Matchmaker: argument of type 'NoneType' is not iterable

[batu8991@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.9.dev202407111727 (2024-07-11 17:27:30 UTC)
Description
(Describe the actions that caused this problem to occur here) Matchmaker did not worked

Log:
UCSF ChimeraX version: 1.9.dev202407111727 (2024-07-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "C:\Users\altay\Desktop\gp66 my view.cxs" format session

Log from Mon Dec 9 16:31:14 2024UCSF ChimeraX version: 1.9.dev202407111727
(2024-07-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "C:\Users\altay\Desktop\Alphafold predictions interacting with
> gp66\gp66_rainbow_xraycrystallography.cxs" format session

Log from Tue Sep 10 13:01:11 2024 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif
> C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/fold_gene2_and_gp66_2024_09_05_13_42_model_2.cif
> C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/fold_gene2_and_gp66_2024_09_05_13_42_model_3.cif
> C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/fold_gene2_and_gp66_2024_09_05_13_42_model_4.cif
> C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/fold_gene2_and_gp66_2024_09_05_13_42_model_0.cif

Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif #1  
---  
Chain | Description  
A | .  
B | .  
  
Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_2.cif #2  
---  
Chain | Description  
A | .  
B | .  
  
Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_3.cif #3  
---  
Chain | Description  
A | .  
B | .  
  
Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_4.cif #4  
---  
Chain | Description  
A | .  
B | .  
  
Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_0.cif #5  
---  
Chain | Description  
A | .  
B | .  
  

> ui tool show AlphaFold

> alphafold pae #1 file
> C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/fold_gene2_and_gp66_2024_09_05_13_42_full_data_1.json

> color #1/B:341 lime

> color #1/B:158 magenta

> color #1/B:509-554 lime

> color #1/B:351-422 magenta

> color #1/B:671-676 lime

> color #1/B:646-656 magenta

> color #1/B:605-610 lime

> color #1/B:839-849 magenta

> ui tool show Matchmaker

> matchmaker #2-5 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif, chain B (#1) with
fold_gene2_and_gp66_2024_09_05_13_42_model_2.cif, chain B (#2), sequence
alignment score = 11074.6  
RMSD between 2051 pruned atom pairs is 0.478 angstroms; (across all 2180
pairs: 2.702)  
  
Matchmaker fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif, chain B (#1) with
fold_gene2_and_gp66_2024_09_05_13_42_model_3.cif, chain B (#3), sequence
alignment score = 11085.7  
RMSD between 2071 pruned atom pairs is 0.504 angstroms; (across all 2180
pairs: 3.689)  
  
Matchmaker fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif, chain B (#1) with
fold_gene2_and_gp66_2024_09_05_13_42_model_4.cif, chain B (#4), sequence
alignment score = 11080.9  
RMSD between 2039 pruned atom pairs is 0.657 angstroms; (across all 2180
pairs: 4.254)  
  
Matchmaker fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif, chain B (#1) with
fold_gene2_and_gp66_2024_09_05_13_42_model_0.cif, chain B (#5), sequence
alignment score = 11088.7  
RMSD between 2093 pruned atom pairs is 0.548 angstroms; (across all 2180
pairs: 3.525)  
  

> select #1/B

17455 atoms, 17778 bonds, 2180 residues, 1 model selected  

> select #1/A

2607 atoms, 2653 bonds, 331 residues, 1 model selected  

> split

Split fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif (#1) into 3 models  
Split fold_gene2_and_gp66_2024_09_05_13_42_model_2.cif (#2) into 3 models  
Split fold_gene2_and_gp66_2024_09_05_13_42_model_3.cif (#3) into 3 models  
Split fold_gene2_and_gp66_2024_09_05_13_42_model_4.cif (#4) into 3 models  
Split fold_gene2_and_gp66_2024_09_05_13_42_model_0.cif (#5) into 3 models  
Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_2.cif A #2.1  
---  
Chain | Description  
A | No description available  
  
Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_2.cif B #2.2  
---  
Chain | Description  
B | No description available  
  
Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_3.cif A #3.1  
---  
Chain | Description  
A | No description available  
  
Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_3.cif B #3.2  
---  
Chain | Description  
B | No description available  
  
Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_4.cif A #4.1  
---  
Chain | Description  
A | No description available  
  
Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_4.cif B #4.2  
---  
Chain | Description  
B | No description available  
  
Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_0.cif A #5.1  
---  
Chain | Description  
A | No description available  
  
Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_0.cif B #5.2  
---  
Chain | Description  
B | No description available  
  

> hide #!1 models

> hide #1.1 models

> hide #1.2 models

> hide #2.2 models

> hide #2.1 models

> hide #!2 models

> hide #1.3 models

> hide #!3 models

> hide #2.3 models

> hide #3.1 models

> hide #3.2 models

> hide #3.3 models

> hide #!4 models

> hide #4.1 models

> hide #4.2 models

> hide #4.3 models

> hide #!5 models

> show #!5 models

> color #5.1 #8ffaf3ff

> show #1.1 models

> show #2.1 models

> hide #2.1 models

> show #4.1 models

> show #3.1 models

> show #2.1 models

> hide #!2 models

> show #!2 models

> hide #5.3 models

> show #5.3 models

> rainbow #1.1#2.1#3.1#4.1#5.1-3

> undo

> select add #5.2

17455 atoms, 17778 bonds, 2180 residues, 1 model selected  

> rainbow sel

Alignment identifier is 5.2/B  

> select #5.2/B:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #5.2/B:1-19

152 atoms, 152 bonds, 19 residues, 1 model selected  

> select #5.2/B:2180

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select #5.2/B:2162-2180

148 atoms, 147 bonds, 19 residues, 1 model selected  

> select #5.2/B:1681-2180

4040 atoms, 4109 bonds, 500 residues, 1 model selected  

> select #5.2/B:1877

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #5.2/B:1877

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #5.2/B:1848

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #5.2/B:1848-1850

25 atoms, 24 bonds, 3 residues, 1 model selected  

> select #5.2/B:1835

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #5.2/B:1835-1845

77 atoms, 76 bonds, 11 residues, 1 model selected  

> select #5.2/B:1840-1841

8 atoms, 7 bonds, 2 residues, 1 model selected  

> select #5.2/B:1840-1945

871 atoms, 890 bonds, 106 residues, 1 model selected  

> select #5.2/B:2013

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #5.2/B:2013-2085

587 atoms, 596 bonds, 73 residues, 1 model selected  

> select
> #5.2/B:18-27,30-40,43-49,106-126,130-132,140-162,165-179,181-195,201-213,224-226,229-232,235-243,268-279,294-308,310-321,324-334,372-387,390-392,396-415,424-445,452-459,471-494,505-508,510-524,548-558,560-568,572-574,576-581,596-609,624-626,635-650,694-720,723-725,747-749,756-758,765-771,789-816,839-844,853-879,882-884,888-899,931-940,945-956,969-978,984-994,1004-1006,1035-1038,1042-1052,1061-1063,1094-1096,1117-1124,1140-1166,1176-1189,1194-1201,1206-1208,1213-1229,1290-1295,1299-1301,1304-1310,1313-1316,1328-1330,1342-1344,1354-1358,1380-1392,1397-1406,1411-1413,1422-1434,1443-1450,1468-1470,1473-1488,1491-1498,1504-1514,1526-1528,1530-1560,1599-1614,1618-1621,1629-1637,1642-1649,1652-1665,1678-1690,1704-1713,1719-1743,1745-1748,1754-1772,1782-1785,1794-1812,1822-1834,1849-1866,1868-1870,1875-1891,1901-1904,1922-1938,1940-1954,1969-1974,1977-1990,1992-2005,2018-2020,2042-2044,2090-2092,2115-2130,2148-2151,2156-2161,2170-2172,2174-2176

8855 atoms, 8918 bonds, 1078 residues, 1 model selected  

> select #5.2/B:2112

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #5.2/B:2112

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #5.2/B:2114-2115

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #5.2/B:2114-2155

334 atoms, 338 bonds, 42 residues, 1 model selected  

> select #5.2/B:2050

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #5.2/B:2050-2053

34 atoms, 33 bonds, 4 residues, 1 model selected  

> select #5.2/B:2109

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #5.2/B:2109-2133

206 atoms, 209 bonds, 25 residues, 1 model selected  

> open 6vr4

6vr4 title:  
Virion-packaged DNA-dependent RNA polymerase of crAss-like phage phi14:2 [more
info...]  
  
