Clipper symmetry: self.structure is None

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 0.91 (2019-08-27)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.91 (2019-08-27)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed 'ChimeraX_ISOLDE-1.0b4.dev0-cp37-cp37m-win_amd64.whl'  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
c:\users\arhue\appdata\local\ucsf\chimerax\cache\0.91\installers\chimerax_isolde-1.0b4.dev0-cp37-cp37m-win_amd64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in
c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-
ISOLDE==1.0b4.dev0) (1.0)  
Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.91 in
c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-
ISOLDE==1.0b4.dev0) (0.91)  
Requirement already satisfied, skipping upgrade: ChimeraX-Clipper==0.10.* in
c:\users\arhue\appdata\local\ucsf\chimerax\0.91\site-packages (from ChimeraX-
ISOLDE==1.0b4.dev0) (0.10.0)  
Installing collected packages: ChimeraX-ISOLDE  
Found existing installation: ChimeraX-ISOLDE 1.0b4.dev0  
Uninstalling ChimeraX-ISOLDE-1.0b4.dev0:  
Successfully uninstalled ChimeraX-ISOLDE-1.0b4.dev0  
Successfully installed ChimeraX-ISOLDE-1.0b4.dev0  
Lock 2321031843208 acquired on
C:\Users\arhue\AppData\Local\UCSF\ChimeraX\Cache\0.91\toolshed\bundle_info.cache.lock  
Lock 2321031843208 released on
C:\Users\arhue\AppData\Local\UCSF\ChimeraX\Cache\0.91\toolshed\bundle_info.cache.lock  
  

WARNING: You are using pip version 19.2.1, however version 20.0.2 is
available.  
You should consider upgrading via the 'python -m pip install --upgrade pip'
command.  
  

> toolshed show ISOLDE

> set selectionWidth 4

Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  

> open 6out

Summary of feedback from opening 6out fetched from pdb  
---  
note | Fetching compressed mmCIF 6out from
http://files.rcsb.org/download/6out.cif  
  
6out title:  
Asymmetric focused reconstruction of human norovirus GI.1 Norwalk strain VLP
asymmetric unit in T=3 symmetry [more info...]  
  
Chain information for 6out #1  
---  
Chain | Description  
A B C | Capsid protein VP1  
  
6out title:  
Asymmetric focused reconstruction of human norovirus GI.1 Norwalk strain VLP
asymmetric unit in T=3 symmetry [more info...]  
  
Chain information for 6out  
---  
Chain | Description  
1.1/A 1.1/B 1.1/C | Capsid protein VP1  
  
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time  
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time  
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time  
  

> close #1.1

> isolde demo cryo_em_intro modelOnly true startIsolde false

6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  
  
Chain information for 6out.pdb #2  
---  
Chain | Description  
A B C | capsid protein VP1  
  
6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  
  
Chain information for 6out.pdb  
---  
Chain | Description  
2.1/A 2.1/B 2.1/C | capsid protein VP1  
  
Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205  

> open 20205 fromDatabase emdb

Summary of feedback from opening 20205 fetched from emdb  
---  
note | Fetching compressed map 20205 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-20205/map/emd_20205.map.gz  
  
Opened emd_20205.map, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at
level 0.287, step 1, values float32  

Invalid "toModel" argument: Must specify 1 structure, got 0 for "#1"  

Invalid "toModel" argument: Must specify 1 structure, got 0 for "#1"  

> clipper associate #2 toModel #2.1

> clipper associate #3 toModel #2

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\clipper\symmetry.py", line 1382, in _box_moved_cb  
self._update_box()  
File "C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\clipper\symmetry.py", line 1395, in _update_box  
atoms = self.structure.atoms  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
File "C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\clipper\symmetry.py", line 1395, in _update_box  
atoms = self.structure.atoms  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\clipper\symmetry.py", line 1382, in _box_moved_cb  
self._update_box()  
File "C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\clipper\symmetry.py", line 1395, in _update_box  
atoms = self.structure.atoms  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
File "C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\clipper\symmetry.py", line 1395, in _update_box  
atoms = self.structure.atoms  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\clipper\symmetry.py", line 1382, in _box_moved_cb  
self._update_box()  
File "C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\clipper\symmetry.py", line 1395, in _update_box  
atoms = self.structure.atoms  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
File "C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\clipper\symmetry.py", line 1395, in _update_box  
atoms = self.structure.atoms  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\clipper\symmetry.py", line 1382, in _box_moved_cb  
self._update_box()  
File "C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\clipper\symmetry.py", line 1395, in _update_box  
atoms = self.structure.atoms  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
File "C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\clipper\symmetry.py", line 1395, in _update_box  
atoms = self.structure.atoms  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\clipper\symmetry.py", line 1382, in _box_moved_cb  
self._update_box()  
File "C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\clipper\symmetry.py", line 1395, in _update_box  
atoms = self.structure.atoms  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
File "C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\clipper\symmetry.py", line 1395, in _update_box  
atoms = self.structure.atoms  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\clipper\symmetry.py", line 1382, in _box_moved_cb  
self._update_box()  
File "C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\clipper\symmetry.py", line 1395, in _update_box  
atoms = self.structure.atoms  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
File "C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\clipper\symmetry.py", line 1395, in _update_box  
atoms = self.structure.atoms  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 419.72
OpenGL renderer: GeForce GTX 1060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tristan Croll]

Hmm... this looks fairly squarely like user error - but will try to replicate exactly what happened and catch it before it leads to a traceback.

[Tristan Croll]

Fixed. The Clipper data layout originally wasn't really designed to allow removing the model without removing the whole tree. But I can see how that will be useful (particularly for interfacing with something like phenix.refine which will want to be able to regularly drop in its most recent coordinates). So now that's possible. Won't yet be that useful to the average user because there is no GUI-exposed way to put a new model in its place, but I'll get to that down the track (I want to provide a way to copy any restraints defined by the user in ISOLDE over to the new model first). At least for now it won't crash.