Opened 2 years ago

Last modified 2 years ago

#9915 assigned defect

PICKLUSTER: not all models have .chains

Reported by: chimerax-bug-report@… Owned by: Luca Genz
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
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  

> toolshed show

Downloading bundle ChimeraX_PICKLUSTER-0.2-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: C:\Users\bbpbe01\AppData\Local\UCSF\ChimeraX\1.4\site-packages  
sysconfig: C:\Users\bbpbe01\AppData\Roaming\Python\Python39\site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: C:\Users\bbpbe01\AppData\Local\UCSF\ChimeraX\1.4\site-packages  
sysconfig: C:\Users\bbpbe01\AppData\Roaming\Python\Python39\site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils:
C:\Users\bbpbe01\AppData\Local\UCSF\ChimeraX\Python39\Include\ChimeraX-
PICKLUSTER  
sysconfig: C:\Users\bbpbe01\AppData\Roaming\Python\Python39\Include\ChimeraX-
PICKLUSTER  
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: C:\Users\bbpbe01\AppData\Local\UCSF\ChimeraX\Python39\Scripts  
sysconfig: C:\Users\bbpbe01\AppData\Roaming\Python\Python39\Scripts  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: C:\Users\bbpbe01\AppData\Local\UCSF\ChimeraX  
sysconfig: C:\Users\bbpbe01\AppData\Roaming\Python  
WARNING: Additional context:  
user = True  
home = None  
root = None  
prefix = None  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils:
C:\Users\bbpbe01\AppData\Local\UCSF\ChimeraX\Python39\Include\UNKNOWN  
sysconfig: C:\Users\bbpbe01\AppData\Roaming\Python\Python39\Include\UNKNOWN  
WARNING: You are using pip version 21.3.1; however, version 23.2.1 is
available.  
You should consider upgrading via the 'C:\Program Files\ChimeraX
1.4\bin\ChimeraX.exe -m pip install --upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing c:\users\bbpbe01\downloads\chimerax_pickluster-0.2-py3-none-any.whl  
Requirement already satisfied: Jinja2>=3.0 in c:\program files\chimerax
1.4\bin\lib\site-packages (from ChimeraX-PICKLUSTER==0.2) (3.0.3)  
Requirement already satisfied: ChimeraX-Core~=1.4 in c:\program files\chimerax
1.4\bin\lib\site-packages (from ChimeraX-PICKLUSTER==0.2) (1.4)  
Requirement already satisfied: ChimeraX-UI~=1.0 in c:\program files\chimerax
1.4\bin\lib\site-packages (from ChimeraX-PICKLUSTER==0.2) (1.18.3)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in c:\program
files\chimerax 1.4\bin\lib\site-packages (from ChimeraX-UI~=1.0->ChimeraX-
PICKLUSTER==0.2) (1.1)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in c:\program
files\chimerax 1.4\bin\lib\site-packages (from ChimeraX-UI~=1.0->ChimeraX-
PICKLUSTER==0.2) (1.0)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program
files\chimerax 1.4\bin\lib\site-packages (from ChimeraX-UI~=1.0->ChimeraX-
PICKLUSTER==0.2) (1.1)  
Requirement already satisfied: MarkupSafe>=2.0 in c:\program files\chimerax
1.4\bin\lib\site-packages (from Jinja2>=3.0->ChimeraX-PICKLUSTER==0.2) (2.1.1)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program
files\chimerax 1.4\bin\lib\site-packages (from ChimeraX-
Graphics~=1.0->ChimeraX-UI~=1.0->ChimeraX-PICKLUSTER==0.2) (1.2)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in c:\program
files\chimerax 1.4\bin\lib\site-packages (from ChimeraX-
Graphics~=1.0->ChimeraX-UI~=1.0->ChimeraX-PICKLUSTER==0.2) (1.0)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in c:\program
files\chimerax 1.4\bin\lib\site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-PICKLUSTER==0.2) (1.0)  
Installing collected packages: ChimeraX-PICKLUSTER  
Successfully installed ChimeraX-PICKLUSTER-0.2  
\---  

Successfully installed ChimeraX-PICKLUSTER-0.2  
Installed ChimeraX-PICKLUSTER (0.2)  

> open "F:\Biotech\Mitarbeiter\Dardan Beqaj\Data\Promotion\Labor\Protein
> interactions\AlphaFOLD
> predictions\MLPs\MLP_bal_C10xM1_83840.result\MLP_bal_C10xM1_83840\MLP_bal_C10xM1_83840_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"
> format pdb

Chain information for
MLP_bal_C10xM1_83840_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
#1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select /B:1-69

551 atoms, 567 bonds, 69 residues, 1 model selected  

> color sel cornflower blue

> select clear

> ui tool show PICKLUSTER

Please register the custom scheme 'pickluster' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

Chain1 is equal to chain2!  

