Opened 3 years ago

Closed 3 years ago

#7992 closed defect (fixed)

Modeller target is None

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:quickstart

> open /Users/manasvinisridharr/Downloads/LjPCNA1.fa

Summary of feedback from opening /Users/manasvinisridharr/Downloads/LjPCNA1.fa  
---  
note | Alignment identifier is LjPCNA1.fa  
  
Opened 1 sequences from LjPCNA1.fa  

> blastprotein LjPCNA1.fa:1

Webservices job id: 2Y4CS41M9RC1ISMJ  

> open pdb:6O09

Summary of feedback from opening 6O09 fetched from pdb  
---  
note | Fetching compressed mmCIF 6o09 from
http://files.rcsb.org/download/6o09.cif  
  
6o09 title:  
Structure of AtPCNA in complex with the PIP motif of ATXR6 [more info...]  
  
Chain information for 6o09 #1  
---  
Chain | Description | UniProt  
A C D F H K | Proliferating cellular nuclear antigen 1 | PCNA1_ARATH  
B E G I J L | Uncharacterized protein | K7MRE7_SOYBN  
  
6o09 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> select clear

Alignment identifier is bp1 [1]  
Associated 6o09 chain C to 6O09_A with 0 mismatches  
Associated 6o09 chain A to 6O09_A with 0 mismatches  
Associated 6o09 chain D to 6O09_A with 0 mismatches  
Associated 6o09 chain F to 6O09_A with 0 mismatches  
Associated 6o09 chain H to 6O09_A with 0 mismatches  
Associated 6o09 chain K to 6O09_A with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp1 [1]  

> open pdb:2ZVV

Summary of feedback from opening 2ZVV fetched from pdb  
---  
notes | Fetching compressed mmCIF 2zvv from
http://files.rcsb.org/download/2zvv.cif  
Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif  
  
2zvv title:  
Crystal structure of Proliferating cellular nuclear antigen 1 and Short
peptide from human P21 [more info...]  
  
Chain information for 2zvv #2  
---  
Chain | Description | UniProt  
A B | Proliferating cellular nuclear antigen 1 | PCNA1_ARATH  
X Y | Cyclin-dependent kinase inhibitor 1 | CDN1A_HUMAN  
  
Non-standard residues in 2zvv #2  
---  
SO4 — sulfate ion  
  
2zvv mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> select clear

> style stick

Changed 16689 atom styles  

> style sphere

Changed 16689 atom styles  

> style ball

Changed 16689 atom styles  

> show cartoons

[Repeated 1 time(s)]

> hide cartoons

> hide atoms

> show atoms

> style stick

Changed 16689 atom styles  

> style sphere

Changed 16689 atom styles  

> lighting full

> lighting soft

> lighting simple

> lighting full

> ui tool show "Selection Inspector"

> rainbow

> undo

> hide #!1 models

> show #2 target m

> ui tool show "Selection Inspector"

> cofr frontCenter

> select add #2

4382 atoms, 4226 bonds, 755 residues, 1 model selected  

> select subtract #2

Nothing selected  

> ui windowfill toggle

[Repeated 1 time(s)]

> hide #2 models

> show #!1 models

> hide #!1 models

> show #2 models

> view

> toolshed show

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #2 cartoons

> hide #2 atoms

> sequence identity "bp1 [1]:1" "bp1 [1]:2"

query vs. 6O09_A: 89.29% identity  
Alignment identifier is bp1 [2]  
Associated 6o09 chain C to 2ZVW_A with 4 mismatches  
Associated 6o09 chain A to 2ZVW_A with 4 mismatches  
Associated 6o09 chain D to 2ZVW_A with 4 mismatches  
Associated 6o09 chain F to 2ZVW_A with 4 mismatches  
Associated 6o09 chain H to 2ZVW_A with 4 mismatches  
Associated 6o09 chain K to 2ZVW_A with 4 mismatches  
Associated 2zvv chain A to 2ZVW_A with 4 mismatches  
Associated 2zvv chain B to 2ZVW_A with 4 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp1 [2]  
Alignment identifier is bp1 [3]  
Associated 6o09 chain C to 2ZVV_A with 0 mismatches  
Associated 6o09 chain A to 2ZVV_A with 0 mismatches  
Associated 6o09 chain D to 2ZVV_A with 0 mismatches  
Associated 6o09 chain F to 2ZVV_A with 0 mismatches  
Associated 6o09 chain H to 2ZVV_A with 0 mismatches  
Associated 6o09 chain K to 2ZVV_A with 0 mismatches  
Associated 2zvv chain A to 2ZVV_A with 0 mismatches  
Associated 2zvv chain B to 2ZVV_A with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp1 [3]  

> sequence identity "bp1 [3]:1" "bp1 [3]:2"

query vs. 2ZVV_A: 89.95% identity  

> ui tool show "Modeller Comparative"

> modeller comparative LjPCNA1.fa:1 numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Alignment LjPCNA1.fa has no associated chains  

> modeller comparative "bp1 [3]:1" numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 302, in launch_modeller  
run(  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 37, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
AttributeError: 'NoneType' object has no attribute 'name'  
  

Populating font family aliases took 186 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.  

AttributeError: 'NoneType' object has no attribute 'name'  
  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
  
See log for complete Python traceback.  
  

> modeller comparative "bp1 [3]:1" numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 302, in launch_modeller  
run(  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 37, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
AttributeError: 'NoneType' object has no attribute 'name'  
  
AttributeError: 'NoneType' object has no attribute 'name'  
  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
  
See log for complete Python traceback.  
  

> modeller comparative "bp1 [3]:2" numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 302, in launch_modeller  
run(  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 37, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
AttributeError: 'NoneType' object has no attribute 'name'  
  
AttributeError: 'NoneType' object has no attribute 'name'  
  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
  
See log for complete Python traceback.  
  

