ISOLDE cannot find symbol atomstruct::Residue::find_atom

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-4.15.0-54-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.91 (2019-09-18)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-09-18)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
/media/yanyan/cpn_ATP_072818/102818/Class3D/job171/run_it025_class001_zflip.mrc

Opened run_it025_class001_zflip.mrc, grid size 280,280,280, pixel 1.08, shown
at level 0.00466, step 2, values float32  

> open
/media/yanyan/cpn_ATP_072818/102818/model/double_subunit_class1_on_class1.pdb

Summary of feedback from opening
/media/yanyan/cpn_ATP_072818/102818/model/double_subunit_class1_on_class1.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
3866 messages similar to the above omitted  
  
Chain information for double_subunit_class1_on_class1.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> toolshed show ISOLDE

> set selectionWidth 4

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1574, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/home/yanyan/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/__init__.py", line 48, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/tools.py", line 214, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "/home/yanyan/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/tool.py", line 168, in __init__  
self.isolde = isolde.Isolde(self)  
File "/home/yanyan/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 307, in __init__  
self._start_gui(gui)  
File "/home/yanyan/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 450, in _start_gui  
self._populate_menus_and_update_params()  
File "/home/yanyan/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 549, in
_populate_menus_and_update_params  
self._update_model_list(None, None, force=True)  
File "/home/yanyan/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 953, in _update_model_list  
from .restraints import MDFF_Mgr  
File "/home/yanyan/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/restraints/__init__.py", line 11, in <module>  
from ..molobject import Restraint_Change_Tracker  
File "/home/yanyan/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/molobject.py", line 41, in <module>  
_c_functions = CFunctions(os.path.splitext(libfile)[0])  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 23, in __init__  
self._c_lib = ctypes_open(library_path)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 261, in ctypes_open  
lib = ctypes.PyDLL(lib_path)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/ctypes/__init__.py", line
364, in __init__  
self._handle = _dlopen(self._name, mode)  
OSError: /home/yanyan/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1275, in <lambda>  
run(ses, "toolshed show %s" % quote_if_necessary(tool_name)))  
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 2737, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 337, in toolshed_show  
bi.start_tool(session, tool_name)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 633, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
/home/yanyan/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
/home/yanyan/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 633, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 430.26
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tristan Croll]

Sigh. I tell people through as many channels as I can to *not* use the Ubuntu builds with ISOLDE...

 

 

[Greg Couch]

Fixed by common Linux ABI.