ISOLDE: isolde/libmolc.so: undefined symbol

[mar2294@…]

The following bug report has been submitted:
Platform:        Linux-4.18.0-17-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.8 (2018-12-17)
Description
After installing ISOLDE 1.0b2 in ChimeraX 0.8, I attempted to launch it via the Tool menu. ISOLDE opens, but I get the error seein in the log contents. The ISOLDE window is open, but it doesn't recognize the PDB and .map files I have open, and I'm unable to get it to load the demo dataset (via the "Load demo" button)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.8 (2018-12-17)  
How to cite UCSF ChimeraX  

> open /home/micah/Downloads/3j5q.pdb

3j5q.pdb title:  
Structure of TRPV1 ion channel In complex with DKTX and RTX determined by
single particle electron cryo-microscopy [more info...]  
  
Chain information for 3j5q.pdb #1  
---  
Chain | Description  
A C F H | DKTX  
B D E G | transient receptor potential cation channel subfamily V member 1  
  

> open /home/micah/Downloads/3j5q.pdb

3j5q.pdb title:  
Structure of TRPV1 ion channel In complex with DKTX and RTX determined by
single particle electron cryo-microscopy [more info...]  
  
Chain information for 3j5q.pdb #2  
---  
Chain | Description  
A C F H | DKTX  
B D E G | transient receptor potential cation channel subfamily V member 1  
  

> open /home/micah/Downloads/TRPV1_DkTx_RTX_sharpened_-150_3.8A.map

Opened TRPV1_DkTx_RTX_sharpened_-150_3.8A.map, grid size 256,256,256, pixel
1.22, shown at level 2.92, step 1, values float32  

> show selAtoms ribbons

> hide selAtoms

> toolshed show ISOLDE

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/info.py", line 579, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 1188, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/home/micah/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/__init__.py", line 31, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/tools.py", line 214, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "/home/micah/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/tool.py", line 159, in __init__  
self.isolde = isolde.Isolde(self)  
File "/home/micah/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 315, in __init__  
self._start_gui(gui)  
File "/home/micah/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 443, in _start_gui  
self._populate_menus_and_update_params()  
File "/home/micah/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 532, in
_populate_menus_and_update_params  
self._update_model_list(None, None, force=True)  
File "/home/micah/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 919, in _update_model_list  
from .restraints import MDFF_Mgr  
File "/home/micah/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/restraints/__init__.py", line 11, in <module>  
from ..molobject import Restraint_Change_Tracker  
File "/home/micah/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/molobject.py", line 42, in <module>  
_c_functions = CFunctions(os.path.splitext(libfile)[0])  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/atomic/molc.py", line 23, in __init__  
self._c_lib = ctypes_open(library_path)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/atomic/molc.py", line 261, in ctypes_open  
lib = ctypes.PyDLL(lib_path)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/ctypes/__init__.py", line 348, in
__init__  
self._handle = _dlopen(self._name, mode)  
OSError: /home/micah/.local/share/ChimeraX/0.8/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/lib/python3.6/site-packages/chimerax/ui/gui.py",
line 941, in <lambda>  
run(ses, "toolshed show %s" % quote_if_necessary(tool_name)))  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2587, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/commands/toolshed.py", line 337, in toolshed_show  
bi.start_tool(session, tool_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/info.py", line 585, 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/micah/.local/share/ChimeraX/0.8/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/micah/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE  
  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/info.py", line 585, 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 410.104
OpenGL renderer: GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tom Goddard]

This error is because an ISOLDE library appears not to find a Residue.find_atom() method in ChimeraX. This suggests that your ISOLDE version and ChimeraX version are not compatible. You are using ChimeraX 0.8 and ISOLDE 1.0b2 and I think those go together. Tristan who developed ISOLDE will have to look at it.

[mar2294@…]

Hello,

Yes, after submitting the bug I emailed Tristan.

It seems it's an issue with ISOLDE and the Ubuntu-specific version of 
ChimeraX. Switching to the Generic Linux ChimeraX solved the problem.

Thanks for the response!

Micah

On 4/19/19 3:46 PM, ChimeraX wrote:

[tic20@…]

As per our discussion off-list, ISOLDE is currently incompatible with the Ubuntu-specific builds of ChimeraX (I’ll add a note to the ToolShed page to make this clear). It’s not clear to me whether this bug report comes from before or after you switched to the “generic Linux” ChimeraX build - if the latter, from the traceback ISOLDE is still seeing the Ubuntu ChimeraX libraries, so you’ll need to uninstall the .deb package.
 

[tic20@…]

Ah - I see we cross-posted. Never mind my last message then!

 

[Tristan Croll]

Tidying up open tickets. While one could argue that the incompatibility of ISOLDE with the Ubuntu builds is technically a bug, it's not one that's really addressable in the near term.