Error deleting atoms

[goddard@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.17134
ChimeraX Version: 0.8 (2018-08-24)
Description
Opening the attached script causes a C++ error when it deletes atoms.

Log:
UCSF ChimeraX version: 0.8 (2018-08-24)  
How to cite UCSF ChimeraX  

open D:\demos\antibiotic\ecoli_ribosome.cxc

open 4v7s

4v7s title:  
Crystal structure of the E. coli ribosome bound to telithromycin.
[more&nbspinfo...;]  
  
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  
  

lighting simple

delete /ca-dz

Traceback (most recent call last):  
  File "C:\Program Files\ChimeraX-Aug-24-2018\bin\lib\site-
packages\chimerax\ui\gui.py", line 504, in customEvent  
    func(*args, **kw)  
  File "C:\Program Files\ChimeraX-Aug-24-2018\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 278, in defer  
    cxcmd(session, topic)  
  File "C:\Program Files\ChimeraX-Aug-24-2018\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 377, in cxcmd  
    ti.execute()  
  File "C:\Program Files\ChimeraX-Aug-24-2018\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 205, in execute  
    cmd.run(cmd_text)  
  File "C:\Program Files\ChimeraX-Aug-24-2018\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2561, in run  
    result = ci.function(session, **kw_args)  
  File "C:\Program Files\ChimeraX-Aug-24-2018\bin\lib\site-
packages\chimerax\core\commands\open.py", line 41, in open  
    from_database=from_database, ignore_cache=ignore_cache, **kw))  
  File "C:\Program Files\ChimeraX-Aug-24-2018\bin\lib\site-
packages\chimerax\core\commands\open.py", line 110, in open  
    models = handle_unknown_kw(session.models.open, paths, format=format,
name=name, **kw)  
  File "C:\Program Files\ChimeraX-Aug-24-2018\bin\lib\site-
packages\chimerax\core\commands\open.py", line 62, in handle_unknown_kw  
    return f(*args, **kw)  
  File "C:\Program Files\ChimeraX-Aug-24-2018\bin\lib\site-
packages\chimerax\core\models.py", line 549, in open  
    session, filenames, format=format, name=name, **kw)  
  File "C:\Program Files\ChimeraX-Aug-24-2018\bin\lib\site-
packages\chimerax\core\io.py", line 444, in open_multiple_data  
    models, status = open_data(session, fspec, format=format, name=name, **kw)  
  File "C:\Program Files\ChimeraX-Aug-24-2018\bin\lib\site-
packages\chimerax\core\io.py", line 402, in open_data  
    models, status = open_func(*args, **kw)  
  File "C:\Program Files\ChimeraX-Aug-24-2018\bin\lib\site-
packages\chimerax\core\scripting.py", line 115, in open_command_script  
    run(session, text)  
  File "C:\Program Files\ChimeraX-Aug-24-2018\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
    results = command.run(text, log=log)  
  File "C:\Program Files\ChimeraX-Aug-24-2018\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2561, in run  
    result = ci.function(session, **kw_args)  
  File "C:\Program Files\ChimeraX-Aug-24-2018\bin\lib\site-
packages\chimerax\std_commands\delete.py", line 22, in delete  
    delete_atoms(session, atoms)  
  File "C:\Program Files\ChimeraX-Aug-24-2018\bin\lib\site-
packages\chimerax\std_commands\delete.py", line 35, in delete_atoms  
    atoms.delete()  
  File "C:\Program Files\ChimeraX-Aug-24-2018\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 649, in delete  
    args = [ctypes.c_void_p, ctypes.c_size_t])(self._c_pointers, len(self))  
RuntimeError: unknown C++ exception  
  

RuntimeError: unknown C++ exception  
  
File "C:\Program Files\ChimeraX-Aug-24-2018\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 649, in delete  
args = [ctypes.c_void_p, ctypes.c_size_t])(self._c_pointers, len(self))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 391.58
OpenGL renderer: Quadro P6000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
File attachment: ecoli_ribosome.cxc

ecoli_ribosome.cxc​

[goddard@…]

Added by email2trac

[Eric Pettersen]

This error doesn't occur in the Mac daily build or in my personal Mac build. It does occur on the Windows machine I tried it on (james). Ugh.

[Eric Pettersen]

The new create-pseudobond-across-deleted-gap code was potentially looking at dead pseudobonds (destruction hadn't yet run to clean them up).