> ui tool show PICKLUSTER

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> sequence chain #1/A

Alignment identifier is 1/A  

> ui tool show PICKLUSTER

Please register the custom scheme 'pickluster' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

Cluster information for
MLP_bal_C10xM1_83840_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb['A',
'B']  
---  
Cluster | Residues  
1 | [['A', 'ARG', 58], ['A', 'ARG', 146], ['A', 'GLY', 148], ['A', 'ASP',
149], ['A', 'PRO', 150], ['A', 'ALA', 331], ['A', 'SER', 332], ['A', 'LEU',
333], ['A', 'ASP', 343], ['A', 'TYR', 345], ['A', 'GLU', 352], ['A', 'GLY',
353], ['A', 'TYR', 354], ['A', 'ASN', 356], ['A', 'ARG', 357], ['A', 'ALA',
358], ['A', 'ALA', 359], ['A', 'LEU', 360], ['A', 'THR', 361], ['A', 'ALA',
362], ['A', 'GLU', 363], ['A', 'PHE', 365], ['A', 'VAL', 366], ['A', 'ALA',
367], ['A', 'ASP', 368], ['A', 'PRO', 369], ['A', 'ALA', 371], ['A', 'PRO',
372], ['A', 'GLY', 373], ['A', 'GLN', 374], ['A', 'ARG', 375], ['A', 'MET',
376], ['A', 'TRP', 378], ['B', 'MET', 1], ['B', 'SER', 2], ['B', 'ASN', 3],
['B', 'PRO', 4], ['B', 'PHE', 5], ['B', 'ASP', 6], ['B', 'LEU', 15], ['B',
'ASN', 17], ['B', 'GLN', 21], ['B', 'HIS', 22], ['B', 'SER', 23], ['B', 'LEU',
24], ['B', 'TRP', 25], ['B', 'PRO', 26], ['B', 'PHE', 28], ['B', 'ALA', 29],
['B', 'PRO', 32], ['B', 'ALA', 33], ['B', 'GLY', 34], ['B', 'TRP', 35], ['B',
'ARG', 44], ['B', 'LEU', 48], ['B', 'VAL', 51], ['B', 'GLU', 52], ['B', 'TRP',
55], ['B', 'LEU', 58], ['B', 'ARG', 59], ['B', 'PRO', 60], ['B', 'LEU', 63],
['B', 'GLU', 66], ['B', 'ALA', 67]]  
  