Chain information for 6vr4 #6  
---  
Chain | Description | UniProt  
A B | DNA-dependent RNA polymerase | S0A2C3_9CAUD 1-2180  
  
Non-standard residues in 6vr4 #6  
---  
CL — chloride ion  
NA — sodium ion  
  
6vr4 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> ui tool show Matchmaker

> matchmaker #!6 to #1.1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif A, chain A (#1.1)
with 6vr4, chain B (#6), sequence alignment score = 16.8  
RMSD between 4 pruned atom pairs is 0.901 angstroms; (across all 21 pairs:
12.544)  
  

> ui tool show Matchmaker

> matchmaker #5.2 to #6

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6vr4, chain A (#6) with
fold_gene2_and_gp66_2024_09_05_13_42_model_0.cif B, chain B (#5.2), sequence
alignment score = 10889.8  
RMSD between 1752 pruned atom pairs is 0.898 angstroms; (across all 2166
pairs: 2.573)  
  

> select add #1

20269 atoms, 20640 bonds, 2537 residues, 5 models selected  

> select add #2

40332 atoms, 41071 bonds, 5049 residues, 9 models selected  

> select add #3

60395 atoms, 61502 bonds, 7561 residues, 13 models selected  

> select add #4

80458 atoms, 81933 bonds, 10073 residues, 17 models selected  

> select add #5.1

83065 atoms, 84586 bonds, 10404 residues, 18 models selected  

> select add #5.3

83066 atoms, 84586 bonds, 10405 residues, 19 models selected  

> delete

Missing or invalid "atoms" argument: empty atom specifier  

> close session

> open
> C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif
> C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/fold_gene2_and_gp66_2024_09_05_13_42_model_2.cif
> C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/fold_gene2_and_gp66_2024_09_05_13_42_model_3.cif
> C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/fold_gene2_and_gp66_2024_09_05_13_42_model_4.cif
> C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/fold_gene2_and_gp66_2024_09_05_13_42_model_0.cif

Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif #1  
---  
Chain | Description  
A | .  
B | .  
  
Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_2.cif #2  
---  
Chain | Description  
A | .  
B | .  
  
Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_3.cif #3  
---  
Chain | Description  
A | .  
B | .  
  
Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_4.cif #4  
---  
Chain | Description  
A | .  
B | .  
  
Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_0.cif #5  
---  
Chain | Description  
A | .  
B | .  
  

> close session

> open 6vr4

6vr4 title:  
Virion-packaged DNA-dependent RNA polymerase of crAss-like phage phi14:2 [more
info...]  
  
Chain information for 6vr4 #1  
---  
Chain | Description | UniProt  
A B | DNA-dependent RNA polymerase | S0A2C3_9CAUD 1-2180  
  
Non-standard residues in 6vr4 #1  
---  
CL — chloride ion  
NA — sodium ion  
  
6vr4 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> select /A

17359 atoms, 17667 bonds, 1 pseudobond, 2181 residues, 2 models selected  

> split

Split 6vr4 (#1) into 2 models  
Chain information for 6vr4 A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 6vr4 B #1.2  
---  
Chain | Description  
B | No description available  
  

> select add #1.1

17359 atoms, 17667 bonds, 1 pseudobond, 2181 residues, 2 models selected  

> rainbow sel

> hide #!1.1 models

> show #!1.1 models

> select add #1

34715 atoms, 35334 bonds, 2 pseudobonds, 4359 residues, 5 models selected  

> select subtract #1

Nothing selected  
Alignment identifier is 1  

> select #1.1/A:1361 #1.2/B:1361

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1.1/A:1361-1365 #1.2/B:1361-1365

