C:\Program Files\ChimeraX-Dec-14-2017\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2557, in run

result = ci.function(session, kw_args)

File "C:\Program Files\ChimeraX-Dec-14-2017\bin\lib\site-packages\chimerax\core\commands\delete.py", line 22, in delete

atoms.delete()

File "C:\Program Files\ChimeraX-Dec-14-2017\bin\lib\site-packages\chimerax\core\atomic\molarray.py", line 584, in delete

args = [ctypes.c_void_p, ctypes.c_size_t])(self._c_pointers, len(self))

RuntimeError: Unknown exception

RuntimeError: Unknown exception

File "C:\Program Files\ChimeraX-Dec-14-2017\bin\lib\site-packages\chimerax\core\atomic\molarray.py", line 584, in delete
args = [ctypes.c_void_p, ctypes.c_size_t])(self._c_pointers, len(self))

See log for complete Python traceback.

If you wish to report this error, send mail to chimerax-bugs@… and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created.

Error processing trigger "graphics update"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX-Dec-14-2017\bin\lib\site-packages\chimerax\core\triggerset.py", line 126, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX-Dec-14-2017\bin\lib\site-packages\chimerax\core\atomic\structure.py", line 2415, in _update_graphics_if_needed
s[i]._update_graphics_if_needed()
File "C:\Program Files\ChimeraX-Dec-14-2017\bin\lib\site-packages\chimerax\core\atomic\structure.py", line 340, in _update_graphics_if_needed
self._update_graphics(gc)
File "C:\Program Files\ChimeraX-Dec-14-2017\bin\lib\site-packages\chimerax\core\atomic\structure.py", line 356, in _update_graphics
pbg._update_graphics(changes)
File "C:\Program Files\ChimeraX-Dec-14-2017\bin\lib\site-packages\chimerax\core\atomic\pbgroup.py", line 191, in _update_graphics
vpb = self._shown_pbonds(self.pseudobonds)
File "C:\Program Files\ChimeraX-Dec-14-2017\bin\lib\site-packages\chimerax\core\atomic\pbgroup.py", line 220, in _shown_pbonds
dpb = pbonds.showns
File "C:\Program Files\ChimeraX-Dec-14-2017\bin\lib\site-packages\chimerax\core\atomic\molc.py", line 171, in get_prop
cget(self._c_pointers, n, pointer(values))
RuntimeError: Unknown exception

[Eric Pettersen]

Same problem/fix as #957