Calculation of interface was successful  
Interactions in clusters in
MLP_bal_C10xM1_83840_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb['A',
'B']  
---  
Cluster | Interactions  
1 | [[['A', 'ARG', 58], ['B', 'ALA', 67]], [['A', 'ARG', 58], ['B', 'GLU',
66]], [['A', 'ARG', 58], ['B', 'LEU', 63]], [['A', 'ARG', 146], ['B', 'GLU',
66]], [['A', 'GLY', 148], ['B', 'LEU', 63]], [['A', 'ASP', 149], ['B', 'LEU',
63]], [['A', 'PRO', 150], ['B', 'LEU', 63]], [['A', 'ALA', 331], ['B', 'MET',
1]], [['A', 'ALA', 331], ['B', 'PHE', 28]], [['A', 'ALA', 331], ['B', 'PRO',
4]], [['A', 'ALA', 331], ['B', 'SER', 2]], [['A', 'SER', 332], ['B', 'PHE',
28]], [['A', 'SER', 332], ['B', 'ALA', 29]], [['A', 'LEU', 333], ['B', 'TRP',
25]], [['A', 'LEU', 333], ['B', 'PRO', 26]], [['A', 'LEU', 333], ['B', 'ALA',
29]], [['A', 'LEU', 333], ['B', 'PHE', 28]], [['A', 'LEU', 333], ['B', 'PHE',
5]], [['A', 'LEU', 333], ['B', 'PRO', 4]], [['A', 'ASP', 343], ['B', 'ASN',
3]], [['A', 'ASP', 343], ['B', 'PRO', 4]], [['A', 'TYR', 345], ['B', 'PHE',
5]], [['A', 'TYR', 345], ['B', 'PRO', 4]], [['A', 'TYR', 345], ['B', 'ASN',
3]], [['A', 'GLU', 352], ['B', 'PRO', 60]], [['A', 'GLU', 352], ['B', 'LEU',
58]], [['A', 'GLU', 352], ['B', 'LEU', 63]], [['A', 'GLU', 352], ['B', 'ARG',
59]], [['A', 'GLU', 352], ['B', 'GLN', 21]], [['A', 'GLU', 352], ['B', 'TRP',
55]], [['A', 'GLY', 353], ['B', 'LEU', 58]], [['A', 'TYR', 354], ['B', 'LEU',
58]], [['A', 'ASN', 356], ['B', 'LEU', 58]], [['A', 'ASN', 356], ['B', 'GLU',
52]], [['A', 'ARG', 357], ['B', 'LEU', 58]], [['A', 'ARG', 357], ['B', 'GLU',
52]], [['A', 'ALA', 358], ['B', 'GLU', 52]], [['A', 'ALA', 358], ['B', 'TRP',
55]], [['A', 'ALA', 358], ['B', 'VAL', 51]], [['A', 'ALA', 358], ['B', 'LEU',
58]], [['A', 'ALA', 359], ['B', 'LEU', 48]], [['A', 'ALA', 359], ['B', 'GLU',
52]], [['A', 'ALA', 359], ['B', 'VAL', 51]], [['A', 'LEU', 360], ['B', 'GLU',
52]], [['A', 'THR', 361], ['B', 'LEU', 58]], [['A', 'THR', 361], ['B', 'TRP',
55]], [['A', 'ALA', 362], ['B', 'VAL', 51]], [['A', 'ALA', 362], ['B', 'HIS',
22]], [['A', 'ALA', 362], ['B', 'TRP', 55]], [['A', 'ALA', 362], ['B', 'LEU',
24]], [['A', 'ALA', 362], ['B', 'SER', 23]], [['A', 'GLU', 363], ['B', 'PHE',
5]], [['A', 'GLU', 363], ['B', 'LEU', 24]], [['A', 'GLU', 363], ['B', 'ARG',
44]], [['A', 'GLU', 363], ['B', 'ASP', 6]], [['A', 'GLU', 363], ['B', 'LEU',
48]], [['A', 'PHE', 365], ['B', 'SER', 23]], [['A', 'PHE', 365], ['B', 'HIS',
22]], [['A', 'VAL', 366], ['B', 'PHE', 5]], [['A', 'VAL', 366], ['B', 'SER',
23]], [['A', 'VAL', 366], ['B', 'TRP', 25]], [['A', 'VAL', 366], ['B', 'LEU',
24]], [['A', 'VAL', 366], ['B', 'TRP', 35]], [['A', 'ALA', 367], ['B', 'PRO',
32]], [['A', 'ALA', 367], ['B', 'TRP', 35]], [['A', 'ALA', 367], ['B', 'SER',
23]], [['A', 'ALA', 367], ['B', 'TRP', 25]], [['A', 'ALA', 367], ['B', 'LEU',
15]], [['A', 'ASP', 368], ['B', 'TRP', 25]], [['A', 'ASP', 368], ['B', 'PRO',
32]], [['A', 'ASP', 368], ['B', 'TRP', 35]], [['A', 'PRO', 369], ['B', 'TRP',
25]], [['A', 'PRO', 369], ['B', 'PRO', 32]], [['A', 'ALA', 371], ['B', 'ALA',
33]], [['A', 'ALA', 371], ['B', 'TRP', 35]], [['A', 'PRO', 372], ['B', 'GLY',
34]], [['A', 'PRO', 372], ['B', 'ALA', 33]], [['A', 'PRO', 372], ['B', 'TRP',
35]], [['A', 'GLY', 373], ['B', 'ASN', 17]], [['A', 'GLY', 373], ['B', 'GLY',
34]], [['A', 'GLY', 373], ['B', 'TRP', 35]], [['A', 'GLY', 373], ['B', 'GLN',
21]], [['A', 'GLY', 373], ['B', 'ALA', 33]], [['A', 'GLN', 374], ['B', 'TRP',
35]], [['A', 'ARG', 375], ['B', 'GLN', 21]], [['A', 'ARG', 375], ['B', 'ASN',
17]], [['A', 'ARG', 375], ['B', 'HIS', 22]], [['A', 'ARG', 375], ['B', 'TRP',
35]], [['A', 'ARG', 375], ['B', 'TRP', 55]], [['A', 'MET', 376], ['B', 'TRP',
25]], [['A', 'MET', 376], ['B', 'PHE', 5]], [['A', 'TRP', 378], ['B', 'ASN',
3]], [['A', 'TRP', 378], ['B', 'PHE', 5]], [['A', 'TRP', 378], ['B', 'ASP',
6]]]  
  