> modeller comparative "bp1 [3]:2" numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 302, in launch_modeller  
run(  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 37, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
AttributeError: 'NoneType' object has no attribute 'name'  
  
AttributeError: 'NoneType' object has no attribute 'name'  
  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
  
See log for complete Python traceback.  
  

> modeller comparative "bp1 [3]:2" numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 302, in launch_modeller  
run(  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 37, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
AttributeError: 'NoneType' object has no attribute 'name'  
  
AttributeError: 'NoneType' object has no attribute 'name'  
  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
  
See log for complete Python traceback.  
  

> modeller comparative "bp1 [3]:2" numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 302, in launch_modeller  
run(  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 37, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
AttributeError: 'NoneType' object has no attribute 'name'  
  
AttributeError: 'NoneType' object has no attribute 'name'  
  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
  
See log for complete Python traceback.  
  

> modeller comparative "bp1 [3]:2" numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 302, in launch_modeller  
run(  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 37, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
AttributeError: 'NoneType' object has no attribute 'name'  
  
AttributeError: 'NoneType' object has no attribute 'name'  
  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
  
See log for complete Python traceback.  
  

> modeller comparative "bp1 [3]:2" numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 302, in launch_modeller  
run(  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 37, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
AttributeError: 'NoneType' object has no attribute 'name'  
  
AttributeError: 'NoneType' object has no attribute 'name'  
  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
  
See log for complete Python traceback.  
  

> modeller comparative "bp1 [3]:2" numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 302, in launch_modeller  
run(  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 37, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
AttributeError: 'NoneType' object has no attribute 'name'  
  
AttributeError: 'NoneType' object has no attribute 'name'  
  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
  
See log for complete Python traceback.  
  

> select add #2

4382 atoms, 4226 bonds, 755 residues, 1 model selected  

> select subtract #2

Nothing selected  

> ui tool show "Modeller Comparative"

> modeller comparative "bp1 [3]:1" numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 302, in launch_modeller  
run(  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 37, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
AttributeError: 'NoneType' object has no attribute 'name'  
  
AttributeError: 'NoneType' object has no attribute 'name'  
  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
  
See log for complete Python traceback.  
  

> modeller comparative "bp1 [3]:1" numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 302, in launch_modeller  
run(  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 37, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
AttributeError: 'NoneType' object has no attribute 'name'  
  
AttributeError: 'NoneType' object has no attribute 'name'  
  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
  
See log for complete Python traceback.  
  

> modeller comparative LjPCNA1.fa:1 numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Alignment LjPCNA1.fa has no associated chains  

> modeller comparative "bp1 [3]:1" numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 302, in launch_modeller  
run(  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 37, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
AttributeError: 'NoneType' object has no attribute 'name'  
  
AttributeError: 'NoneType' object has no attribute 'name'  
  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
  
See log for complete Python traceback.  
  

> help help:user/tools/modeller.html

[Repeated 4 time(s)]

> modeller comparative "bp1 [3]:1" numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 302, in launch_modeller  
run(  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 37, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
AttributeError: 'NoneType' object has no attribute 'name'  
  
AttributeError: 'NoneType' object has no attribute 'name'  
  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
  
See log for complete Python traceback.  
  

> modeller comparative "bp1 [3]:1" numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 302, in launch_modeller  
run(  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 37, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
AttributeError: 'NoneType' object has no attribute 'name'  
  
AttributeError: 'NoneType' object has no attribute 'name'  
  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
  
See log for complete Python traceback.  
  

> modeller comparative "bp1 [3]:1" numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 302, in launch_modeller  
run(  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 37, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
AttributeError: 'NoneType' object has no attribute 'name'  
  
AttributeError: 'NoneType' object has no attribute 'name'  
  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
  
See log for complete Python traceback.  
  

> show #!1 models

> hide #2 models

> show #!1 cartoons

> hide #!1 atoms

> show #2 models

> sequence identity "bp1 [3]:1" "bp1 [3]:2"

query vs. 2ZVV_A: 89.95% identity  

> ui tool show "Modeller Comparative"

Traceback (most recent call last):  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 338, in _update_sequence_menus  
row, role = self.targets_layout.getWidgetPosition(mb)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/enum.py",
line 384, in __call__  
return cls.__new__(cls, value)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/enum.py",
line 702, in __new__  
raise ve_exc  
ValueError: 3 is not a valid QFormLayout.ItemRole  
  
ValueError: 3 is not a valid QFormLayout.ItemRole  
  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/enum.py",
line 702, in __new__  
raise ve_exc  
  
See log for complete Python traceback.  
  

> modeller comparative "bp1 [3]:2" numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 302, in launch_modeller  
run(  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 37, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
AttributeError: 'NoneType' object has no attribute 'name'  
  
AttributeError: 'NoneType' object has no attribute 'name'  
  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
  
See log for complete Python traceback.  
  

> modeller comparative "bp1 [3]:1" numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 302, in launch_modeller  
run(  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 37, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
AttributeError: 'NoneType' object has no attribute 'name'  
  
AttributeError: 'NoneType' object has no attribute 'name'  
  
File
"/Users/manasvinisridharr/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Model Number: MGND3HN/A
      Chip: Unknown
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 8419.41.10
      OS Loader Version: 8419.41.10

Software:

    System Software Overview:

      System Version: macOS 13.0 (22A380)
      Kernel Version: Darwin 22.1.0
      Time since boot: 17 hours, 14 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Sequence
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Modeller target is None

comment:2 by Eric Pettersen, 3 years ago

Resolution: → fixed
Status: accepted → closed

Fix: ​https://github.com/RBVI/ChimeraX/commit/f0996199abf5fcd491d66a213c1cf50e4b931070

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