Opened 3 years ago

Closed 3 years ago

#7427 closed defect (can't reproduce)

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

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc: Tom Goddard
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: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/chrismuriel/Desktop/modified_aligned/VasH_VFischeri_model_iTasser_T_newfit_02-coot-0.pdb
> format pdb

Chain information for VasH_VFischeri_model_iTasser_T_newfit_02-coot-0.pdb #1  
---  
Chain | Description  
T | No description available  
  

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Alignment identifier is 1/T  

> select
> /T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294

447 atoms, 441 bonds, 56 residues, 1 model selected  

> select
> /T:12-25,35-44,63-73,89-96,109-132,141-153,170-180,198-206,214-217,228-230,233-245,271-276,282-288,298-320,329-337,343-357,369-371,374-379,389-392,396-414,419-426,430-440

1818 atoms, 1810 bonds, 231 residues, 1 model selected  

> select
> /T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294

447 atoms, 441 bonds, 56 residues, 1 model selected  

> cartoon sel

Alignment identifier is 1/T  

> select /T:1

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

> select /T:1-181

1334 atoms, 1349 bonds, 181 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light coral

> color sel peach puff

> color sel navajo white

> color sel light pink

> select
> /T:12-25,35-44,63-73,89-96,109-132,141-153,170-180,198-206,214-217,228-230,233-245,271-276,282-288,298-320,329-337,343-357,369-371,374-379,389-392,396-414,419-426,430-440

1818 atoms, 1810 bonds, 231 residues, 1 model selected  

> select
> /T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294

447 atoms, 441 bonds, 56 residues, 1 model selected  

> select
> /T:12-25,35-44,63-73,89-96,109-132,141-153,170-180,198-206,214-217,228-230,233-245,271-276,282-288,298-320,329-337,343-357,369-371,374-379,389-392,396-414,419-426,430-440

1818 atoms, 1810 bonds, 231 residues, 1 model selected  

> select /T:334

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

> select /T:334-346

106 atoms, 109 bonds, 13 residues, 1 model selected  

> select /T:442

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

> select /T:321-442

945 atoms, 961 bonds, 122 residues, 1 model selected  

> select /T:297-298

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select /T:297-442

1136 atoms, 1155 bonds, 146 residues, 1 model selected  

> color sel light green

> color sel dark sea green

> color sel aquamarine

> color sel dark sea green

> select
> /T:12-25,35-44,63-73,89-96,109-132,141-153,170-180,198-206,214-217,228-230,233-245,271-276,282-288,298-320,329-337,343-357,369-371,374-379,389-392,396-414,419-426,430-440

1818 atoms, 1810 bonds, 231 residues, 1 model selected  

> select
> /T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294

447 atoms, 441 bonds, 56 residues, 1 model selected  

> select /T:1-5

34 atoms, 33 bonds, 5 residues, 1 model selected  

> select /T:1-180

1328 atoms, 1343 bonds, 180 residues, 1 model selected  

> color sel pink

[Repeated 1 time(s)]

> select
> /T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294

447 atoms, 441 bonds, 56 residues, 1 model selected  

> open
> /Users/chrismuriel/Desktop/modified_aligned/VasH_VCholerae_model_iTasser_newfit_01-coot-0.pdb
> format pdb

VasH_VCholerae_model_iTasser_newfit_01-coot-0.pdb title:  
Alphafold monomer V2.0 prediction for transcriptional regulator vash (Q9KN48)
[more info...]  
  
Chain information for VasH_VCholerae_model_iTasser_newfit_01-coot-0.pdb #2  
---  
Chain | Description | UniProt  
A | transcriptional regulator vash | VASH_VIBCH  
  
Destroying pre-existing alignment with identifier 1/T  
Alignment identifier is 1/T  

> select #1/T:1

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

> select #1/T:1-180

1328 atoms, 1343 bonds, 180 residues, 1 model selected  

> color sel salmon

> undo

Destroying pre-existing alignment with identifier 1/T  
Alignment identifier is 1/T  

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

> hide #1 models

> show #1 models

> hide #1 models

> ui tool show "Color Actions"

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

[Repeated 2 time(s)]Alignment identifier is 1/T  

> select #2

4173 atoms, 4251 bonds, 530 residues, 1 model selected  
Alignment identifier is 2/A  

> ~select #2

Nothing selected  

> select #2/A:1

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

> select #2/A:1-180

1459 atoms, 1492 bonds, 180 residues, 1 model selected  

> color sel salmon

> color sel misty rose

> color sel bisque

> color sel blanched almond

[Repeated 3 time(s)]