> ui tool show PICKLUSTER

Please register the custom scheme 'pickluster' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

Cluster information for
MLP_bal_C10xM1_83840_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb['A',
'B']  
---  
Cluster | Residues  
1 | [['A', 'ARG', 58], ['A', 'ARG', 146], ['A', 'GLY', 148], ['A', 'ASP',
149], ['A', 'PRO', 150], ['A', 'ALA', 331], ['A', 'SER', 332], ['A', 'LEU',
333], ['A', 'ASP', 343], ['A', 'TYR', 345], ['A', 'GLU', 352], ['A', 'GLY',
353], ['A', 'TYR', 354], ['A', 'ASN', 356], ['A', 'ARG', 357], ['A', 'ALA',
358], ['A', 'ALA', 359], ['A', 'LEU', 360], ['A', 'THR', 361], ['A', 'ALA',
362], ['A', 'GLU', 363], ['A', 'PHE', 365], ['A', 'VAL', 366], ['A', 'ALA',
367], ['A', 'ASP', 368], ['A', 'PRO', 369], ['A', 'ALA', 371], ['A', 'PRO',
372], ['A', 'GLY', 373], ['A', 'GLN', 374], ['A', 'ARG', 375], ['A', 'MET',
376], ['A', 'TRP', 378], ['B', 'MET', 1], ['B', 'SER', 2], ['B', 'ASN', 3],
['B', 'PRO', 4], ['B', 'PHE', 5], ['B', 'ASP', 6], ['B', 'LEU', 15], ['B',
'ASN', 17], ['B', 'GLN', 21], ['B', 'HIS', 22], ['B', 'SER', 23], ['B', 'LEU',
24], ['B', 'TRP', 25], ['B', 'PRO', 26], ['B', 'PHE', 28], ['B', 'ALA', 29],
['B', 'PRO', 32], ['B', 'ALA', 33], ['B', 'GLY', 34], ['B', 'TRP', 35], ['B',
'ARG', 44], ['B', 'LEU', 48], ['B', 'VAL', 51], ['B', 'GLU', 52], ['B', 'TRP',
55], ['B', 'LEU', 58], ['B', 'ARG', 59], ['B', 'PRO', 60], ['B', 'LEU', 63],
['B', 'GLU', 66], ['B', 'ALA', 67]]  
  
Calculation of interface was successful  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 335, in interceptRequest  
self._callback(info)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\ui\htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\gui.py",
line 399, in thread_safe  
func(*args, **kw)  
File "C:\Users\bbpbe01\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\PICKLUSTER\tool.py", line 263, in handle_scheme  
path = str(query["path"][0])  
KeyError: 'path'  
  
KeyError: 'path'  
  
File "C:\Users\bbpbe01\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\PICKLUSTER\tool.py", line 263, in handle_scheme  
path = str(query["path"][0])  
  
See log for complete Python traceback.  
  

> close session

> open "F:\Biotech\Mitarbeiter\Dardan Beqaj\Data\Promotion\Labor\Protein
> interactions\AlphaFOLD
> predictions\MLPs\MLP_bal_C10xM1_83840.result\MLP_bal_C10xM1_83840\MLP_bal_C10xM1_83840_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"
> format pdb

Chain information for
MLP_bal_C10xM1_83840_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
#1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show "Color Actions"

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> help help:user

> Coloring

Unknown command: Coloring  

> ui tool show AlphaFold

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file "F:\\\Biotech\\\Mitarbeiter\\\Dardan
> Beqaj\\\Data\\\Promotion\\\Labor\\\Protein interactions\\\AlphaFOLD
> predictions\\\MLPs\\\MLP_bal_C10xM1_83840.result\\\MLP_bal_C10xM1_83840\\\MLP_bal_C10xM1_83840_scores_rank_001_alphafold2_multimer_v3_model_4_seed_000.json"

> ui tool show "Model Loops"

> ui tool show "Modeller Comparative"

> ui tool show AlphaFold

> alphafold pae #1 file "F:\\\Biotech\\\Mitarbeiter\\\Dardan
> Beqaj\\\Data\\\Promotion\\\Labor\\\Protein interactions\\\AlphaFOLD
> predictions\\\MLPs\\\MLP_bal_C10xM1_83840.result\\\MLP_bal_C10xM1_83840\\\MLP_bal_C10xM1_83840_scores_rank_001_alphafold2_multimer_v3_model_4_seed_000.json"

> color bfactor #1 palette alphafold

4909 atoms, 669 residues, atom bfactor range 24.4 to 98.9  

> alphafold pae #1 colorDomains true

> alphafold pae #1 file "F:\\\Biotech\\\Mitarbeiter\\\Dardan
> Beqaj\\\Data\\\Promotion\\\Labor\\\Protein interactions\\\AlphaFOLD
> predictions\\\MLPs\\\MLP_bal_C10xM1_83840.result\\\MLP_bal_C10xM1_83840\\\MLP_bal_C10xM1_83840_scores_rank_001_alphafold2_multimer_v3_model_4_seed_000.json"

> color bfactor #1 palette alphafold

4909 atoms, 669 residues, atom bfactor range 24.4 to 98.9  

> ui mousemode right "color key"

> ui mousemode right translate

> undo

[Repeated 1 time(s)]

> alphafold pae #1 file "F:\\\Biotech\\\Mitarbeiter\\\Dardan
> Beqaj\\\Data\\\Promotion\\\Labor\\\Protein interactions\\\AlphaFOLD
> predictions\\\MLPs\\\MLP_bal_C10xM1_83840.result\\\MLP_bal_C10xM1_83840\\\MLP_bal_C10xM1_83840_scores_rank_001_alphafold2_multimer_v3_model_4_seed_000.json"

> color bfactor #1 palette alphafold

4909 atoms, 669 residues, atom bfactor range 24.4 to 98.9  

> ui mousemode right "color key"

> key blue:min white: #d7eaf8:max

> key blue:min white: #cccccc:max

> key blue:min white: #f0f0f0:max

> key blue:min white: #acacac:max

> key blue:min white: #c1c1c1:max

> key blue:min white: #f1f1f1:max

> key blue:min white: white:max

> key blue:min white: #2c2c2c:max

> key blue:min white: orange:max

> key blue:min white: white:max

> key blue:min white: yellow:max

> key blue:min white: #2c2c2c:max

> key blue:min white: white:max

> key blue:min white: #2c2c2c:max

> key blue:min white: cornflowerblue:max

> key blue:min white: white:max

> key blue:min white: #2c2c2c:max

> key blue:min white: grey:max

> key blue:min white: blue:max

> key blue:min white: white:max

> key blue:min white: black:max

> key blue:min white: #dddddd:max

> key blue:min white: #ddddc8:max

> key blue:min white: white:max

> key blue:min white: #ececec:max

> key blue:min white: lightgrey:max

> key blue:min white: #f0f0f0:max

> key blue:min white: #fefefe:max

> key blue:min white: white:max

> key blue:min white: #824f00:max

> key blue:min white: white:max

> key blue:min white: #004fa7:max

> key blue:min white: yellow:max

> key blue:min white: #004fa7:max

> key blue:min white: white:max

> key blue:min white: #2c2c2c:max

> key blue:min white: grey:max

> key blue:min white: blue:max

> key blue:min white: blue:max white:

> key blue:min white: blue:max blue:

> key blue:min white: #d6e6f3:max blue:

> key blue:min white: #cccccc:max blue:

> key blue:min white: #f0f0f0:max blue:

> key blue:min white: #dddddd:max blue:

> key blue:min white: white:max blue:

> key blue:min white: #dddddd:max blue:

> key blue:min white: white:max blue:

> key blue:min white: grey:max blue:

> key blue:min white: cornflowerblue:max blue:

> key blue:min #dbe9f4: cornflowerblue:max blue:

> key blue:min #cccccc: cornflowerblue:max blue:

> key blue:min #f0f0f0: cornflowerblue:max blue:

> key blue:min #c1c1c1: cornflowerblue:max blue:

> key blue:min #f1f1f1: cornflowerblue:max blue:

> key blue:min white: cornflowerblue:max blue:

> key blue:min #2c2c2c: cornflowerblue:max blue:

> key blue:min grey: cornflowerblue:max blue:

> key blue:min red: cornflowerblue:max blue:

> key blue:min #e7ffff: cornflowerblue:max blue:

> key blue:min white: cornflowerblue:max blue:

> key blue:min #2c2c2c: cornflowerblue:max blue:

> key blue:min grey: cornflowerblue:max blue:

> key blue:min yellow: cornflowerblue:max blue:

> key #dae9f7:min yellow: cornflowerblue:max blue:

> key #cccccc:min yellow: cornflowerblue:max blue:

> key #9ca6c8:min yellow: cornflowerblue:max blue:

> key #dedede:min yellow: cornflowerblue:max blue:

> key #dddddd:min yellow: cornflowerblue:max blue:

> key white:min yellow: cornflowerblue:max blue:

> key #606060:min yellow: cornflowerblue:max blue:

> key black:min yellow: cornflowerblue:max blue:

> key white:min yellow: cornflowerblue:max blue:

> key black:min yellow: cornflowerblue:max blue:

> key white:min yellow: cornflowerblue:max blue:

> key grey:min yellow: cornflowerblue:max blue:

> key orange:min yellow: cornflowerblue:max blue:

> key orange:min yellow: cornflowerblue:max blue: white:

> key orange:min yellow: cornflowerblue:max blue: blue:

> key orange:min yellow: cornflowerblue:max #d7e9f7: blue:

> key orange:min yellow: cornflowerblue:max #cccccc: blue:

> key orange:min yellow: cornflowerblue:max #c8a3b7: blue:

> key orange:min yellow: cornflowerblue:max #0000e5: blue:

> key orange:min yellow: cornflowerblue:max #4591c8: blue:

> key orange:min yellow: cornflowerblue:max white: blue:

> key orange:min yellow: cornflowerblue:max cornflowerblue: blue:

> key orange:min yellow: #daebf9:max cornflowerblue: blue:

> key orange:min yellow: #cccccc:max cornflowerblue: blue:

> key orange:min yellow: #c8b8c6:max cornflowerblue: blue:

> key orange:min yellow: #c6c8b8:max cornflowerblue: blue:

> key orange:min yellow: #dddddd:max cornflowerblue: blue:

> key orange:min yellow: #007591:max cornflowerblue: blue:

> key orange:min yellow: white:max cornflowerblue: blue:

> key orange:min yellow: #1f1f1f:max cornflowerblue: blue:

> key orange:min yellow: #4f004f:max cornflowerblue: blue:

> key orange:min yellow: #2c2c2c:max cornflowerblue: blue:

> key orange:min yellow: grey:max cornflowerblue: blue:

> key orange:min yellow: white:max cornflowerblue: blue:

> key orange:min yellow: #2c2c2c:max cornflowerblue: blue:

> key orange:min yellow: grey:max cornflowerblue: blue:

> key orange:min yellow: yellow:max cornflowerblue: blue:

> key orange:min #dcecf9: yellow:max cornflowerblue: blue:

> key orange:min #cccccc: yellow:max cornflowerblue: blue:

> key orange:min #787878: yellow:max cornflowerblue: blue:

> key orange:min #f0f0f0: yellow:max cornflowerblue: blue:

> key orange:min black: yellow:max cornflowerblue: blue:

> key orange:min #c1c1c1: yellow:max cornflowerblue: blue:

> key orange:min #f1f1f1: yellow:max cornflowerblue: blue:

> key orange:min white: yellow:max cornflowerblue: blue:

> key orange:min #fbfbfb: yellow:max cornflowerblue: blue:

> key orange:min white: yellow:max cornflowerblue: blue:

> key orange:min red: yellow:max cornflowerblue: blue:

> key orange:min #2c2c2c: yellow:max cornflowerblue: blue:

> key orange:min white: yellow:max cornflowerblue: blue:

> key orange:min orange: yellow:max cornflowerblue: blue:

> key #daebf9:min orange: yellow:max cornflowerblue: blue:

> key #cccccc:min orange: yellow:max cornflowerblue: blue:

> key #c6bec8:min orange: yellow:max cornflowerblue: blue:

> key #c7c8c3:min orange: yellow:max cornflowerblue: blue:

> key white:min orange: yellow:max cornflowerblue: blue:

> key #cf9d66:min orange: yellow:max cornflowerblue: blue:

> key white:min orange: yellow:max cornflowerblue: blue:

> key #2c2c2c:min orange: yellow:max cornflowerblue: blue:

> key alphafold :min : :max : :

[Repeated 1 time(s)]

> key tickLength 8.0

> key alphafold :min : :max : :

> key alphafold :min : : : :

> key alphafold :min : : : :max

> ui mousemode right translate

> save "F:/Biotech/Mitarbeiter/Dardan Beqaj/Data/Promotion/Labor/Protein
> interactions/AlphaFOLD
> predictions/MLPs/MLP_bal_C10xM1_83840.result/plDDT_coloration.cxs"

> ui tool show PICKLUSTER

Please register the custom scheme 'pickluster' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 559, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1325, in start_tool  
return cls._get_func(api, "start_tool")(session, bi, ti)  
File "C:\Users\bbpbe01\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\PICKLUSTER\\__init__.py", line 50, in start_tool  
return tool.PICKLUSTER(session, ti.name)  
File "C:\Users\bbpbe01\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\PICKLUSTER\tool.py", line 59, in __init__  
for chain in model.chains:  
AttributeError: 'ColorKeyModel' object has no attribute 'chains'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\gui.py",
line 1685, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\cmd.py",
line 219, in ui_tool_show  
bi.start_tool(session, name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 564, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool PICKLUSTER
in bundle ChimeraX-PICKLUSTER:  
'ColorKeyModel' object has no attribute 'chains'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool PICKLUSTER
in bundle ChimeraX-PICKLUSTER:  
'ColorKeyModel' object has no attribute 'chains'  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 564, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  

> ui tool show PICKLUSTER

Please register the custom scheme 'pickluster' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 559, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1325, in start_tool  
return cls._get_func(api, "start_tool")(session, bi, ti)  
File "C:\Users\bbpbe01\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\PICKLUSTER\\__init__.py", line 50, in start_tool  
return tool.PICKLUSTER(session, ti.name)  
File "C:\Users\bbpbe01\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\PICKLUSTER\tool.py", line 59, in __init__  
for chain in model.chains:  
AttributeError: 'ColorKeyModel' object has no attribute 'chains'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\gui.py",
line 1685, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\cmd.py",
line 219, in ui_tool_show  
bi.start_tool(session, name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 564, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool PICKLUSTER
in bundle ChimeraX-PICKLUSTER:  
'ColorKeyModel' object has no attribute 'chains'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool PICKLUSTER
in bundle ChimeraX-PICKLUSTER:  
'ColorKeyModel' object has no attribute 'chains'  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 564, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.9171
OpenGL renderer: Intel(R) HD Graphics 530
OpenGL vendor: Intel

Python: 3.9.11
Locale: de_DE.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: FUJITSU
Model: ESPRIMO P957
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 8,362,655,744
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-6500 CPU @ 3.20GHz
OSLanguage: de-DE

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    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-PICKLUSTER: 0.2
    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
    comtypes: 1.1.10
    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: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    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
    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
    pywin32: 303
    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
    WMI: 1.5.1

Change History (1)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Third Party
Owner: set to Luca Genz
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → PICKLUSTER: not all models have .chains

A ColorKeyModel was open, which does not have a 'chains' attribute. In your loop you could screen for AtomicStructure instances, i.e.:

from chimerax.atomic import AtomicStructure
if not isinstance(model, AtomicStructure):

continue

or just loop through atomic structures to begin with:

from chimerax.atomic import all_atomic_structures
for index, model in enumerate(all_atomic_structures(session)):

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