86 atoms, 86 bonds, 10 residues, 2 models selected  
1 [ID: 1] region chains A,B [1360-1364] RMSD: 67.152  
  

> delete /B

> save
> C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/gp66_rainbow_cryoEM.cxs

——— End of log from Tue Sep 10 13:01:11 2024 ———

opened ChimeraX session  

> cartoon style sel xsection oval modeHelix default

> show sel cartoons

> color sel bypolymer

> color #1.1 #ffaaffff

> select add #1.1

17359 atoms, 17667 bonds, 1 pseudobond, 2181 residues, 2 models selected  

> select subtract #1.1

Nothing selected  

> select add #1.1

17359 atoms, 17667 bonds, 1 pseudobond, 2181 residues, 2 models selected  

> cartoon style (#!1.1 & sel) modeHelix tube sides 20

> cartoon style (#!1.1 & sel & coil) xsection oval

> cartoon style (#!1.1 & sel) xsection barbell modeHelix default

> cartoon style (#!1.1 & sel) xsection rectangle modeHelix default

> cartoon style (#!1.1 & sel) xsection oval modeHelix default

> cartoon style (#!1.1 & sel & coil) xsection oval

> cartoon style (#!1.1 & sel) xsection barbell modeHelix default

No Surface models open  
[Repeated 1 time(s)]

> select subtract #1.1

Nothing selected  

> select clear

> select /A:211

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:200

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:200-216

129 atoms, 128 bonds, 17 residues, 1 model selected  

> color sel cyan

> select /A:902

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:902-1011

879 atoms, 895 bonds, 110 residues, 1 model selected  

> color sel orange

> color sel blue

> select /A:1269

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:1269-1311

337 atoms, 342 bonds, 43 residues, 1 model selected  

> select /A:1232

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:1232-1371

1076 atoms, 1097 bonds, 140 residues, 1 model selected  

> color sel orange

> view orient

> undo

> select
> /A:17-50,105-125,139-162,164-196,200-215,217-221,223-243,267-280,293-309,312-321,323-335,371-393,395-417,423-445,451-461,471-495,504-509,513-523,547-583,595-610,634-651,693-726,746-750,755-772,788-817,838-843,852-878,881-885,887-900,930-939,944-956,968-979,983-995,1001-1007,1034-1039,1043-1053,1116-1125,1139-1167,1175-1191,1193-1202,1205-1209,1212-1229,1289-1296,1303-1315,1327-1331,1341-1345,1353-1359,1379-1393,1396-1404,1413-1418,1422-1434,1442-1451,1467-1499,1504-1515,1525-1560,1598-1612,1618-1623,1628-1639,1641-1665,1677-1691,1703-1713,1718-1742,1753-1773,1781-1785,1793-1813,1821-1834,1848-1871,1874-1895,1900-1905,1921-1955,1963-2006,2017-2021,2090-2093,2111-2128,2130-2134,2146-2153,2155-2162

9909 atoms, 10011 bonds, 1222 residues, 1 model selected  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3174, in run  
self.log_parse_error()  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3301, in log_parse_error  
text_color, err_color,  
^^^^^^^^^^  
NameError: name 'text_color' is not defined  
  
NameError: name 'text_color' is not defined  
  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3301, in log_parse_error  
text_color, err_color,  
^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> save myview

Cannot determine format for 'myview'  

> save "C:/Users/altay/Desktop/gp66 my view.cxs"

——— End of log from Mon Dec 9 16:31:14 2024 ———

opened ChimeraX session  

> select add #1

17359 atoms, 17667 bonds, 1 pseudobond, 2181 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select /A:842

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:842-1120

2191 atoms, 2231 bonds, 279 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel hot pink

> color sel pale violet red

[Repeated 1 time(s)]

> color sel purple

> color sel blue

> color sel chartreuse

> undo

[Repeated 5 time(s)]

