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Opened 3 days ago
Closed 43 hours ago
#20453 closed defect (duplicate)
glClear: invalid framebuffer operation on statusbar expose
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-26.5-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Try to install ISOLDE
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/leightongo/Desktop/40c7.cxs
Log from Tue Dec 9 10:35:55 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/leightongo/Desktop/40c7_complex.pdb format pdb
Chain information for 40c7_complex.pdb #1
---
Chain | Description
A E M S | No description available
B F N T | No description available
C H P V | No description available
D G O U | No description available
40 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select add #1
36621 atoms, 37042 bonds, 2448 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select subtract #1
Nothing selected
> combine #1
[Repeated 2 time(s)]
> hide #2 models
> hide #3 models
> hide #4 models
> ui mousemode right select
Drag select of 895 residues
> select up
15371 atoms, 15545 bonds, 1024 residues, 1 model selected
> select up
18311 atoms, 18521 bonds, 1224 residues, 1 model selected
> select up
36621 atoms, 37042 bonds, 2448 residues, 1 model selected
> select down
18311 atoms, 18521 bonds, 1224 residues, 1 model selected
> delete sel
Drag select of 477 residues
> select up
8015 atoms, 8103 bonds, 536 residues, 1 model selected
> select up
9155 atoms, 9261 bonds, 612 residues, 1 model selected
> select up
18310 atoms, 18521 bonds, 1224 residues, 1 model selected
> select down
9155 atoms, 9261 bonds, 612 residues, 1 model selected
> delete sel
> hide #1 models
> show #2 models
Drag select of 155 residues
> select up
3701 atoms, 3742 bonds, 254 residues, 1 model selected
> select up
8373 atoms, 8473 bonds, 564 residues, 1 model selected
> select up
36621 atoms, 37042 bonds, 2448 residues, 1 model selected
> select down
8373 atoms, 8473 bonds, 564 residues, 1 model selected
> delete sel
Drag select of 28 residues
> select up
680 atoms, 684 bonds, 41 residues, 1 model selected
> select up
782 atoms, 787 bonds, 48 residues, 1 model selected
> select up
28248 atoms, 28569 bonds, 1884 residues, 1 model selected
> select down
782 atoms, 787 bonds, 48 residues, 1 model selected
> combine #1
> close #5
> delete sel
Drag select of 122 residues
> select up
3323 atoms, 3356 bonds, 215 residues, 1 model selected
> select up
7433 atoms, 7519 bonds, 492 residues, 1 model selected
> select up
27466 atoms, 27782 bonds, 1836 residues, 1 model selected
> select down
7433 atoms, 7519 bonds, 492 residues, 1 model selected
> delete sel
Drag select of 51 residues
> select up
1187 atoms, 1201 bonds, 84 residues, 1 model selected
> select up
1722 atoms, 1742 bonds, 120 residues, 1 model selected
> select up
20033 atoms, 20263 bonds, 1344 residues, 1 model selected
> select down
1722 atoms, 1742 bonds, 120 residues, 1 model selected
> delete sel
> combine #2
Drag select of 630 residues
> select up
14040 atoms, 14186 bonds, 936 residues, 2 models selected
> select up
18312 atoms, 18522 bonds, 1224 residues, 2 models selected
> select up
36622 atoms, 37042 bonds, 2448 residues, 2 models selected
> select down
18312 atoms, 18522 bonds, 1224 residues, 2 models selected
> delete sel
Undo failed, probably because structures have been modified.
> hide #2 models
> show #2 models
> hide #5 models
> show #5 models
> close #5
> show #1 models
> hide #1 models
> hide #2 models
> show #3 models
Drag select of 634 residues
> select up
10695 atoms, 10812 bonds, 719 residues, 1 model selected
> select up
14235 atoms, 14399 bonds, 952 residues, 1 model selected
> select up
36621 atoms, 37042 bonds, 2448 residues, 1 model selected
> select down
14235 atoms, 14399 bonds, 952 residues, 1 model selected
> delete sel
Drag select of 816 residues
> select up
12984 atoms, 13132 bonds, 868 residues, 1 model selected
> select up
13231 atoms, 13382 bonds, 884 residues, 1 model selected
> select up
22386 atoms, 22643 bonds, 1496 residues, 1 model selected
> select down
13231 atoms, 13382 bonds, 884 residues, 1 model selected
> delete sel
> hide #3 models
> show #2 models
> show #1 models
> show #3 models
> hide #3 models
> hide #2 models
> hide #1 models
> show #4 models
Drag select of 145 residues
> select up
3620 atoms, 3658 bonds, 239 residues, 1 model selected
> select up
7433 atoms, 7519 bonds, 492 residues, 1 model selected
> select up
36621 atoms, 37042 bonds, 2448 residues, 1 model selected
> select down
7433 atoms, 7519 bonds, 492 residues, 1 model selected
> delete sel
Drag select of 510 residues
> select up
8946 atoms, 9045 bonds, 602 residues, 1 model selected
> select up
11659 atoms, 11789 bonds, 780 residues, 1 model selected
Drag select of 182 residues
> select up
4213 atoms, 4258 bonds, 280 residues, 1 model selected
> select up
9155 atoms, 9260 bonds, 612 residues, 1 model selected
> select up
29188 atoms, 29523 bonds, 1956 residues, 1 model selected
> select down
9155 atoms, 9260 bonds, 612 residues, 1 model selected
> delete sel
Drag select of 87 residues
> select up
1601 atoms, 1619 bonds, 109 residues, 1 model selected
> select up
1722 atoms, 1742 bonds, 120 residues, 1 model selected
> select up
20033 atoms, 20263 bonds, 1344 residues, 1 model selected
> select down
1722 atoms, 1742 bonds, 120 residues, 1 model selected
> delete sel
Drag select of 218 residues
> select up
5227 atoms, 5282 bonds, 351 residues, 1 model selected
> select up
9155 atoms, 9260 bonds, 612 residues, 1 model selected
> select up
18311 atoms, 18521 bonds, 1224 residues, 1 model selected
> select down
9155 atoms, 9260 bonds, 612 residues, 1 model selected
> delete sel
> show #3 models
> show #2 models
> show #1 models
> color #1 #ff9300ff
> color #2 #0433ffff
> color #3 #00f900ff
> combine #1-4
> hide #4 models
> hide #3 models
> hide #2 models
> hide #1 models
> hide #5 models
> show #5 models
> hide #5 models
> show #4 models
> show #3 models
> show #2 models
> show #1 models
> mmaker #1 to #2
Computing secondary structure
[Repeated 1 time(s)] 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 copy of 40c7_complex.pdb, chain N (#2) with 40c7_complex.pdb, chain
B (#1), sequence alignment score = 1044.6
RMSD between 220 pruned atom pairs is 0.452 angstroms; (across all 220 pairs:
0.452)
> mmaker #3 to #2
Computing secondary structure
[Repeated 1 time(s)] 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 copy of 40c7_complex.pdb, chain N (#2) with copy of
40c7_complex.pdb, chain T (#3), sequence alignment score = 1009.8
RMSD between 220 pruned atom pairs is 0.472 angstroms; (across all 220 pairs:
0.472)
> mmaker #4 to #2
Computing secondary structure
[Repeated 1 time(s)] 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 copy of 40c7_complex.pdb, chain N (#2) with copy of
40c7_complex.pdb, chain F (#4), sequence alignment score = 1044.6
RMSD between 219 pruned atom pairs is 0.479 angstroms; (across all 220 pairs:
0.498)
Drag select of 63 residues
> select up
2189 atoms, 2197 bonds, 131 residues, 4 models selected
> select up
3128 atoms, 3148 bonds, 192 residues, 4 models selected
> show sel atoms
> style sel stick
Changed 3128 atom styles
> color sel byhetero
> hide #4 models
> hide #3 models
> hide #2 models
> select clear
> sequence chain #1/B
Alignment identifier is 1/B
> select #1/B
3357 atoms, 3397 bonds, 220 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light salmon
> color sel lime green
> color sel turquoise
> color sel cornflower blue
> select #1/D
3294 atoms, 3335 bonds, 224 residues, 1 model selected
> color sel navy
> color sel indigo
> select #1/A
782 atoms, 787 bonds, 48 residues, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross resSeparation 5 interModel false intraMol false
> ignoreHiddenModels true select true color #ed7258 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
236 contacts
atom1 atom2 overlap distance
40c7_complex.pdb #1/A GLU 19 CG 40c7_complex.pdb #1/D ARG 26 O 0.783 2.397
40c7_complex.pdb #1/A GLU 19 HG2 40c7_complex.pdb #1/D ARG 26 O 0.691 1.789
40c7_complex.pdb #1/A HIS 43 CE1 40c7_complex.pdb #1/B ASN 34 O 0.599 2.581
40c7_complex.pdb #1/A GLU 39 CD 40c7_complex.pdb #1/B TRP 56 NE1 0.597 2.728
40c7_complex.pdb #1/A ARG 38 NH1 40c7_complex.pdb #1/B THR 59 CG2 0.586 2.739
40c7_complex.pdb #1/A HIS 43 NE2 40c7_complex.pdb #1/B ASN 34 HB2 0.572 2.068
40c7_complex.pdb #1/A ARG 15 NH2 40c7_complex.pdb #1/D VAL 2 CG2 0.500 2.825
40c7_complex.pdb #1/A GLU 39 OE2 40c7_complex.pdb #1/B TRP 56 CD1 0.499 2.681
40c7_complex.pdb #1/A ARG 38 NH1 40c7_complex.pdb #1/B THR 59 HG23 0.476 2.149
40c7_complex.pdb #1/A GLU 39 HB3 40c7_complex.pdb #1/B LYS 36 NZ 0.476 2.149
40c7_complex.pdb #1/A HIS 43 CE1 40c7_complex.pdb #1/B LYS 36 HE3 0.469 2.231
40c7_complex.pdb #1/A GLU 27 OE1 40c7_complex.pdb #1/B PHE 62 HE2 0.457 2.023
40c7_complex.pdb #1/A ARG 38 HH11 40c7_complex.pdb #1/B THR 59 CG2 0.443 2.257
40c7_complex.pdb #1/A HIS 43 HE1 40c7_complex.pdb #1/B LYS 36 CE 0.440 2.260
40c7_complex.pdb #1/A GLU 19 CG 40c7_complex.pdb #1/D ARG 26 HB3 0.435 2.265
40c7_complex.pdb #1/A GLU 19 OE2 40c7_complex.pdb #1/D ARG 26 C 0.432 2.748
40c7_complex.pdb #1/A HIS 43 CE1 40c7_complex.pdb #1/B LYS 36 CE 0.423 2.977
40c7_complex.pdb #1/A GLU 39 OE1 40c7_complex.pdb #1/B TRP 56 CE2 0.419 2.761
40c7_complex.pdb #1/A GLU 19 OE1 40c7_complex.pdb #1/D GLU 1 CA 0.415 2.765
40c7_complex.pdb #1/A GLU 19 OE1 40c7_complex.pdb #1/D GLU 1 C 0.413 2.767
40c7_complex.pdb #1/A GLU 19 OE2 40c7_complex.pdb #1/D ARG 26 O 0.390 2.570
40c7_complex.pdb #1/A GLN 20 OE1 40c7_complex.pdb #1/D GLU 1 N 0.384 2.321
40c7_complex.pdb #1/A HIS 43 NE2 40c7_complex.pdb #1/B ASN 34 CB 0.380 2.960
40c7_complex.pdb #1/A ARG 38 CD 40c7_complex.pdb #1/B THR 59 HG23 0.370 2.330
40c7_complex.pdb #1/A GLN 20 CD 40c7_complex.pdb #1/D GLU 1 N 0.357 2.968
40c7_complex.pdb #1/A ARG 8 NE 40c7_complex.pdb #1/D ASP 101 C 0.355 2.970
40c7_complex.pdb #1/A GLU 19 CD 40c7_complex.pdb #1/D ARG 26 HB3 0.354 2.346
40c7_complex.pdb #1/A GLU 19 CD 40c7_complex.pdb #1/D ARG 26 O 0.340 2.840
40c7_complex.pdb #1/A GLU 19 CD 40c7_complex.pdb #1/D GLU 1 H3 0.337 2.363
40c7_complex.pdb #1/A GLU 39 HB3 40c7_complex.pdb #1/B LYS 36 CE 0.322 2.378
40c7_complex.pdb #1/A GLN 42 O 40c7_complex.pdb #1/B ASN 35 HB3 0.313 2.167
40c7_complex.pdb #1/A ARG 8 HE 40c7_complex.pdb #1/D ASP 101 C 0.306 2.394
40c7_complex.pdb #1/A GLU 19 HG2 40c7_complex.pdb #1/D ARG 26 C 0.305 2.395
40c7_complex.pdb #1/A GLU 27 OE1 40c7_complex.pdb #1/B PHE 62 CE2 0.303 2.877
40c7_complex.pdb #1/A ARG 8 HD2 40c7_complex.pdb #1/D ASP 101 HB3 0.289 1.711
40c7_complex.pdb #1/A GLU 19 OE1 40c7_complex.pdb #1/D GLU 1 N 0.288 2.417
40c7_complex.pdb #1/A GLU 19 OE2 40c7_complex.pdb #1/D ARG 26 CB 0.277 2.903
40c7_complex.pdb #1/A HIS 43 HE1 40c7_complex.pdb #1/B LYS 36 HE3 0.276 1.724
40c7_complex.pdb #1/A ARG 8 HE 40c7_complex.pdb #1/D ASP 101 O 0.257 1.823
40c7_complex.pdb #1/A ARG 15 HH22 40c7_complex.pdb #1/D VAL 2 CG2 0.257 2.443
40c7_complex.pdb #1/A ARG 38 HH11 40c7_complex.pdb #1/B THR 59 HG23 0.256 1.744
40c7_complex.pdb #1/A ARG 8 CD 40c7_complex.pdb #1/D ASP 101 O 0.256 2.924
40c7_complex.pdb #1/A GLU 19 CG 40c7_complex.pdb #1/D ARG 26 CB 0.248 3.152
40c7_complex.pdb #1/A ARG 8 HD2 40c7_complex.pdb #1/D ASP 101 CB 0.246 2.454
40c7_complex.pdb #1/A GLU 39 CB 40c7_complex.pdb #1/B LYS 36 NZ 0.243 3.082
40c7_complex.pdb #1/A GLN 20 OE1 40c7_complex.pdb #1/D GLU 1 HB2 0.242 2.238
40c7_complex.pdb #1/A GLU 19 HG2 40c7_complex.pdb #1/D ARG 26 HB3 0.236 1.764
40c7_complex.pdb #1/A GLN 20 OE1 40c7_complex.pdb #1/D GLU 1 H1 0.225 1.855
40c7_complex.pdb #1/A GLU 19 HG2 40c7_complex.pdb #1/D ARG 26 CB 0.221 2.479
40c7_complex.pdb #1/A GLN 20 OE1 40c7_complex.pdb #1/D GLU 1 CB 0.218 2.962
40c7_complex.pdb #1/A GLU 39 CD 40c7_complex.pdb #1/B TRP 56 CD1 0.217 3.183
40c7_complex.pdb #1/A GLU 19 CG 40c7_complex.pdb #1/D ARG 26 C 0.216 3.184
40c7_complex.pdb #1/A ARG 38 CD 40c7_complex.pdb #1/B THR 59 CG2 0.206 3.194
40c7_complex.pdb #1/A GLU 19 OE1 40c7_complex.pdb #1/D GLU 1 H3 0.205 1.875
40c7_complex.pdb #1/A GLN 42 OE1 40c7_complex.pdb #1/B ASN 35 O 0.205 2.755
40c7_complex.pdb #1/A ARG 15 NH2 40c7_complex.pdb #1/D VAL 2 HG22 0.202 2.423
40c7_complex.pdb #1/A ARG 8 NE 40c7_complex.pdb #1/D ASP 101 O 0.194 2.511
40c7_complex.pdb #1/A ARG 15 HH22 40c7_complex.pdb #1/D VAL 2 HG22 0.193 1.807
40c7_complex.pdb #1/A ARG 38 HD3 40c7_complex.pdb #1/B THR 59 HG23 0.185 1.815
40c7_complex.pdb #1/A GLU 19 CD 40c7_complex.pdb #1/D ARG 26 CB 0.180 3.220
40c7_complex.pdb #1/A GLU 19 CD 40c7_complex.pdb #1/D GLU 1 N 0.175 3.150
40c7_complex.pdb #1/A GLU 19 OE2 40c7_complex.pdb #1/D ARG 26 HB3 0.166 2.314
40c7_complex.pdb #1/A ARG 15 NE 40c7_complex.pdb #1/D PHE 27 HB3 0.162 2.463
40c7_complex.pdb #1/A GLN 20 CD 40c7_complex.pdb #1/D GLU 1 H1 0.155 2.545
40c7_complex.pdb #1/A GLU 19 CB 40c7_complex.pdb #1/D GLU 1 H3 0.152 2.548
40c7_complex.pdb #1/A GLN 42 O 40c7_complex.pdb #1/B ASN 35 CB 0.140 3.040
40c7_complex.pdb #1/A GLU 19 HG2 40c7_complex.pdb #1/D ARG 26 CA 0.137 2.563
40c7_complex.pdb #1/A GLU 39 HB3 40c7_complex.pdb #1/B LYS 36 HE2 0.137 1.863
40c7_complex.pdb #1/A GLU 19 CB 40c7_complex.pdb #1/D GLU 1 N 0.134 3.191
40c7_complex.pdb #1/A ARG 15 CZ 40c7_complex.pdb #1/D PHE 27 HB3 0.133 2.567
40c7_complex.pdb #1/A GLN 20 CD 40c7_complex.pdb #1/D GLU 1 H2 0.122 2.578
40c7_complex.pdb #1/A ARG 38 NH1 40c7_complex.pdb #1/B THR 59 HG22 0.122 2.503
40c7_complex.pdb #1/A GLU 19 CD 40c7_complex.pdb #1/D GLU 1 C 0.120 3.280
40c7_complex.pdb #1/A ARG 8 CD 40c7_complex.pdb #1/D ASP 101 HB3 0.118 2.582
40c7_complex.pdb #1/A ARG 38 CZ 40c7_complex.pdb #1/B THR 59 HG23 0.118 2.582
40c7_complex.pdb #1/A GLU 39 OE1 40c7_complex.pdb #1/B TRP 56 CZ2 0.116 3.064
40c7_complex.pdb #1/A GLU 39 CD 40c7_complex.pdb #1/B TRP 56 CE2 0.116 3.284
40c7_complex.pdb #1/A ARG 15 NH2 40c7_complex.pdb #1/D VAL 2 HG23 0.116 2.509
40c7_complex.pdb #1/A ARG 15 CD 40c7_complex.pdb #1/D PHE 27 HB3 0.113 2.587
40c7_complex.pdb #1/A GLU 39 CB 40c7_complex.pdb #1/B LYS 36 CE 0.105 3.295
40c7_complex.pdb #1/A ARG 38 HD3 40c7_complex.pdb #1/B THR 59 CG2 0.101 2.599
40c7_complex.pdb #1/A HIS 43 HE1 40c7_complex.pdb #1/B LYS 36 CD 0.089 2.611
40c7_complex.pdb #1/A GLN 42 OE1 40c7_complex.pdb #1/B LYS 36 HA 0.084 2.396
40c7_complex.pdb #1/A GLN 20 CG 40c7_complex.pdb #1/D GLU 1 H2 0.081 2.619
40c7_complex.pdb #1/A ARG 31 CZ 40c7_complex.pdb #1/B GLU 61 OE1 0.081 3.099
40c7_complex.pdb #1/A ARG 15 HD2 40c7_complex.pdb #1/D PHE 27 CB 0.076 2.624
40c7_complex.pdb #1/A ARG 15 HH21 40c7_complex.pdb #1/D VAL 2 CG2 0.075 2.625
40c7_complex.pdb #1/A GLU 39 OE1 40c7_complex.pdb #1/B LYS 36 HG2 0.073 2.407
40c7_complex.pdb #1/A GLU 39 CD 40c7_complex.pdb #1/B TRP 56 HE1 0.068 2.632
40c7_complex.pdb #1/A GLN 20 OE1 40c7_complex.pdb #1/D GLU 1 CA 0.067 3.113
40c7_complex.pdb #1/A HIS 43 CE1 40c7_complex.pdb #1/B ASN 34 HB2 0.063 2.637
40c7_complex.pdb #1/A GLU 39 CB 40c7_complex.pdb #1/B LYS 36 HE2 0.060 2.640
40c7_complex.pdb #1/A ARG 15 HD2 40c7_complex.pdb #1/D PHE 27 HB3 0.057 1.943
40c7_complex.pdb #1/A GLU 19 HG3 40c7_complex.pdb #1/D ARG 26 O 0.053 2.427
40c7_complex.pdb #1/A GLU 39 HB3 40c7_complex.pdb #1/B LYS 36 HZ1 0.035 1.965
40c7_complex.pdb #1/A ARG 8 HD2 40c7_complex.pdb #1/D ASP 101 O 0.034 2.446
40c7_complex.pdb #1/A ARG 8 CD 40c7_complex.pdb #1/D ASP 101 CB 0.032 3.368
40c7_complex.pdb #1/A ARG 15 HH12 40c7_complex.pdb #1/D LYS 98 CE 0.031 2.669
40c7_complex.pdb #1/A GLU 19 CD 40c7_complex.pdb #1/D GLU 1 O 0.031 3.149
40c7_complex.pdb #1/A GLU 39 OE1 40c7_complex.pdb #1/B LYS 36 CG 0.031 3.149
40c7_complex.pdb #1/A GLU 39 HB3 40c7_complex.pdb #1/B LYS 36 HZ3 0.029 1.971
40c7_complex.pdb #1/A ARG 8 HH21 40c7_complex.pdb #1/D THR 102 C 0.026 2.674
40c7_complex.pdb #1/A GLU 19 CD 40c7_complex.pdb #1/D ARG 26 C 0.023 3.377
40c7_complex.pdb #1/A ARG 15 NH1 40c7_complex.pdb #1/D TYR 32 CE2 0.017 3.308
40c7_complex.pdb #1/A HIS 43 NE2 40c7_complex.pdb #1/B LYS 36 HE3 0.011 2.629
40c7_complex.pdb #1/A GLN 20 CG 40c7_complex.pdb #1/D GLU 1 N 0.008 3.317
40c7_complex.pdb #1/A GLU 39 OE1 40c7_complex.pdb #1/B LYS 36 CE -0.012 3.192
40c7_complex.pdb #1/A ARG 15 CD 40c7_complex.pdb #1/D PHE 27 CB -0.015 3.415
40c7_complex.pdb #1/A ARG 15 HH12 40c7_complex.pdb #1/D LYS 98 CD -0.016 2.716
40c7_complex.pdb #1/A GLU 39 OE1 40c7_complex.pdb #1/B LYS 36 HE2 -0.017 2.497
40c7_complex.pdb #1/A GLN 20 OE1 40c7_complex.pdb #1/D GLU 1 H2 -0.021 2.101
40c7_complex.pdb #1/A SER 5 HB3 40c7_complex.pdb #1/B LYS 36 HZ1 -0.024 2.024
40c7_complex.pdb #1/A ARG 38 CZ 40c7_complex.pdb #1/B THR 59 CG2 -0.027 3.427
40c7_complex.pdb #1/A GLU 19 HB3 40c7_complex.pdb #1/D GLU 1 H3 -0.030 2.030
40c7_complex.pdb #1/A ARG 38 NE 40c7_complex.pdb #1/B THR 59 HG23 -0.031 2.656
40c7_complex.pdb #1/A GLU 35 OE2 40c7_complex.pdb #1/D ASP 101 CB -0.038 3.218
40c7_complex.pdb #1/A ARG 31 HH21 40c7_complex.pdb #1/B TYR 55 CZ -0.048 2.748
40c7_complex.pdb #1/A GLU 19 HB3 40c7_complex.pdb #1/D GLU 1 N -0.057 2.682
40c7_complex.pdb #1/A GLU 19 OE2 40c7_complex.pdb #1/D PHE 27 HD1 -0.058 2.538
40c7_complex.pdb #1/A ARG 15 CZ 40c7_complex.pdb #1/D PHE 27 CB -0.059 3.459
40c7_complex.pdb #1/A HIS 43 NE2 40c7_complex.pdb #1/B ASN 34 CA -0.059 3.399
40c7_complex.pdb #1/A ARG 15 HH12 40c7_complex.pdb #1/D LYS 98 HE2 -0.062 2.062
40c7_complex.pdb #1/A HIS 43 CE1 40c7_complex.pdb #1/B LYS 36 CD -0.063 3.463
40c7_complex.pdb #1/A SER 5 CB 40c7_complex.pdb #1/B LYS 36 HZ1 -0.064 2.764
40c7_complex.pdb #1/A GLU 39 OE1 40c7_complex.pdb #1/B TRP 56 NE1 -0.069 2.774
40c7_complex.pdb #1/A ARG 15 NH2 40c7_complex.pdb #1/D VAL 2 CA -0.069 3.394
40c7_complex.pdb #1/A GLU 39 CB 40c7_complex.pdb #1/B LYS 36 HZ3 -0.069 2.769
40c7_complex.pdb #1/A ARG 15 HH21 40c7_complex.pdb #1/D VAL 2 CA -0.072 2.772
40c7_complex.pdb #1/A GLU 19 CB 40c7_complex.pdb #1/D ARG 26 HB3 -0.082 2.782
40c7_complex.pdb #1/A GLU 19 CG 40c7_complex.pdb #1/D ARG 26 CA -0.084 3.484
40c7_complex.pdb #1/A GLU 19 OE1 40c7_complex.pdb #1/D GLU 1 O -0.092 3.052
40c7_complex.pdb #1/A GLU 39 OE2 40c7_complex.pdb #1/B TRP 56 NE1 -0.092 2.797
40c7_complex.pdb #1/A ARG 15 NH1 40c7_complex.pdb #1/D TYR 32 HE2 -0.092 2.717
40c7_complex.pdb #1/A ARG 31 NE 40c7_complex.pdb #1/B GLU 61 OE1 -0.095 2.800
40c7_complex.pdb #1/A HIS 43 ND1 40c7_complex.pdb #1/B ASN 34 O -0.099 2.804
40c7_complex.pdb #1/A ARG 15 NE 40c7_complex.pdb #1/D PHE 27 CB -0.106 3.431
40c7_complex.pdb #1/A HIS 43 CG 40c7_complex.pdb #1/B ASN 34 O -0.109 3.289
40c7_complex.pdb #1/A ARG 8 CD 40c7_complex.pdb #1/D ASP 101 C -0.114 3.514
40c7_complex.pdb #1/A ARG 31 HH21 40c7_complex.pdb #1/B TYR 55 CE1 -0.118 2.818
40c7_complex.pdb #1/A ARG 15 HH11 40c7_complex.pdb #1/D TYR 32 CE2 -0.119 2.819
40c7_complex.pdb #1/A HIS 43 CE1 40c7_complex.pdb #1/B ASN 34 CB -0.119 3.519
40c7_complex.pdb #1/A ARG 38 HH11 40c7_complex.pdb #1/B THR 59 HG22 -0.123 2.123
40c7_complex.pdb #1/A ARG 15 HH21 40c7_complex.pdb #1/D VAL 2 N -0.123 2.748
40c7_complex.pdb #1/A ARG 15 HH21 40c7_complex.pdb #1/D VAL 2 HG23 -0.125 2.125
40c7_complex.pdb #1/A SER 5 HB3 40c7_complex.pdb #1/B LYS 36 NZ -0.126 2.751
40c7_complex.pdb #1/A ARG 15 NH2 40c7_complex.pdb #1/D PHE 27 CD1 -0.126 3.451
40c7_complex.pdb #1/A GLN 42 O 40c7_complex.pdb #1/B ASN 35 HD22 -0.134 2.214
40c7_complex.pdb #1/A GLU 35 OE2 40c7_complex.pdb #1/D ASP 101 HB2 -0.134 2.614
40c7_complex.pdb #1/A GLN 42 OE1 40c7_complex.pdb #1/B LYS 36 CA -0.140 3.320
40c7_complex.pdb #1/A ARG 15 NH2 40c7_complex.pdb #1/D VAL 2 CB -0.143 3.468
40c7_complex.pdb #1/A HIS 43 HE1 40c7_complex.pdb #1/B LYS 36 CG -0.146 2.846
40c7_complex.pdb #1/A GLU 39 CB 40c7_complex.pdb #1/B LYS 36 HZ1 -0.147 2.847
40c7_complex.pdb #1/A GLU 27 HB3 40c7_complex.pdb #1/B PHE 62 CE2 -0.149 2.849
40c7_complex.pdb #1/A GLN 42 O 40c7_complex.pdb #1/B ASN 35 ND2 -0.153 2.858
40c7_complex.pdb #1/A GLN 42 O 40c7_complex.pdb #1/B ASN 35 CG -0.156 3.336
40c7_complex.pdb #1/A HIS 43 CE1 40c7_complex.pdb #1/B ASN 34 C -0.161 3.561
40c7_complex.pdb #1/A GLU 39 OE2 40c7_complex.pdb #1/B TRP 56 HD1 -0.166 2.646
40c7_complex.pdb #1/A ARG 8 NH2 40c7_complex.pdb #1/D THR 102 C -0.176 3.501
40c7_complex.pdb #1/A ARG 15 NH1 40c7_complex.pdb #1/D LYS 98 CE -0.189 3.514
40c7_complex.pdb #1/A GLU 19 CG 40c7_complex.pdb #1/D GLU 1 H3 -0.192 2.892
40c7_complex.pdb #1/A ARG 15 NH1 40c7_complex.pdb #1/D PHE 27 HB3 -0.193 2.818
40c7_complex.pdb #1/A HIS 43 CD2 40c7_complex.pdb #1/B ASN 34 O -0.195 3.375
40c7_complex.pdb #1/A GLU 39 CA 40c7_complex.pdb #1/B LYS 36 HE2 -0.195 2.895
40c7_complex.pdb #1/A ARG 15 NH1 40c7_complex.pdb #1/D PHE 27 CB -0.201 3.526
40c7_complex.pdb #1/A ARG 8 HH21 40c7_complex.pdb #1/D THR 102 CA -0.203 2.903
40c7_complex.pdb #1/A ARG 15 NH1 40c7_complex.pdb #1/D LYS 98 CD -0.205 3.530
40c7_complex.pdb #1/A GLN 20 HG2 40c7_complex.pdb #1/D GLU 1 H2 -0.210 2.210
40c7_complex.pdb #1/A SER 5 CB 40c7_complex.pdb #1/B LYS 36 NZ -0.211 3.536
40c7_complex.pdb #1/A GLU 39 OE1 40c7_complex.pdb #1/B TRP 56 CD1 -0.212 3.392
40c7_complex.pdb #1/A HIS 43 NE2 40c7_complex.pdb #1/B LYS 36 CE -0.212 3.552
40c7_complex.pdb #1/A GLU 19 OE2 40c7_complex.pdb #1/D GLU 1 C -0.213 3.393
40c7_complex.pdb #1/A GLU 19 OE2 40c7_complex.pdb #1/D GLU 1 O -0.214 3.174
40c7_complex.pdb #1/A GLU 39 OE1 40c7_complex.pdb #1/B TRP 56 CD2 -0.225 3.405
40c7_complex.pdb #1/A ARG 15 NH1 40c7_complex.pdb #1/D LYS 98 HE2 -0.227 2.852
40c7_complex.pdb #1/A ARG 15 NH2 40c7_complex.pdb #1/D VAL 2 HA -0.233 2.858
40c7_complex.pdb #1/A GLU 19 OE2 40c7_complex.pdb #1/D ARG 26 CA -0.235 3.415
40c7_complex.pdb #1/A ARG 31 NH2 40c7_complex.pdb #1/B TYR 55 CZ -0.237 3.562
40c7_complex.pdb #1/A ARG 15 HH11 40c7_complex.pdb #1/D TYR 32 HE2 -0.238 2.238
40c7_complex.pdb #1/A GLU 39 CG 40c7_complex.pdb #1/B LYS 36 HZ3 -0.238 2.938
40c7_complex.pdb #1/A ARG 31 CZ 40c7_complex.pdb #1/B GLU 61 OE2 -0.241 3.421
40c7_complex.pdb #1/A GLU 19 OE2 40c7_complex.pdb #1/D PHE 27 CD1 -0.242 3.422
40c7_complex.pdb #1/A ARG 31 CZ 40c7_complex.pdb #1/B GLU 61 CD -0.242 3.642
40c7_complex.pdb #1/A ARG 8 HH21 40c7_complex.pdb #1/D THR 102 N -0.243 2.868
40c7_complex.pdb #1/A GLN 20 HG2 40c7_complex.pdb #1/D GLU 1 N -0.249 2.874
40c7_complex.pdb #1/A HIS 43 NE2 40c7_complex.pdb #1/B ASN 34 O -0.249 2.969
40c7_complex.pdb #1/A GLU 19 OE1 40c7_complex.pdb #1/D GLU 1 HA -0.252 2.732
40c7_complex.pdb #1/A GLU 19 CB 40c7_complex.pdb #1/D ARG 26 CB -0.255 3.655
40c7_complex.pdb #1/A HIS 43 HE1 40c7_complex.pdb #1/B LYS 36 HG3 -0.261 2.261
40c7_complex.pdb #1/A GLU 19 CD 40c7_complex.pdb #1/D GLU 1 CA -0.269 3.669
40c7_complex.pdb #1/A GLU 39 CG 40c7_complex.pdb #1/B LYS 36 NZ -0.274 3.599
40c7_complex.pdb #1/A HIS 43 HE1 40c7_complex.pdb #1/B ASN 34 O -0.277 2.757
40c7_complex.pdb #1/A HIS 43 NE2 40c7_complex.pdb #1/B ASN 34 C -0.277 3.617
40c7_complex.pdb #1/A GLN 42 OE1 40c7_complex.pdb #1/B LYS 36 CG -0.280 3.460
40c7_complex.pdb #1/A ARG 8 NE 40c7_complex.pdb #1/D THR 102 N -0.282 3.532
40c7_complex.pdb #1/A ARG 8 HE 40c7_complex.pdb #1/D THR 102 N -0.284 2.909
40c7_complex.pdb #1/A GLU 27 OE1 40c7_complex.pdb #1/B PHE 62 CZ -0.287 3.467
40c7_complex.pdb #1/A GLU 39 OE2 40c7_complex.pdb #1/B TRP 56 CG -0.289 3.469
40c7_complex.pdb #1/A GLU 27 CB 40c7_complex.pdb #1/B PHE 62 CE2 -0.293 3.693
40c7_complex.pdb #1/A GLU 39 OE1 40c7_complex.pdb #1/B LYS 36 CD -0.294 3.474
40c7_complex.pdb #1/A ARG 38 NE 40c7_complex.pdb #1/B THR 59 CG2 -0.296 3.621
40c7_complex.pdb #1/A GLU 39 CG 40c7_complex.pdb #1/B TRP 56 NE1 -0.297 3.622
40c7_complex.pdb #1/A ARG 31 NH2 40c7_complex.pdb #1/B GLU 61 CD -0.307 3.632
40c7_complex.pdb #1/A ARG 15 NH2 40c7_complex.pdb #1/D VAL 2 N -0.308 3.558
40c7_complex.pdb #1/A ARG 8 HD2 40c7_complex.pdb #1/D ASP 101 C -0.311 3.011
40c7_complex.pdb #1/A GLU 19 HB2 40c7_complex.pdb #1/D GLU 1 N -0.312 2.937
40c7_complex.pdb #1/A ARG 15 CZ 40c7_complex.pdb #1/D PHE 27 CD1 -0.312 3.712
40c7_complex.pdb #1/A ARG 15 HH21 40c7_complex.pdb #1/D VAL 2 HA -0.317 2.317
40c7_complex.pdb #1/A GLU 27 CD 40c7_complex.pdb #1/B PHE 62 HE2 -0.317 3.017
40c7_complex.pdb #1/A GLU 27 CD 40c7_complex.pdb #1/B PHE 62 CE2 -0.322 3.722
40c7_complex.pdb #1/A HIS 43 HE1 40c7_complex.pdb #1/B LYS 36 HE2 -0.325 2.325
40c7_complex.pdb #1/A ARG 8 HH21 40c7_complex.pdb #1/D THR 102 O -0.332 2.412
40c7_complex.pdb #1/A ARG 31 NE 40c7_complex.pdb #1/B GLU 61 CD -0.332 3.657
40c7_complex.pdb #1/A GLU 19 OE2 40c7_complex.pdb #1/D ARG 26 HB2 -0.338 2.818
40c7_complex.pdb #1/A ARG 38 HD2 40c7_complex.pdb #1/B THR 59 HG23 -0.340 2.340
40c7_complex.pdb #1/A ARG 15 HD2 40c7_complex.pdb #1/D PHE 27 CA -0.340 3.040
40c7_complex.pdb #1/A ARG 8 NH2 40c7_complex.pdb #1/D THR 102 N -0.345 3.595
40c7_complex.pdb #1/A ARG 31 NH2 40c7_complex.pdb #1/B TYR 55 CE1 -0.345 3.670
40c7_complex.pdb #1/A GLU 39 O 40c7_complex.pdb #1/B LYS 36 CE -0.356 3.536
40c7_complex.pdb #1/A HIS 43 CE1 40c7_complex.pdb #1/B LYS 36 CG -0.357 3.757
40c7_complex.pdb #1/A HIS 43 CD2 40c7_complex.pdb #1/B ASN 34 CA -0.357 3.757
40c7_complex.pdb #1/A ARG 31 HE 40c7_complex.pdb #1/B GLU 61 OE1 -0.367 2.447
40c7_complex.pdb #1/A ARG 15 NH2 40c7_complex.pdb #1/D PHE 27 HD1 -0.367 2.992
40c7_complex.pdb #1/A HIS 43 CE1 40c7_complex.pdb #1/B LYS 36 HE2 -0.369 3.069
40c7_complex.pdb #1/A GLU 27 CG 40c7_complex.pdb #1/B PHE 62 CZ -0.369 3.769
40c7_complex.pdb #1/A GLU 19 CG 40c7_complex.pdb #1/D GLU 1 N -0.371 3.696
40c7_complex.pdb #1/A GLU 39 CA 40c7_complex.pdb #1/B LYS 36 CE -0.371 3.771
40c7_complex.pdb #1/A GLN 34 HE22 40c7_complex.pdb #1/B TYR 55 OH -0.372 2.472
40c7_complex.pdb #1/A ARG 38 HD2 40c7_complex.pdb #1/B THR 59 CG2 -0.373 3.073
40c7_complex.pdb #1/A GLN 42 HB2 40c7_complex.pdb #1/B ASN 35 O -0.379 2.859
40c7_complex.pdb #1/A ARG 8 NE 40c7_complex.pdb #1/D ASP 101 CA -0.380 3.705
40c7_complex.pdb #1/A HIS 43 CD2 40c7_complex.pdb #1/B ASN 34 HB2 -0.381 3.081
40c7_complex.pdb #1/A ARG 8 HD2 40c7_complex.pdb #1/D ASP 101 CA -0.385 3.085
40c7_complex.pdb #1/A HIS 43 CD2 40c7_complex.pdb #1/B ASN 34 CB -0.388 3.788
40c7_complex.pdb #1/A ARG 8 CD 40c7_complex.pdb #1/D ASP 101 CA -0.389 3.789
40c7_complex.pdb #1/A ARG 8 NH2 40c7_complex.pdb #1/D THR 102 O -0.390 3.095
40c7_complex.pdb #1/A ARG 15 HG3 40c7_complex.pdb #1/D ARG 26 O -0.393 2.873
236 contacts
> style sel stick
Changed 154 atom styles
> sequence chain #1/D
Alignment identifier is 1/D
> select add #1
9155 atoms, 9260 bonds, 236 pseudobonds, 612 residues, 2 models selected
> style sel stick
Changed 9155 atom styles
> save /Users/leightongo/Desktop/40c7.cxs
——— End of log from Tue Dec 9 10:35:55 2025 ———
> view name session-start
opened ChimeraX session
> set bgColor white
> ui mousemode right select
Drag select of 643 atoms, 185 residues, 209 pseudobonds, 605 bonds
> select up
2921 atoms, 2952 bonds, 209 pseudobonds, 188 residues, 2 models selected
> select up
2948 atoms, 2980 bonds, 209 pseudobonds, 188 residues, 2 models selected
> select up
3651 atoms, 3694 bonds, 209 pseudobonds, 237 residues, 2 models selected
> select up
7433 atoms, 7519 bonds, 209 pseudobonds, 492 residues, 2 models selected
> select up
9155 atoms, 9260 bonds, 236 pseudobonds, 612 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> open
> /Users/leightongo/Downloads/fold_49d12_a1pro/fold_49d12_a1pro_model_0.cif
Chain information for fold_49d12_a1pro_model_0.cif #6
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> open
> /Users/leightongo/Downloads/fold_49d12_a1pro/fold_49d12_a1pro_model_0.cif
Chain information for fold_49d12_a1pro_model_0.cif #7
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> close #7
> select subtract #1
Nothing selected
> select add #6
4050 atoms, 4142 bonds, 535 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> mmaker #6 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 40c7_complex.pdb, chain B (#1) with fold_49d12_a1pro_model_0.cif,
chain B (#6), sequence alignment score = 765
RMSD between 193 pruned atom pairs is 0.881 angstroms; (across all 215 pairs:
2.110)
> hide #!1 models
> select subtract #6
Nothing selected
Drag select of 97 residues
> select up
1182 atoms, 1199 bonds, 157 residues, 1 model selected
> select up
3588 atoms, 3672 bonds, 477 residues, 1 model selected
> select up
4050 atoms, 4142 bonds, 535 residues, 1 model selected
> select down
3588 atoms, 3672 bonds, 477 residues, 1 model selected
> hide sel cartoons
> ui mousemode right translate
> select #6/C:cys
36 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> ui tool show "Build Structure"
> bond sel
Created 2 bonds
> bond length #6/C:17@CB#6/C:17@SG 1.521
> bond length #6/C:37@CA#6/C:37@C 1.521
> bond length #6/C:17@N#6/C:17@CA 1.521
> bond length #6/C:17@CA#6/C:17@C 1.521
> bond length #6/C:37@CA#6/C:37@CB 1.521
> bond length #6/C:17@CA#6/C:17@CB 1.521
> bond length #6/C:37@C#6/C:37@O 1.521
> bond length #6/C:17@C#6/C:17@O 1.521
> bond length #6/C:37@N#6/C:37@CA 1.521
> bond length #6/C:37@CB#6/C:37@SG 1.521
> bond length #6/C:46@N#6/C:46@CA 1.521
> bond length #6/C:21@N#6/C:21@CA 1.521
> bond length #6/C:46@CA#6/C:46@C 1.521
> bond length #6/C:21@CA#6/C:21@C 1.521
> bond length #6/C:46@CA#6/C:46@CB 1.521
> bond length #6/C:21@CA#6/C:21@CB 1.521
> bond length #6/C:13@N#6/C:13@CA 1.521
> bond length #6/C:46@C#6/C:46@O 1.521
> bond length #6/C:21@C#6/C:21@O 1.521
> bond length #6/C:46@CB#6/C:46@SG 1.521
> bond length #6/C:21@CB#6/C:21@SG 1.521
> bond length #6/C:33@N#6/C:33@CA 1.521
> bond length #6/C:33@CA#6/C:33@C 1.521
> bond length #6/C:13@CA#6/C:13@C 1.521
> bond length #6/C:33@CA#6/C:33@CB 1.521
> bond length #6/C:13@CA#6/C:13@CB 1.521
> bond length #6/C:33@C#6/C:33@O 1.521
> bond length #6/C:13@C#6/C:13@O 1.521
> bond length #6/C:33@CB#6/C:33@SG 1.521
> bond length #6/C:13@CB#6/C:13@SG 1.521
> bond length #6/C:17@CB#6/C:17@SG 1.531
> bond length #6/C:37@CA#6/C:37@C 1.531
> bond length #6/C:17@N#6/C:17@CA 1.531
> bond length #6/C:17@CA#6/C:17@C 1.531
> bond length #6/C:37@CA#6/C:37@CB 1.531
> bond length #6/C:17@CA#6/C:17@CB 1.531
> bond length #6/C:37@C#6/C:37@O 1.531
> bond length #6/C:17@C#6/C:17@O 1.531
> bond length #6/C:37@N#6/C:37@CA 1.531
> bond length #6/C:37@CB#6/C:37@SG 1.531
> bond length #6/C:46@N#6/C:46@CA 1.531
> bond length #6/C:21@N#6/C:21@CA 1.531
> bond length #6/C:46@CA#6/C:46@C 1.531
> bond length #6/C:21@CA#6/C:21@C 1.531
> bond length #6/C:46@CA#6/C:46@CB 1.531
> bond length #6/C:21@CA#6/C:21@CB 1.531
> bond length #6/C:13@N#6/C:13@CA 1.531
> bond length #6/C:46@C#6/C:46@O 1.531
> bond length #6/C:21@C#6/C:21@O 1.531
> bond length #6/C:46@CB#6/C:46@SG 1.531
> bond length #6/C:21@CB#6/C:21@SG 1.531
> bond length #6/C:33@N#6/C:33@CA 1.531
> bond length #6/C:33@CA#6/C:33@C 1.531
> bond length #6/C:13@CA#6/C:13@C 1.531
> bond length #6/C:33@CA#6/C:33@CB 1.531
> bond length #6/C:13@CA#6/C:13@CB 1.531
> bond length #6/C:33@C#6/C:33@O 1.531
> bond length #6/C:13@C#6/C:13@O 1.531
> bond length #6/C:33@CB#6/C:33@SG 1.531
> bond length #6/C:13@CB#6/C:13@SG 1.531
> bond length #6/C:17@CB#6/C:17@SG 1.541
> bond length #6/C:37@CA#6/C:37@C 1.541
> bond length #6/C:17@N#6/C:17@CA 1.541
> bond length #6/C:17@CA#6/C:17@C 1.541
> bond length #6/C:37@CA#6/C:37@CB 1.541
> bond length #6/C:17@CA#6/C:17@CB 1.541
> bond length #6/C:37@C#6/C:37@O 1.541
> bond length #6/C:17@C#6/C:17@O 1.541
> bond length #6/C:37@N#6/C:37@CA 1.541
> bond length #6/C:37@CB#6/C:37@SG 1.541
> bond length #6/C:46@N#6/C:46@CA 1.541
> bond length #6/C:21@N#6/C:21@CA 1.541
> bond length #6/C:46@CA#6/C:46@C 1.541
> bond length #6/C:21@CA#6/C:21@C 1.541
> bond length #6/C:46@CA#6/C:46@CB 1.541
> bond length #6/C:21@CA#6/C:21@CB 1.541
> bond length #6/C:13@N#6/C:13@CA 1.541
> bond length #6/C:46@C#6/C:46@O 1.541
> bond length #6/C:21@C#6/C:21@O 1.541
> bond length #6/C:46@CB#6/C:46@SG 1.541
> bond length #6/C:21@CB#6/C:21@SG 1.541
> bond length #6/C:33@N#6/C:33@CA 1.541
> bond length #6/C:33@CA#6/C:33@C 1.541
> bond length #6/C:13@CA#6/C:13@C 1.541
> bond length #6/C:33@CA#6/C:33@CB 1.541
> bond length #6/C:13@CA#6/C:13@CB 1.541
> bond length #6/C:33@C#6/C:33@O 1.541
> bond length #6/C:13@C#6/C:13@O 1.541
> bond length #6/C:33@CB#6/C:33@SG 1.541
> bond length #6/C:13@CB#6/C:13@SG 1.541
> bond length #6/C:17@CB#6/C:17@SG 1.551
> bond length #6/C:37@CA#6/C:37@C 1.551
> bond length #6/C:17@N#6/C:17@CA 1.551
> bond length #6/C:17@CA#6/C:17@C 1.551
> bond length #6/C:37@CA#6/C:37@CB 1.551
> bond length #6/C:17@CA#6/C:17@CB 1.551
> bond length #6/C:37@C#6/C:37@O 1.551
> bond length #6/C:17@C#6/C:17@O 1.551
> bond length #6/C:37@N#6/C:37@CA 1.551
> bond length #6/C:37@CB#6/C:37@SG 1.551
> bond length #6/C:46@N#6/C:46@CA 1.551
> bond length #6/C:21@N#6/C:21@CA 1.551
> bond length #6/C:46@CA#6/C:46@C 1.551
> bond length #6/C:21@CA#6/C:21@C 1.551
> bond length #6/C:46@CA#6/C:46@CB 1.551
> bond length #6/C:21@CA#6/C:21@CB 1.551
> bond length #6/C:13@N#6/C:13@CA 1.551
> bond length #6/C:46@C#6/C:46@O 1.551
> bond length #6/C:21@C#6/C:21@O 1.551
> bond length #6/C:46@CB#6/C:46@SG 1.551
> bond length #6/C:21@CB#6/C:21@SG 1.551
> bond length #6/C:33@N#6/C:33@CA 1.551
> bond length #6/C:33@CA#6/C:33@C 1.551
> bond length #6/C:13@CA#6/C:13@C 1.551
> bond length #6/C:33@CA#6/C:33@CB 1.551
> bond length #6/C:13@CA#6/C:13@CB 1.551
> bond length #6/C:33@C#6/C:33@O 1.551
> bond length #6/C:13@C#6/C:13@O 1.551
> bond length #6/C:33@CB#6/C:33@SG 1.551
> bond length #6/C:13@CB#6/C:13@SG 1.551
> bond length #6/C:17@CB#6/C:17@SG 1.561
> bond length #6/C:37@CA#6/C:37@C 1.561
> bond length #6/C:17@N#6/C:17@CA 1.561
> bond length #6/C:17@CA#6/C:17@C 1.561
> bond length #6/C:37@CA#6/C:37@CB 1.561
> bond length #6/C:17@CA#6/C:17@CB 1.561
> bond length #6/C:37@C#6/C:37@O 1.561
> bond length #6/C:17@C#6/C:17@O 1.561
> bond length #6/C:37@N#6/C:37@CA 1.561
> bond length #6/C:37@CB#6/C:37@SG 1.561
> bond length #6/C:46@N#6/C:46@CA 1.561
> bond length #6/C:21@N#6/C:21@CA 1.561
> bond length #6/C:46@CA#6/C:46@C 1.561
> bond length #6/C:21@CA#6/C:21@C 1.561
> bond length #6/C:46@CA#6/C:46@CB 1.561
> bond length #6/C:21@CA#6/C:21@CB 1.561
> bond length #6/C:13@N#6/C:13@CA 1.561
> bond length #6/C:46@C#6/C:46@O 1.561
> bond length #6/C:21@C#6/C:21@O 1.561
> bond length #6/C:46@CB#6/C:46@SG 1.561
> bond length #6/C:21@CB#6/C:21@SG 1.561
> bond length #6/C:33@N#6/C:33@CA 1.561
> bond length #6/C:33@CA#6/C:33@C 1.561
> bond length #6/C:13@CA#6/C:13@C 1.561
> bond length #6/C:33@CA#6/C:33@CB 1.561
> bond length #6/C:13@CA#6/C:13@CB 1.561
> bond length #6/C:33@C#6/C:33@O 1.561
> bond length #6/C:13@C#6/C:13@O 1.561
> bond length #6/C:33@CB#6/C:33@SG 1.561
> bond length #6/C:13@CB#6/C:13@SG 1.561
> bond length #6/C:17@CB#6/C:17@SG 1.571
> bond length #6/C:37@CA#6/C:37@C 1.571
> bond length #6/C:17@N#6/C:17@CA 1.571
> bond length #6/C:17@CA#6/C:17@C 1.571
> bond length #6/C:37@CA#6/C:37@CB 1.571
> bond length #6/C:17@CA#6/C:17@CB 1.571
> bond length #6/C:37@C#6/C:37@O 1.571
> bond length #6/C:17@C#6/C:17@O 1.571
> bond length #6/C:37@N#6/C:37@CA 1.571
> bond length #6/C:37@CB#6/C:37@SG 1.571
> bond length #6/C:46@N#6/C:46@CA 1.571
> bond length #6/C:21@N#6/C:21@CA 1.571
> bond length #6/C:46@CA#6/C:46@C 1.571
> bond length #6/C:21@CA#6/C:21@C 1.571
> bond length #6/C:46@CA#6/C:46@CB 1.571
> bond length #6/C:21@CA#6/C:21@CB 1.571
> bond length #6/C:13@N#6/C:13@CA 1.571
> bond length #6/C:46@C#6/C:46@O 1.571
> bond length #6/C:21@C#6/C:21@O 1.571
> bond length #6/C:46@CB#6/C:46@SG 1.571
> bond length #6/C:21@CB#6/C:21@SG 1.571
> bond length #6/C:33@N#6/C:33@CA 1.571
> bond length #6/C:33@CA#6/C:33@C 1.571
> bond length #6/C:13@CA#6/C:13@C 1.571
> bond length #6/C:33@CA#6/C:33@CB 1.571
> bond length #6/C:13@CA#6/C:13@CB 1.571
> bond length #6/C:33@C#6/C:33@O 1.571
> bond length #6/C:13@C#6/C:13@O 1.571
> bond length #6/C:33@CB#6/C:33@SG 1.571
> bond length #6/C:13@CB#6/C:13@SG 1.571
> bond length #6/C:17@CB#6/C:17@SG 1.581
> bond length #6/C:37@CA#6/C:37@C 1.581
> bond length #6/C:17@N#6/C:17@CA 1.581
> bond length #6/C:17@CA#6/C:17@C 1.581
> bond length #6/C:37@CA#6/C:37@CB 1.581
> bond length #6/C:17@CA#6/C:17@CB 1.581
> bond length #6/C:37@C#6/C:37@O 1.581
> bond length #6/C:17@C#6/C:17@O 1.581
> bond length #6/C:37@N#6/C:37@CA 1.581
> bond length #6/C:37@CB#6/C:37@SG 1.581
> bond length #6/C:46@N#6/C:46@CA 1.581
> bond length #6/C:21@N#6/C:21@CA 1.581
> bond length #6/C:46@CA#6/C:46@C 1.581
> bond length #6/C:21@CA#6/C:21@C 1.581
> bond length #6/C:46@CA#6/C:46@CB 1.581
> bond length #6/C:21@CA#6/C:21@CB 1.581
> bond length #6/C:13@N#6/C:13@CA 1.581
> bond length #6/C:46@C#6/C:46@O 1.581
> bond length #6/C:21@C#6/C:21@O 1.581
> bond length #6/C:46@CB#6/C:46@SG 1.581
> bond length #6/C:21@CB#6/C:21@SG 1.581
> bond length #6/C:33@N#6/C:33@CA 1.581
> bond length #6/C:33@CA#6/C:33@C 1.581
> bond length #6/C:13@CA#6/C:13@C 1.581
> bond length #6/C:33@CA#6/C:33@CB 1.581
> bond length #6/C:13@CA#6/C:13@CB 1.581
> bond length #6/C:33@C#6/C:33@O 1.581
> bond length #6/C:13@C#6/C:13@O 1.581
> bond length #6/C:33@CB#6/C:33@SG 1.581
> bond length #6/C:13@CB#6/C:13@SG 1.581
> bond length #6/C:17@CB#6/C:17@SG 1.591
> bond length #6/C:37@CA#6/C:37@C 1.591
> bond length #6/C:17@N#6/C:17@CA 1.591
> bond length #6/C:17@CA#6/C:17@C 1.591
> bond length #6/C:37@CA#6/C:37@CB 1.591
> bond length #6/C:17@CA#6/C:17@CB 1.591
> bond length #6/C:37@C#6/C:37@O 1.591
> bond length #6/C:17@C#6/C:17@O 1.591
> bond length #6/C:37@N#6/C:37@CA 1.591
> bond length #6/C:37@CB#6/C:37@SG 1.591
> bond length #6/C:46@N#6/C:46@CA 1.591
> bond length #6/C:21@N#6/C:21@CA 1.591
> bond length #6/C:46@CA#6/C:46@C 1.591
> bond length #6/C:21@CA#6/C:21@C 1.591
> bond length #6/C:46@CA#6/C:46@CB 1.591
> bond length #6/C:21@CA#6/C:21@CB 1.591
> bond length #6/C:13@N#6/C:13@CA 1.591
> bond length #6/C:46@C#6/C:46@O 1.591
> bond length #6/C:21@C#6/C:21@O 1.591
> bond length #6/C:46@CB#6/C:46@SG 1.591
> bond length #6/C:21@CB#6/C:21@SG 1.591
> bond length #6/C:33@N#6/C:33@CA 1.591
> bond length #6/C:33@CA#6/C:33@C 1.591
> bond length #6/C:13@CA#6/C:13@C 1.591
> bond length #6/C:33@CA#6/C:33@CB 1.591
> bond length #6/C:13@CA#6/C:13@CB 1.591
> bond length #6/C:33@C#6/C:33@O 1.591
> bond length #6/C:13@C#6/C:13@O 1.591
> bond length #6/C:33@CB#6/C:33@SG 1.591
> bond length #6/C:13@CB#6/C:13@SG 1.591
> bond length #6/C:17@CB#6/C:17@SG 1.601
> bond length #6/C:37@CA#6/C:37@C 1.601
> bond length #6/C:17@N#6/C:17@CA 1.601
> bond length #6/C:17@CA#6/C:17@C 1.601
> bond length #6/C:37@CA#6/C:37@CB 1.601
> bond length #6/C:17@CA#6/C:17@CB 1.601
> bond length #6/C:37@C#6/C:37@O 1.601
> bond length #6/C:17@C#6/C:17@O 1.601
> bond length #6/C:37@N#6/C:37@CA 1.601
> bond length #6/C:37@CB#6/C:37@SG 1.601
> bond length #6/C:46@N#6/C:46@CA 1.601
> bond length #6/C:21@N#6/C:21@CA 1.601
> bond length #6/C:46@CA#6/C:46@C 1.601
> bond length #6/C:21@CA#6/C:21@C 1.601
> bond length #6/C:46@CA#6/C:46@CB 1.601
> bond length #6/C:21@CA#6/C:21@CB 1.601
> bond length #6/C:13@N#6/C:13@CA 1.601
> bond length #6/C:46@C#6/C:46@O 1.601
> bond length #6/C:21@C#6/C:21@O 1.601
> bond length #6/C:46@CB#6/C:46@SG 1.601
> bond length #6/C:21@CB#6/C:21@SG 1.601
> bond length #6/C:33@N#6/C:33@CA 1.601
> bond length #6/C:33@CA#6/C:33@C 1.601
> bond length #6/C:13@CA#6/C:13@C 1.601
> bond length #6/C:33@CA#6/C:33@CB 1.601
> bond length #6/C:13@CA#6/C:13@CB 1.601
> bond length #6/C:33@C#6/C:33@O 1.601
> bond length #6/C:13@C#6/C:13@O 1.601
> bond length #6/C:33@CB#6/C:33@SG 1.601
> bond length #6/C:13@CB#6/C:13@SG 1.601
> bond sel
Created 0 bonds
> bond sel
Created 0 bonds
> bond sel reasonable false
Created 598 bonds
> ~bond sel
> bond sel
Created 32 bonds
> hide #6.1 models
> ui mousemode right select
> select clear
> select #6/C:46@SG
1 atom, 1 residue, 1 model selected
> select add #6/C:13@SG
2 atoms, 2 residues, 1 model selected
> ui tool show "Build Structure"
> bond sel reasonable false
Created 1 bond
> select clear
> select ~sel & ##selected
Nothing selected
> select #6/C
462 atoms, 473 bonds, 30 pseudobonds, 58 residues, 2 models selected
> help graphics
> graphics selection color black
> graphics selection linewidth 2
Expected a keyword
> graphics selection width 2
> graphics selection width 3
> save /Users/leightongo/Desktop/image1.png supersample 3
Desktop color scheme is dark
Desktop color scheme is light
> hide #!6 models
> show #!1 models
> select add #6
4050 atoms, 4145 bonds, 30 pseudobonds, 535 residues, 2 models selected
> select subtract #6
Nothing selected
> sequcence chain #1/A
Unknown command: sequcence chain #1/A
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:48
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/A:29-48
325 atoms, 326 bonds, 20 residues, 1 model selected
> color sel white
Drag select of 81 residues
> select up
2799 atoms, 2831 bonds, 183 residues, 1 model selected
> select up
6651 atoms, 6732 bonds, 444 residues, 1 model selected
> select up
9155 atoms, 9260 bonds, 612 residues, 1 model selected
> hide sel cartoons
> select clear
> select #1/C
1722 atoms, 1741 bonds, 120 residues, 1 model selected
> show sel cartoons
> select ~sel & ##selected
7433 atoms, 7519 bonds, 236 pseudobonds, 492 residues, 2 models selected
> select #1/A
782 atoms, 787 bonds, 48 residues, 1 model selected
> show sel cartoons
> select #1/C
1722 atoms, 1741 bonds, 120 residues, 1 model selected
> hide sel cartoons
> select #1/A:cys
40 atoms, 38 bonds, 4 residues, 1 model selected
> show sel atoms
> select #1/A:48
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/A:48
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/A:48
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/A:5-6
32 atoms, 32 bonds, 2 residues, 1 model selected
> select #1/A:5-6
32 atoms, 32 bonds, 2 residues, 1 model selected
> select #1/A:5
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:5
11 atoms, 10 bonds, 1 residue, 1 model selected
> open /Users/leightongo/Downloads/a1procomplex_refine_026.pdb
Chain information for a1procomplex_refine_026.pdb #7
---
Chain | Description
A E I M | No description available
B | No description available
C | No description available
D | No description available
F | No description available
G | No description available
H P | No description available
J | No description available
K | No description available
L | No description available
N | No description available
O | No description available
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
17904 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> mmaker #7 to #1
Computing secondary structure
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 40c7_complex.pdb, chain B (#1) with a1procomplex_refine_026.pdb,
chain A (#7), sequence alignment score = 1052.7
RMSD between 160 pruned atom pairs is 1.301 angstroms; (across all 219 pairs:
1.774)
> select add #1
9155 atoms, 9260 bonds, 236 pseudobonds, 612 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #7
34902 atoms, 35293 bonds, 4 pseudobonds, 2399 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select add #6
38952 atoms, 39438 bonds, 34 pseudobonds, 2934 residues, 4 models selected
> select subtract #6
34902 atoms, 35293 bonds, 4 pseudobonds, 2399 residues, 2 models selected
> select add #1
44057 atoms, 44553 bonds, 240 pseudobonds, 3011 residues, 4 models selected
> show sel cartoons
> close #2-4#1
> close #5
> save /Users/leightongo/Desktop/40c7.cxs
> select #7/A-C
8179 atoms, 8278 bonds, 1 pseudobond, 555 residues, 2 models selected
> combine sel
> hide #!7 models
> select add #7
34902 atoms, 35293 bonds, 4 pseudobonds, 2399 residues, 2 models selected
> select subtract #7
Nothing selected
> hide #!1 models
> show #!1 models
> show #!7 models
> hide #!7 models
> combine #7/A-C
> hide #!1 models
> close #2
> show #!1 models
Drag select of 370 residues
> select up
6328 atoms, 6399 bonds, 429 residues, 1 model selected
> select up
8666 atoms, 8772 bonds, 591 residues, 1 model selected
> select up
34902 atoms, 35293 bonds, 2399 residues, 1 model selected
> select down
8666 atoms, 8772 bonds, 591 residues, 1 model selected
> delete sel
Drag select of 249 residues
> select up
5397 atoms, 5456 bonds, 368 residues, 1 model selected
> select up
8329 atoms, 8429 bonds, 567 residues, 1 model selected
> select up
26236 atoms, 26521 bonds, 1808 residues, 1 model selected
> select down
8329 atoms, 8429 bonds, 567 residues, 1 model selected
> delete sel
Drag select of 36 residues
> select up
548 atoms, 554 bonds, 37 residues, 1 model selected
> select up
17907 atoms, 18092 bonds, 1241 residues, 1 model selected
> select down
548 atoms, 554 bonds, 37 residues, 1 model selected
> delete sel
Drag select of 347 residues, 1 pseudobonds
> select up
6512 atoms, 6589 bonds, 1 pseudobond, 432 residues, 2 models selected
> select up
8718 atoms, 8823 bonds, 1 pseudobond, 590 residues, 2 models selected
> delete sel
Drag select of 77 residues
> show sel atoms
> style sel stick
Changed 1139 atom styles
> color sel byhetero
> select #1/L:63-end
151 atoms, 152 bonds, 9 residues, 1 model selected
> color sel white
> color sel byhetero
> select ~sel & ##selected
8490 atoms, 8563 bonds, 2 pseudobonds, 605 residues, 2 models selected
> hide sel atoms
> select #1/L
541 atoms, 547 bonds, 36 residues, 1 model selected
> help combine
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/leightongo/Desktop/movie1.mp4
Movie saved to /Users/leightongo/Desktop/movie1.mp4
> toolshed show
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,2
Model Number: MK1A3LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 Performance and 2 Efficiency)
Memory: 32 GB
System Firmware Version: 18000.120.36
OS Loader Version: 18000.120.36
Software:
System Software Overview:
System Version: macOS 26.5 (25F71)
Kernel Version: Darwin 25.5.0
Time since boot: 3 days, 3 hours, 6 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
DELL P2723QE:
Resolution: 6016 x 3384
UI Looks like: 3008 x 1692 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
DELL P2723QE:
Resolution: 3384 x 6016
UI Looks like: 1692 x 3008 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: 90
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FocalBlur: 0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-HelloWorld: 0.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
ChimeraX-MutationScores: 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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
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: 2.5.2
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
Change History (2)
comment:1 by , 45 hours ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → glClear: invalid framebuffer operation on statusbar expose |
comment:2 by , 43 hours ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Note:
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This ChimeraX error is due to a Qt window toolkit bug on macOS 26. We have worked around it in the ChimeraX 1.12 release candidate and daily builds currently on the ChimeraX download web page.