> select #2/A:181

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

> select #2/A:181-191

82 atoms, 81 bonds, 11 residues, 1 model selected  

> color sel blanched almond

> select #2/A:192

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

> select #2/A:192-212

154 atoms, 153 bonds, 21 residues, 1 model selected  

> color sel blanched almond

> select #2/A:212-213

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #2/A:212-213

14 atoms, 13 bonds, 2 residues, 1 model selected  

> color sel blanched almond

[Repeated 1 time(s)]

> select #2/A:214-215

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

> select #2/A:214-422

1655 atoms, 1685 bonds, 209 residues, 1 model selected  

> select #2/A:421-423

20 atoms, 19 bonds, 3 residues, 1 model selected  

> select #2/A:410-423

114 atoms, 115 bonds, 14 residues, 1 model selected  

> select #2/A:214

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

> select #2/A:214-389

1385 atoms, 1409 bonds, 176 residues, 1 model selected  

> select #2/A:214

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

> select #2/A:214-359

1132 atoms, 1151 bonds, 146 residues, 1 model selected  

> color sel azure

> select
> #2/A:3-11,17-32,68-75,85-89,93-99,130-137,140-191,198-212,227-236,255-263,280-283,294-296,299-311,337-342,348-354,364-386,395-403,409-422,432-435,475-477,481-499,504-510,515-524

2124 atoms, 2136 bonds, 261 residues, 1 model selected  

> select
> #2/A:36-42,49-51,79-82,106-113,122-129,217-220,245-249,288-292,328-333,357-360

424 atoms, 424 bonds, 54 residues, 1 model selected  

> show #1 models

> select #2

4173 atoms, 4251 bonds, 530 residues, 1 model selected  

> ~select #2

Nothing selected  

> hide #2 models

> hide #1 models

> show #1 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> hide #1 models

> show #2 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #2 models

Alignment identifier is 1/T  
Destroying pre-existing alignment with identifier 2/A  
Alignment identifier is 2/A  

> select
> #2/A:3-11,17-32,68-75,85-89,93-99,130-137,140-191,198-212,227-236,255-263,280-283,294-296,299-311,337-342,348-354,364-386,395-403,409-422,432-435,475-477,481-499,504-510,515-524

2124 atoms, 2136 bonds, 261 residues, 1 model selected  

> select
> #1/T:12-25,35-44,63-73,89-96,109-132,141-153,170-180,198-206,214-217,228-230,233-245,271-276,282-288,298-320,329-337,343-357,369-371,374-379,389-392,396-414,419-426,430-440

1818 atoms, 1810 bonds, 231 residues, 1 model selected  

> select #1/T:1-2

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select #1/T:1-180

1328 atoms, 1343 bonds, 180 residues, 1 model selected  

> color sel cornflower blue

> color sel crimson

> color sel gray

> color sel saddle brown

> color sel chocolate

> color sel tomato

> color sel orange red

> color sel light sea green

> color sel orange red

> color sel violet

> select #1/T:442

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

> select #1/T:296-442

1143 atoms, 1163 bonds, 147 residues, 1 model selected  

> color sel light sea green

[Repeated 1 time(s)]

> select #1/T:301

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

> select #1/T:301-442

1113 atoms, 1132 bonds, 142 residues, 1 model selected  

> color sel turquoise

> select #1/T:290-296

51 atoms, 52 bonds, 7 residues, 1 model selected  

> select #1/T:290-300

74 atoms, 75 bonds, 11 residues, 1 model selected  

> color sel navajo white

> undo

[Repeated 7 time(s)]

> select #1/T:299-300

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select #1/T:299-442

1123 atoms, 1142 bonds, 144 residues, 1 model selected  

> color sel turquoise

> color sel light sea green

[Repeated 2 time(s)]

> color sel dodger blue

> select
> #1/T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294

447 atoms, 441 bonds, 56 residues, 1 model selected  

> select
> #1/T:12-25,35-44,63-73,89-96,109-132,141-153,170-180,198-206,214-217,228-230,233-245,271-276,282-288,298-320,329-337,343-357,369-371,374-379,389-392,396-414,419-426,430-440

1818 atoms, 1810 bonds, 231 residues, 1 model selected  

> select #1/T:296

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

> select #1/T:296-300

30 atoms, 30 bonds, 5 residues, 1 model selected  

> select #1/T:298

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

> select #1/T:298-300

18 atoms, 17 bonds, 3 residues, 1 model selected  

> color sel dodger blue

> select
> #1/T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294

447 atoms, 441 bonds, 56 residues, 1 model selected  

> select #1/T:287

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

> select #1/T:287-290

32 atoms, 31 bonds, 4 residues, 1 model selected  

> select #1/T:295

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

> select #1/T:295-298

27 atoms, 27 bonds, 4 residues, 1 model selected  

> select #1/T:293-294

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

> select #1/T:293-295

23 atoms, 22 bonds, 3 residues, 1 model selected  

> select #1/T:296

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

> select #1/T:296-297

12 atoms, 12 bonds, 2 residues, 1 model selected  

> color sel peach puff

> color sel navajo white

> select
> #1/T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294

447 atoms, 441 bonds, 56 residues, 1 model selected  

> select
> #1/T:12-25,35-44,63-73,89-96,109-132,141-153,170-180,198-206,214-217,228-230,233-245,271-276,282-288,298-320,329-337,343-357,369-371,374-379,389-392,396-414,419-426,430-440

1818 atoms, 1810 bonds, 231 residues, 1 model selected  

> select #1/T:296-297

12 atoms, 12 bonds, 2 residues, 1 model selected  

> select #1/T:296-298

20 atoms, 20 bonds, 3 residues, 1 model selected  

> select #1/T:296-442

1143 atoms, 1163 bonds, 147 residues, 1 model selected  

> color sel dodger blue

[Repeated 1 time(s)]

> select
> #1/T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294

447 atoms, 441 bonds, 56 residues, 1 model selected  

> select #1/T:296-442

1143 atoms, 1163 bonds, 147 residues, 1 model selected  

> select
> #1/T:12-25,35-44,63-73,89-96,109-132,141-153,170-180,198-206,214-217,228-230,233-245,271-276,282-288,298-320,329-337,343-357,369-371,374-379,389-392,396-414,419-426,430-440

1818 atoms, 1810 bonds, 231 residues, 1 model selected  

> select
> #1/T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294

447 atoms, 441 bonds, 56 residues, 1 model selected  

> select
> #1/T:12-25,35-44,63-73,89-96,109-132,141-153,170-180,198-206,214-217,228-230,233-245,271-276,282-288,298-320,329-337,343-357,369-371,374-379,389-392,396-414,419-426,430-440

1818 atoms, 1810 bonds, 231 residues, 1 model selected  
Alignment identifier is 1/T  

> select
> #1/T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294

447 atoms, 441 bonds, 56 residues, 1 model selected  

> select
> #1/T:12-25,35-44,63-73,89-96,109-132,141-153,170-180,198-206,214-217,228-230,233-245,271-276,282-288,298-320,329-337,343-357,369-371,374-379,389-392,396-414,419-426,430-440

1818 atoms, 1810 bonds, 231 residues, 1 model selected  

> select #1/T:1

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

> select #1/T:1-180

1328 atoms, 1343 bonds, 180 residues, 1 model selected  

> label sel attribute label_specifier

> redo

> label sel attribute label_specifier

> ~label sel atoms

[Repeated 2 time(s)]

> ~label sel residues

> select strand

871 atoms, 865 bonds, 110 residues, 2 models selected  

> undo

> select coil

2713 atoms, 2708 bonds, 370 residues, 2 models selected  

> select #1/T:287-288

19 atoms, 18 bonds, 2 residues, 1 model selected  

> select #1/T:287-300

99 atoms, 100 bonds, 14 residues, 1 model selected  

> select #1/T:292

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

> select #1/T:292-300

60 atoms, 61 bonds, 9 residues, 1 model selected  

> select #1/T:296

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

> select #1/T:296-300

30 atoms, 30 bonds, 5 residues, 1 model selected  

> select #1/T:291-292

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select #1/T:291-300

67 atoms, 68 bonds, 10 residues, 1 model selected  

> select #1/T:291

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

> select #1/T:291-298

57 atoms, 58 bonds, 8 residues, 1 model selected  

> select #1/T:292-293

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select #1/T:292-300

60 atoms, 61 bonds, 9 residues, 1 model selected  

> select #1/T:294

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

> select #1/T:294-300

46 atoms, 46 bonds, 7 residues, 1 model selected  

> select #1/T:291

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

> select #1/T:291-296

44 atoms, 45 bonds, 6 residues, 1 model selected  

> select #1/T:291

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

> select #1/T:291-298

57 atoms, 58 bonds, 8 residues, 1 model selected  

> select #1/T:290-291

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #1/T:290-297

56 atoms, 57 bonds, 8 residues, 1 model selected  

> select #1/T:290

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

> select #1/T:290-295

44 atoms, 44 bonds, 6 residues, 1 model selected  

> select #1/T:296

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

> select #1/T:296-300

30 atoms, 30 bonds, 5 residues, 1 model selected  

> color sel dodger blue

[Repeated 1 time(s)]

> select
> #1/T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294

447 atoms, 441 bonds, 56 residues, 1 model selected  

> select #1/T:1

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

> select #1/T:1-221

1616 atoms, 1636 bonds, 221 residues, 1 model selected  

> select #1/T:1

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

> select #1/T:1-119

873 atoms, 885 bonds, 119 residues, 1 model selected  

> select #1/T:1-5

34 atoms, 33 bonds, 5 residues, 1 model selected  

> select #1/T:1-180

1328 atoms, 1343 bonds, 180 residues, 1 model selected  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> label sel atoms attribute alt_loc

> show #2 models

> hide #!1 models

> select #1/T:9-10

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

> select #1/T:9-10

16 atoms, 15 bonds, 2 residues, 1 model selected  
Destroying pre-existing alignment with identifier 1/T  
Alignment identifier is 1/T  

> select #1/T:1

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

> select #1/T:1-132

978 atoms, 990 bonds, 132 residues, 1 model selected  

> select #1/T:1

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

> select #1/T:1-132

978 atoms, 990 bonds, 132 residues, 1 model selected  

> select #1/T:1-130

962 atoms, 974 bonds, 130 residues, 1 model selected  

> select #1/T:1-134

988 atoms, 1000 bonds, 134 residues, 1 model selected  

> select #1/T:1-22

156 atoms, 155 bonds, 22 residues, 1 model selected  

> select #1/T:1-22

156 atoms, 155 bonds, 22 residues, 1 model selected  

> select #1/T:1-126

929 atoms, 941 bonds, 126 residues, 1 model selected  

> select #1/T:1-126

929 atoms, 941 bonds, 126 residues, 1 model selected  

> select #1/T:1

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

> select #1/T:1-132

978 atoms, 990 bonds, 132 residues, 1 model selected  

Window position QRect(1497,-531 100x30) outside any known screen, using
primary screen  

Height must be a number  
[Repeated 4 time(s)]

> hide #2 models

> show #!1 models

> show #2 models

> hide #!1 models

Destroying pre-existing alignment with identifier 1/T  
Alignment identifier is 1/T  

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

[Repeated 1 time(s)]

> select #1/T:1

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

> select #1/T:1-132

978 atoms, 990 bonds, 132 residues, 1 model selected  
Destroying pre-existing alignment with identifier 1/T  
Alignment identifier is 1/T  

> ui tool show "Color Actions"

> color #2 darkgrey transparency 0

> select #2

4173 atoms, 4251 bonds, 530 residues, 1 model selected  
Alignment identifier is 2/A  

> select #2/A:1

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

> select #2/A:1-111

890 atoms, 913 bonds, 111 residues, 1 model selected  

> select #2/A:1-2

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #2/A:1-113

905 atoms, 929 bonds, 113 residues, 1 model selected  

> select #2/A:1-3

23 atoms, 22 bonds, 3 residues, 1 model selected  

> select #2/A:1-192

1548 atoms, 1581 bonds, 192 residues, 1 model selected  

> color sel dark turquoise

> color sel cornflower blue

> select #2/A:193-195

20 atoms, 19 bonds, 3 residues, 1 model selected  

> select #2/A:193-212

147 atoms, 146 bonds, 20 residues, 1 model selected  

> color sel cornflower blue

> select
> #2/A:3-11,17-32,68-75,85-89,93-99,130-137,140-191,198-212,227-236,255-263,280-283,294-296,299-311,337-342,348-354,364-386,395-403,409-422,432-435,475-477,481-499,504-510,515-524

2124 atoms, 2136 bonds, 261 residues, 1 model selected  

> select #2/A:193-212

147 atoms, 146 bonds, 20 residues, 1 model selected  

> select #2/A:193-194

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

> select #2/A:193-387

1520 atoms, 1544 bonds, 195 residues, 1 model selected  

> color sel plum

[Repeated 1 time(s)]

> select #2/A:395-396

23 atoms, 23 bonds, 2 residues, 1 model selected  

> select #2/A:395-530

1048 atoms, 1067 bonds, 136 residues, 1 model selected  

> color sel pale green

[Repeated 1 time(s)]

> color sel spring green

> color sel lime green

> select
> #2/A:36-42,49-51,79-82,106-113,122-129,217-220,245-249,288-292,328-333,357-360

424 atoms, 424 bonds, 54 residues, 1 model selected  

> show #!1 models

> hide #!1 models

> show #!1 models

> select #2

4173 atoms, 4251 bonds, 530 residues, 1 model selected  

> ~select #2

Nothing selected  

> hide #!1 models

> show #!1 models

> hide #!1 models

> select #2/A:395-530

1048 atoms, 1067 bonds, 136 residues, 1 model selected  

> select #2/A:393-394

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

> select #2/A:193-394

1577 atoms, 1601 bonds, 202 residues, 1 model selected  

> color sel blue violet

[Repeated 1 time(s)]

> show #!1 models

> hide #2 models

> hide #!1 models

> show #2 models

> show #!1 models

> hide #2 models

> hide #!1 models

> show #2 models

> select #2

4173 atoms, 4251 bonds, 530 residues, 1 model selected  

> ~select #2

Nothing selected  

> show #!1 models

> hide #!1 models

> view

> label #2 atoms attribute alt_loc

> label #2 atoms attribute num_alt_locs

> label #2 atoms attribute alt_loc

[Repeated 1 time(s)]

> show #!1 models

> label #1-2 atoms attribute alt_loc

> hide #!2 models

Window position QRect(1229,-751 654x459) outside any known screen, using
primary screen  

> save /Users/chrismuriel/Desktop/2022_vasHmodel_VF.tif width 1358 height 824
> supersample 3 transparentBackground true

> show #!2 models

> hide #!1 models

Window position QRect(1229,-751 654x459) outside any known screen, using
primary screen  

> save /Users/chrismuriel/Desktop/2022_vasHmodel_VC.tif width 1358 height 824
> supersample 3 transparentBackground true

> show #!1 models

Window position QRect(1229,-751 654x459) outside any known screen, using
primary screen  

> save /Users/chrismuriel/Desktop/2022_alignment_vasHmodel_VC_VF.tif width
> 1358 height 824 supersample 3 transparentBackground true

Window position QRect(1177,-756 654x459) outside any known screen, using
primary screen  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2251, in <lambda>  
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 648, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
KeyError: <chimerax.seq-view.tool.SequenceViewer object at 0x7fe926bc9190>  
  
KeyError:  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 648, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
  
See log for complete Python traceback.  
  

Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x60000feb38a0>
contents scale of 1 - updating layer to match.  

[Repeated 3 time(s)]




OpenGL version: 4.1 INTEL-18.7.4
OpenGL renderer: Intel(R) HD Graphics 615
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook
      Model Identifier: MacBook10,1
      Processor Name: Dual-Core Intel Core m3
      Processor Speed: 1.2 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 451.120.7.0.0
      OS Loader Version: 540.120.3~6
      SMC Version (system): 2.42f13

Software:

    System Software Overview:

      System Version: macOS 12.4 (21F79)
      Kernel Version: Darwin 21.5.0
      Time since boot: 58 days 46 minutes

Graphics/Displays:

    Intel HD Graphics 615:

      Chipset Model: Intel HD Graphics 615
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x591e
      Revision ID: 0x0002
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2304 x 1440 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        HP V21:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 1CR042225R  
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort
        Apple TV:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 63.00Hz
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Mirror: Off
          Connection Type: AirPlay

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    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: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    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: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    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
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    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: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → Window Toolkit
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → QMainWindowLayout::tabPosition called with out-of-bounds

comment:2 by Eric Pettersen, 3 years ago

Resolution: → can't reproduce
Status: accepted → closed
Summary: QMainWindowLayout::tabPosition called with out-of-bounds → QMainWindowLayout::tabPosition called with out-of-bounds value

Seemed to occur after "Destroying pre-existing alignment with identifier 1/T", which you can get by clicking the show-sequence link in the chain table when the sequence is already shown, but doing that in my test case with the sequence tiled normally, tabbed, or floating did not produce the "QMainWindowLayout::tabPosition called with out-of-bounds value", which is indicates inconsistent internal Qt state.

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