> color sel bypolymer

> select /A:902

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:902-1101

1558 atoms, 1584 bonds, 200 residues, 1 model selected  

> select /A:1101

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:1101-1102

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:1103

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:902-1103

1574 atoms, 1600 bonds, 202 residues, 1 model selected  

> color sel blue

> select /A:1361

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1361

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1363

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1363

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1365

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1365

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1361

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1361

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1363

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1365

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1365

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1:1361,1363,1365

24 atoms, 21 bonds, 3 residues, 1 model selected  

> show sel atoms

> cartoon style (sel & coil) xsection oval

> cartoon style sel xsection barbell modeHelix default

> select add #1

17359 atoms, 17667 bonds, 1 pseudobond, 2181 residues, 3 models selected  

> cartoon style (#!1.1 & sel & coil) xsection oval

> cartoon style (#!1.1 & sel) xsection barbell modeHelix default

> cartoon style (#!1.1 & sel) xsection rectangle modeHelix default

> cartoon style (#!1.1 & sel) xsection oval modeHelix default

> lighting flat

> select subtract #1

Nothing selected  

> lighting flat

> lighting soft

> lighting full

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting soft

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> set bgColor white

> select #1:1361,1363,1365

24 atoms, 21 bonds, 3 residues, 1 model selected  

> style sel stick

Changed 24 atom styles  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 6vr4 A_A SES surface #1.1.2: minimum, -32.72, mean -4.54,
maximum 10.26  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic sel

Coulombic values for 6vr4 A_A SES surface #1.1.2: minimum, -32.72, mean -4.54,
maximum 10.26  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic sel

Coulombic values for 6vr4 A_A SES surface #1.1.2: minimum, -32.72, mean -4.54,
maximum 10.26  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic sel

Coulombic values for 6vr4 A_A SES surface #1.1.2: minimum, -32.72, mean -4.54,
maximum 10.26  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color bfactor sel

24 atoms, 3 residues, 1 surfaces, atom bfactor range 54.2 to 128  

> undo

[Repeated 5 time(s)]

> hide sel atoms

> hide sel cartoons

> hide sel surfaces

> show sel cartoons

> show sel atoms

> style sel stick

Changed 24 atom styles  

> color sel byhetero

> color bfactor sel

24 atoms, 3 residues, 1 surfaces, atom bfactor range 54.2 to 128  

> color (#!1.1 & sel) red

> view orient

> open C:/Users/altay/Downloads/fold_gene50_and_gp66.zip

Unrecognized file suffix '.zip'  

> save "C:/Users/altay/Downloads/fold_gene50_and_gp66 (1)/gp66 my view.cxs"

> open "C:/Users/altay/Downloads/fold_gene50_and_gp66
> (1)/fold_gene50_and_gp66_model_4.cif"
> "C:/Users/altay/Downloads/fold_gene50_and_gp66
> (1)/fold_gene50_and_gp66_model_0.cif"
> "C:/Users/altay/Downloads/fold_gene50_and_gp66
> (1)/fold_gene50_and_gp66_model_1.cif"
> "C:/Users/altay/Downloads/fold_gene50_and_gp66
> (1)/fold_gene50_and_gp66_model_2.cif"
> "C:/Users/altay/Downloads/fold_gene50_and_gp66
> (1)/fold_gene50_and_gp66_model_3.cif"

Chain information for fold_gene50_and_gp66_model_4.cif #2  
---  
Chain | Description  
A | .  
B | .  
  
Chain information for fold_gene50_and_gp66_model_0.cif #3  
---  
Chain | Description  
A | .  
B | .  
  
Chain information for fold_gene50_and_gp66_model_1.cif #4  
---  
Chain | Description  
A | .  
B | .  
  
Chain information for fold_gene50_and_gp66_model_2.cif #5  
---  
Chain | Description  
A | .  
B | .  
  
Chain information for fold_gene50_and_gp66_model_3.cif #6  
---  
Chain | Description  
A | .  
B | .  
  

> ui tool show Matchmaker

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 571, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1284, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\match_maker\\__init__.py", line 44, in start_tool  
return MatchMakerTool(session, tool_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\match_maker\tool.py", line 166, in __init__  
self._match_value_change()  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\match_maker\tool.py", line 366, in _match_value_change  
match_value = match_widget.value  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 130, in value  
return self.get_value()  
^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 133, in get_value  
self._sleep_check()  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 89, in _sleep_check  
self._items_change()  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 169, in _items_change  
item_names = self._item_names() # updates things  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 47, in _item_names  
values = [v for v in self.list_func() if self.filter_func(v)]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 47, in <listcomp>  
values = [v for v in self.list_func() if self.filter_func(v)]  
^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 22, in <lambda>  
filter_func = lambda x, ff=filter_func, cf=class_filter: ff(x) and
isinstance(x, cf)  
^^^^^  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\match_maker\tool.py", line 60, in <lambda>  
filter_func=lambda s, ref_list=self.ref_structure_list: s != ref_list.value)  
^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 130, in value  
return self.get_value()  
^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 133, in get_value  
self._sleep_check()  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 89, in _sleep_check  
self._items_change()  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 172, in _items_change  
filtered_sel = [self.value_map[v] for v in self.value_map.keys() if v in
prev_value]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 172, in <listcomp>  
filtered_sel = [self.value_map[v] for v in self.value_map.keys() if v in
prev_value]  
^^^^^^^^^^^^^^^  
TypeError: argument of type 'NoneType' is not iterable  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\ui\gui.py", line 1853, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\ui\cmd.py", line 219, in ui_tool_show  
return bi.start_tool(session, name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Matchmaker
in bundle ChimeraX-MatchMaker:  
argument of type 'NoneType' is not iterable  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Matchmaker
in bundle ChimeraX-MatchMaker:  
argument of type 'NoneType' is not iterable  
  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  

> ui tool show Matchmaker

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 79, in showEvent  
self._items_change()  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 172, in _items_change  
filtered_sel = [self.value_map[v] for v in self.value_map.keys() if v in
prev_value]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 172, in <listcomp>  
filtered_sel = [self.value_map[v] for v in self.value_map.keys() if v in
prev_value]  
^^^^^^^^^^^^^^^  
TypeError: argument of type 'NoneType' is not iterable  
  
TypeError: argument of type 'NoneType' is not iterable  
  
File "C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 172, in  
filtered_sel = [self.value_map[v] for v in self.value_map.keys() if v in
prev_value]  
^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.4953
OpenGL renderer: Intel(R) UHD Graphics 770
OpenGL vendor: Intel

Python: 3.11.4
Locale: de_DE.cp1252
Qt version: PyQt6 6.7.0, Qt 6.7.1
Qt runtime version: 6.7.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex Micro Plus 7020
OS: Microsoft Windows 11 Enterprise (Build 22631)
Memory: 34,031,325,184
MaxProcessMemory: 137,438,953,344
CPU: 32 Intel(R) Core(TM) i9-14900
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.7.4
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.13
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.3
    ChimeraX-AtomicLibrary: 14.1.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9.dev202407111727
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-DeepMutationalScan: 1.0
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-Foldseek: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.2
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.7
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.5
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.1.5
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.12.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.3
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.17
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.6
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.1
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.2
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.1
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.1
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.47
    psutil: 5.9.8
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject_hooks: 1.1.0
    PyQt6-commercial: 6.7.0
    PyQt6-Qt6: 6.7.2
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.2
    PyQt6-WebEngineSubwheel-Qt6: 6.7.2
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 26.0.3
    qtconsole: 5.5.2
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.13.0
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    Sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia_utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing_extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.2
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
    WMI: 1.5.1

[Eric Pettersen]

Hi Baturay,

Thanks for reporting this problem. It has been fixed in later versions of ChimeraX, so if you get the 1.9 release candidate or the current daily build then this won't happen to you again.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab