glClear: invalid framebuffer operation

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-26.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/sdvorkin/ERK2_assignments.cxs format session

Log from Tue Dec 9 08:36:39 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/sdvorkin/Kinases/ERK2/Erk2_PDBs/4xCys_2p_CSPs_5v60.cxs format
> session

Log from Mon Oct 27 14:42:46 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/sdvorkin/Kinases/ERK2/Erk2_PDBs/Aloop_2_Sept082025.cxs format
> session

Log from Fri Sep 5 15:44:15 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/sdvorkin/Kinases/ERK2/Erk2_PDBs/hErk2_A_Loop_5v60_AF.cxs format
> session

Log from Wed Sep 3 11:26:32 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/sdvorkin/Kinases/ERK2/Erk2_PDBs/Erk2_AF_vs5v60.cxs format
> session

Log from Tue Aug 26 09:17:22 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/sdvorkin/Kinases/ERK2/5x_Cys_Mut/Fig_ERK2_AF_5xCys.cxs format
> session

Log from Thu Jul 17 13:26:02 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/sdvorkin/Kinases/ERK2/5x_Cys_Mut/ERK2_AF_5xCys.cxs format
> session

Log from Tue Jul 15 13:44:49 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/sdvorkin/Kinases/ERK2/Erk2_PDBs/ERK2_AF_CYS_fig.cxs

Log from Tue Apr 22 13:22:28 2025 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle  
  

> cartoon suppressBackboneDisplay false

> alias rd ui mousemode right distance

> alias ra ui mousemode right label

> alias nmr1 hide #*.2-20 models

UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/sdvorkin/Kinases/Erk2:RSK/Erk2_PDBs/Erk2_AF-P28482-F1-model_v4.pdb

Erk2_AF-P28482-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for mitogen-activated protein kinase 1
(P28482) [more info...]  
  
Chain information for Erk2_AF-P28482-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | mitogen-activated protein kinase 1 | MK01_HUMAN 1-360  
  

> show :cys target a

> color :cys red target a

> set bgColor white

> name N-lobe :start-111

> name C-lobe :112-end

> name P-loop :32-37

> name P-loop-Aro :36

> name hinge :103-107

> name gk :105

> name aC-helix :59-76

> name SB :54,71

> name DFG :167-169

> name A-loop :167-198

> name HRD :147-149

> name C-loop :145-154

> name pho-res :185,187

> name R-spine :86,75,147,210,168

> name C-spine :39,52,156,155,157,108,217,221

> color A-loop medium orchid

> color aC-helix chocolate

> color :cys red target a

> save /Users/sdvorkin/Desktop/image27.png supersample 3

> save /Users/sdvorkin/Kinases/Erk2:RSK/Erk2_PDBs/ERK2_AF_CYS_fig.cxs

——— End of log from Tue Apr 22 13:22:28 2025 ———

opened ChimeraX session  

> show #1 :244 target a

> color #1 :244 cyan target a

> view :137 clip false

> show :137 target a

> show :28 target a

> show :313 target a

> color :313 cyan target a

> show :343 target a

> color :343 cyan target a

> show :343 target a

> show :255 target a

> color :255 cyan target a

> hide :40,216 target a

> show :75 target a

> show :74 target a

> show :53 target a

> show :72 target a

> label :254, 166, 161, 187, 65

> show :347 target a

> show :103 target a

> show :243, 116 target a

> open /Users/sdvorkin/Desktop/FANCL/3zqs.cif

3zqs.cif title:  
Human FANCL central domain [more info...]  
  
Chain information for 3zqs.cif #2  
---  
Chain | Description | UniProt  
A B | E3 UBIQUITIN-PROTEIN LIGASE FANCL | FANCL_HUMAN 109-294  
  
Non-standard residues in 3zqs.cif #2  
---  
NA — sodium ion  
P6G — hexaethylene glycol (polyethylene glycol PEG400)  
PRO — proline  
  
3zqs.cif mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> hide #!1 target m

> split #2/A

Split 3zqs.cif (#2) into 2 models  
Chain information for 3zqs.cif A #2.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 3zqs.cif B #2.2  
---  
Chain | Description  
B | No description available  
  

> color #2/A cyan target ac

> show #2/A 227 target a

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #2/A :227 target a

> open /Users/sdvorkin/Desktop/FANCL/7kzp.cif

Summary of feedback from opening /Users/sdvorkin/Desktop/FANCL/7kzp.cif  
---  
warning | Atom H1 is not in the residue template for UNK /W:1  
note | Fetching CCD ZN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif  
  
7kzp.cif title:  
Structure of the human Fanconi anaemia Core complex [more info...]  
  
Chain information for 7kzp.cif #3  
---  
Chain | Description | UniProt  
A S | Fanconi anemia group A protein | FANCA_HUMAN 1-1455  
B O | Fanconi anemia group B protein | FANCB_HUMAN 1-859  
C | Fanconi anemia group C protein | FANCC_HUMAN 1-558  
E | Fanconi anemia group E protein | FANCE_HUMAN 1-536  
F | Fanconi anemia group F protein | FANCF_HUMAN 1-374  
G H | Fanconi anemia group G protein | FANCG_HUMAN 1-622  
L M | E3 ubiquitin-protein ligase FANCL | FANCL_HUMAN 1-375  
P Q | Fanconi anemia core complex-associated protein 100 | FP100_HUMAN 1-881  
W | Fanconi anemia core complex-associated protein 20 |   
  
Non-standard residues in 7kzp.cif #3  
---  
ZN — zinc ion  
  

> show #!3 target m

> hide #3 target a

> show #3 target c

> split #3 /A

Split 7kzp.cif (#3) into 14 models  
Chain information for 7kzp.cif A #3.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 7kzp.cif B #3.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 7kzp.cif C #3.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 7kzp.cif E #3.4  
---  
Chain | Description  
E | No description available  
  
Chain information for 7kzp.cif F #3.5  
---  
Chain | Description  
F | No description available  
  
Chain information for 7kzp.cif G #3.6  
---  
Chain | Description  
G | No description available  
  
Chain information for 7kzp.cif H #3.7  
---  
Chain | Description  
H | No description available  
  
Chain information for 7kzp.cif L #3.8  
---  
Chain | Description  
L | No description available  
  
Chain information for 7kzp.cif M #3.9  
---  
Chain | Description  
M | No description available  
  
Chain information for 7kzp.cif O #3.10  
---  
Chain | Description  
O | No description available  
  
Chain information for 7kzp.cif P #3.11  
---  
Chain | Description  
P | No description available  
  
Chain information for 7kzp.cif Q #3.12  
---  
Chain | Description  
Q | No description available  
  
Chain information for 7kzp.cif S #3.13  
---  
Chain | Description  
S | No description available  
  
Chain information for 7kzp.cif W #3.14  
---  
Chain | Description  
W | No description available  
  

> color #3/H magenta target c

> color #3/I blue target c

[Repeated 1 time(s)]

> show #3/H :227 target a

> close #2

> close #3

> show #!1 target m

[Repeated 2 time(s)]

> view #1 :300 clip false

> save /Users/sdvorkin/Kinases/ERK2/5x_Cys_Mut/ERK2_AF_5xCys.cxs

——— End of log from Tue Jul 15 13:44:49 2025 ———

opened ChimeraX session  

> show #1 :333 target a

> show #1 :126, 72 target a

> show #1 :126, 95, 217 target a

> color #1 :126, 95, 217 blue target a

> color #1 :198, 256 lime green target a

> show #1 :198, 256 target a

> show #1 :116, 149, 170, 234, 242 target a

> color #1 :116, 149, 170, 234, 242 magenta target a

> color #1 :116, 146, 170, 234, 242 magenta target a

> show #1 :116, 146, 170, 234, 242 target a

> hide :149 target a

> show :209 target a

> color :209 black target a

> show :145, 173 target a

> show :110 target a

> color :110 black target a

> label :146

> label :209

> show :174

> lable :145

Unknown command: lable :145  

> label :145

> label :173

> label :174

> label :352

> show :352

> show :352 target a

> show :347, 343 target a

> label :347, 343

> label :63, 68

> show :63, 68 target a

> show :69 target a

> label :69

> show :199 target a

> label :199 attribute

Missing "attribute" keyword's argument  

> label :333

> show :184 target a

> label :184

> label :188

> show :188

> show :185, 189 190, 181 195 target a

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show :185, 189 190, 181, 195 target a

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show :185, 189, 190, 181, 195 target a

> label :185, 189, 190, 181, 195

> label :185, 189, 190, 181, 195, 170

> label :185, 189, 190, 181, 195, 170, 198

> label :185, 189, 190, 181, 195, 170, 198, 256

> label :185, 189, 190, 181, 195, 170, 198, 256, 200, 203

> show :185, 189, 190, 181, 195, 170, 198, 256, 200, 203 target a

> hide :203 target a

> label :255 target a

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label :255

> label :313

> label :127

> label :110

> label :199

> label :118, 74

> label :116

> label :68

> show :68 target a

> show :ile, val, thr, ala, mat, leu target a

> color :ile, val, thr, ala, mat, leu tan target a

> color :256, 198, 166, 170, 234, 242, 262, 181, 185, 190, 171, 174, 189, 260,
> 307 red target a

> color :cys grey target a

> color :209, 173, 146, 145, 199, 333 gold target a

> label :335, 338, 346

> label :31, 49

> label :26, 28

> label :160

> label :159

> label :75

> label :ala

> label :264

> label :met4

> label :met

> show :met

> label :244

> save /Users/sdvorkin/Kinases/ERK2/5x_Cys_Mut/ERK2_AF_5xCys.cxs

> save /Users/sdvorkin/Kinases/ERK2/5x_Cys_Mut/Fig_ERK2_AF_5xCys.cxs

> hide :ile, leu, val, mat, thr, ala target a

> color :ile, leu, val, mat, thr, ala target tan ca

Invalid "target" argument: Character 't' is not an allowed target, must be one
of acrsbmpfl  

> color :ile, leu, val, mat, thr, ala target tan ac

Invalid "target" argument: Character 't' is not an allowed target, must be one
of acrsbmpfl  

> color :ile, leu, val, mat, thr, ala tan target ac

> ~label #1 residues

> hide :ile, leu, val, met, thr, ala target a

> color :cys red target a

> hide :40, 216 target a

> show :143 target a

> show :145 target a

> show :145, 198, 209 target a

> show :val target a

> color :val magenta target a

> color :val cyan target a

> hide :val target a

> hide :145, 198, 209 target a

> hide :1-11 target ac

> show :145 target a

> save /Users/sdvorkin/Desktop/image1.png supersample 3

> save /Users/sdvorkin/Desktop/image2.png supersample 3

> show :145, 198, 209 target a

> color :198, 209 gold target a

> save /Users/sdvorkin/Desktop/image3.png supersample 3

> save /Users/sdvorkin/Desktop/image4.png supersample 3

> save /Users/sdvorkin/Kinases/ERK2/5x_Cys_Mut/Fig_ERK2_AF_5xCys.cxs

——— End of log from Thu Jul 17 13:26:02 2025 ———

opened ChimeraX session  

> view :127 clip false

> view :307 clip false

> show :307 target a

> show :145, 146, 174, 188, 209 target a

> label :145, 146, 174, 188, 209 target a

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label :145, 146, 174, 188, 209

> open /Users/sdvorkin/Kinases/ERK2/Erk2_PDBs/5v60.pdb

5v60.pdb title:  
Phospho-ERK2 bound to amp-PCP [more info...]  
  
Chain information for 5v60.pdb #2  
---  
Chain | Description | UniProt  
A | mitogen-activated protein kinase 1 | MK01_HUMAN 8-360  
  
Non-standard residues in 5v60.pdb #2  
---  
ACP — phosphomethylphosphonic acid adenylate ester (adenosine-5'-[β,
γ-methylene]triphosphate)  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MG — magnesium ion  
  

> matchmaker #1 to # 2

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 5v60.pdb, chain A (#2) with Erk2_AF-P28482-F1-model_v4.pdb, chain A
(#1), sequence alignment score = 1753.3  
RMSD between 321 pruned atom pairs is 0.736 angstroms; (across all 349 pairs:
1.743)  
  

> show #2 :145, 146, 174, 188, 209 target a

> hide #!1 models

> hide #2 :GOL, MG target a

> hide #2 :GOL, MG, HOH target a

> hide #2 target a

> show #2 :145, 146, 174, 188, 209 target a

> color #2 :145, 146, 174, 188, 209 red target a

> label #2 :145, 146, 174, 188, 209

> show #!1 models

> color #2 :145, 146, 174, 188, 209, 198 red target a

> show #2 :145, 146, 174, 188, 209, 198 target a

> label #2 :145, 146, 174, 188, 209

> label #1 :289

> undo

> show #2 :198

> label #2 :198

> show #2 :184

> color #2 :184 red target a

> color #1 :184 gold target a

> show #1 :184

> label #1 :184

> label #2 :184

> color #1 :174 gold target a

> show #1,2 :val, leu, thr, ala target a

> show #1,2 :val, leu, thr, ala, ile target a

> label #1,2 :74

> label #1,2 :173

> color #1 :173 gold target a

> color #2 :173 red target a

> show #1,2 :val, leu, thr, ala, met target a

> label #1,2 :256

> label #1,2 :281

> undo

> label #1,2 :181

> label #1,2 :137

> label #1,2 :90

> label #1,2 :21, 28

> label #1,2 :21, 28, 53, 104

> undo

> show #1,2 :val, leu, thr, ala, met target a

> hide #1 :1-8 target ac

> hide #1 :1-11 target ac

> show #1,2 :val, leu, thr, ala, met, ile target a

> hide #1 :1-11 target ac

> ~label #1-2 residues

> label #1 :21, 28, 53, 104, 90

> label #1 :21, 28, 53, 104, 90, 51

> label #1 :188, 173, 143, 145, 146, 148, 181

> label #1 :188, 173, 143, 145, 146, 148, 181, 234

> label #1 :188, 173, 143, 145, 146, 148, 181, 234, 256

> label #1 :188, 173, 143, 145, 146, 148, 181, 234, 256, 199, 333

> label #1 :188, 173, 143, 145, 146, 148, 181, 234, 256, 199, 333, 184, 185,
> 209, 198

> label #1 :188, 173, 143, 145, 146, 148, 181, 234, 256, 199, 333, 184, 185,
> 209, 198, 206

> label # :184, 181, 173

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label #2 :184, 181, 173

> label #2 :241, 264, 267, 237, 200

> label #2 :241, 264, 267, 237, 200, 255, 252

> label #2 :241, 264, 267, 237, 200, 255, 252, 265

> label #2 :74

> label #2 :170

> label #2 :188

> label #2 :115

> show :#2 :148 target a

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #2 :148 target a

> label #2 :189

> label #1 :189

> label #1 :108

> show #1 :157 target a

> label #1 :157

> show #1 :308 target a

> label #1 :308

> show #1,2 :thr

> show #1,2 :thr target a

> label #1 :166, 163

> label #1 :244,127,254

> label #1 :244,127,254, 227, 278

> label #1 :244,127,254, 227, 278, 273

> label #1 :244,127,254, 227, 278, 273, 243

> label #1 :244,127,254, 227, 278, 273, 243, 294

> label #1 ::338

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label #1 :338

> label #1 :345

> undo

> label #1 :349, 335

> label #1 :346

> label #1 :69

> label #1 :343

> label #1 :356

> label #1 :256

> label #1 :351

> label #1 :83

> show #1 :30 target a

> show #2 :30 target a

> show #2 :78 target a

> view #2 :294 clip false

> save /Users/sdvorkin/Kinases/ERK2/Erk2_PDBs/Erk2_AF_vs5v60.cxs

——— End of log from Tue Aug 26 09:17:22 2025 ———

opened ChimeraX session  

> hide #!2 models

> color #1 tan target ac

> color #1 :ile,leu,val,met,thr,ala green target a

> color :65,127,166,254 cyan target a

> color :127,254 blue target a

> color :143,171,174,189,195 red target a

> color :74 gold target a

> ~label #1 residues

> color :159,160 gold target a

> color :181 gold target a

> color :185, 190 red target a

> hide #1:phe,tyr target a

> save /Users/sdvorkin/Desktop/image1.png supersample 3

> save /Users/sdvorkin/Desktop/image2.png supersample 3

> hide #1 models

> show #!2 models

> hide #2:phe,tyr target a

> color #2 tan target c

> color #2 tan target ac

> ~label #2 residues

> show #1 models

> hide #1 models

> color #2 :ile,leu,val,met,thr,ala green target a

> color #2 :65,127,166,254 cyan target a

> color#2 :127,254 blue target a

Unknown command: color#2 :127,254 blue target a  

> color #2 :127,254 blue target a

> show #2 :65,127,166,254 target a

> color #2 :143,171,174,189,195 red target a

> color :74 gold target a

> color :159,160, 181 gold target a

> color :185, 190 red target a

> hide :148

> color :167-198 medium orchid target c

> color :59-76 chocolate target c

> save /Users/sdvorkin/Desktop/image3.png supersample 3

> hide #2 :1-166, 199-end target ac

> undo

> hide #2 :1-143, 148-166, 199-206, 219-end target ac

> save /Users/sdvorkin/Desktop/image4.png supersample 3

> save /Users/sdvorkin/Desktop/image5.png supersample 3

> hide #1 :1-143, 148-166, 199-206, 219-end target ac

> show #1 target m

> hide #!2 target m

> save /Users/sdvorkin/Desktop/image6.png supersample 3

> save /Users/sdvorkin/Desktop/image7.png supersample 3

> show #1 target m

> show #1#!2 target m

> hide #!2 models

> hide #1 models

> show #!2 models

> save /Users/sdvorkin/Desktop/image8.png supersample 3

> show #1 models

> hide #!2 models

> show #!2 models

> hide #1 models

> save /Users/sdvorkin/Desktop/image9.png supersample 3

> show :181, 185 target a

> save /Users/sdvorkin/Kinases/ERK2/Erk2_PDBs/hErk2_A_Loop_5v60_AF.cxs

——— End of log from Wed Sep 3 11:26:32 2025 ———

opened ChimeraX session  

> open /Users/sdvorkin/Kinases/ERK2/Erk2_PDBs/5UMO.cif

5UMO.cif title:  
Structure of extracellular signal-regulated kinase [more info...]  
  
Chain information for 5UMO.cif #3  
---  
Chain | Description | UniProt  
A | Mitogen-activated protein kinase 1 | MK01_RAT 4-354  
  
Non-standard residues in 5UMO.cif #3  
---  
SO4 — sulfate ion  
  

> matchmaker #3 to #2

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 5v60.pdb, chain A (#2) with 5UMO.cif, chain A (#3), sequence
alignment score = 1768.6  
RMSD between 274 pruned atom pairs is 0.855 angstroms; (across all 343 pairs:
2.341)  
  

> open /Users/sdvorkin/Kinases/ERK2/Erk2_PDBs/4S31.cif

4S31.cif title:  
Crystal structure of mitogen-activated protein kinase 1 wtERK2 at 1.45A [more
info...]  
  
Chain information for 4S31.cif #4  
---  
Chain | Description | UniProt  
A | Mitogen-activated protein kinase 1 | MK01_RAT 1-358  
  

> matchmaker #5 to #2

No molecules/chains to match specified  

> matchmaker #4 to #2

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 5v60.pdb, chain A (#2) with 4S31.cif, chain A (#4), sequence
alignment score = 1767.4  
RMSD between 287 pruned atom pairs is 0.898 angstroms; (across all 343 pairs:
2.368)  
  

> hide #!4 models

> hide #!3 models

> show #2 target c

> show #!3 models

> show #!4 models

> hide #!2 models

> hide #!3 models

> show #!3 models

> hide #!4 models

> hide #!3 models

> show #!3 models

> show #!4 models

> hide #!4 models

> show #!4 models

> show #2-4 :168 target c

> show #2-4 :168 target a

> show #2-4 :169 target a

> show #2-4 :167 target a

> hide #2-4 :167-169 target a

> hide #2-4 :166 target a

> show #2-4 :166 target a

> show #!2 models

> hide #2 :166 target a

> show #2 :168 target a

> show #3-4 :168 target a

> hide #!3-4 target m

> show #2:argtarget atoms

> show #2:arg target a

> show #2:190 target a

> show #2:187 target a

> open /Users/sdvorkin/Kinases/ERK2/Erk2_PDBs/rat_ERK2_PDBS/2erk.pdb

2erk.pdb title:  
Phosphorylated map kinase ERK2 [more info...]  
  
Chain information for 2erk.pdb #5  
---  
Chain | Description | UniProt  
A | extracellular signal-regulated kinase 2 | MK01_RAT 1-358  
  

> matchmaker #5 to #2

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 5v60.pdb, chain A (#2) with 2erk.pdb, chain A (#5), sequence
alignment score = 1776.4  
RMSD between 333 pruned atom pairs is 0.609 angstroms; (across all 349 pairs:
0.859)  
  

> show #5:180-190 target a

> show #2:180-190 target a

> show #5:207, 196 target a

> show #5:arg target a

> show #5:179 target a

> color #2 light blue target c

> show #!3 models

> open /Users/sdvorkin/Kinases/ERK2/Erk2_PDBs/rat_ERK2_PDBS/4gt3.pdb

4gt3.pdb title:  
ATP-bound form of the ERK2 kinase [more info...]  
  
Chain information for 4gt3.pdb #6  
---  
Chain | Description | UniProt  
A | mitogen-activated protein kinase 1 | MK01_RAT 1-358  
  
Non-standard residues in 4gt3.pdb #6  
---  
ATP — adenosine-5'-triphosphate  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MG — magnesium ion  
PEG — di(hydroxyethyl)ether  
  

> matchmaker #6 to #2

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 5v60.pdb, chain A (#2) with 4gt3.pdb, chain A (#6), sequence
alignment score = 1788.4  
RMSD between 308 pruned atom pairs is 0.920 angstroms; (across all 348 pairs:
2.124)  
  

> hide target a

> show :ile,val,thr,tyr,arg,ala,leu target a

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> color #2 light blue target ac

> show #!4 models

> hide #!4 models

> open /Users/sdvorkin/Downloads/4GSB.cif

4GSB.cif title:  
Monoclinic crystal form of the apo-ERK2 [more info...]  
  
Chain information for 4GSB.cif #7  
---  
Chain | Description | UniProt  
A | Mitogen-activated protein kinase 1 | MK01_RAT 1-358  
  
Non-standard residues in 4GSB.cif #7  
---  
CSO — S-hydroxycysteine  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
PGE — triethylene glycol  
SO4 — sulfate ion  
  

> matchmaker #7 to #2

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 5v60.pdb, chain A (#2) with 4GSB.cif, chain A (#7), sequence
alignment score = 1775.3  
RMSD between 302 pruned atom pairs is 0.902 angstroms; (across all 345 pairs:
2.161)  
  

> show :ile,val,thr,tyr,arg,ala,leu target a

> hide start-160 target ac

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide :start-160 target ac

> hide :220-end target ac

> show #!4 models

> show #1 models

> hide #1 models

> color #3 #94f394ff

> color #4 #b1a9ecff

> color #4 #a697ecff

> color #2 #d3ffffff

> color #2 #a4fefaff

> color #2 #85f5feff

> color #6 #c8db45ff

> color #6 #d7db87ff

> color #5 #efb79bff

> color #5 #ef9d86ff

> color #5 #efa196ff

> color #7 #ed96cdff

> color #7 #ed93c9ff

> color #1 #653f74ff

> color #1 #6b437aff

> color #1 #06047aff

> color #1 #767a76ff

> color #1 #76767aff

> color #1 #353537ff

> show #1 models

> color #1 #707074ff

> hide #1 models

> hide #!2 models

> hide #5 models

> show #!2 models

> show #5 models

> save /Users/sdvorkin/Kinases/ERK2/Erk2_PDBs/Aloop_Sept082025.cxs

> hide #!2 models

> hide #!7 models

> show #!7 models

> hide #5 models

> lighting full

> save /Users/sdvorkin/Desktop/image36.png supersample 3

> save /Users/sdvorkin/Desktop/image37.png supersample 3

> hide #5#!3-4,6-7 target m

> show #!2 models

> show #!6 models

> hide #!6 models

> show #5 models

> save /Users/sdvorkin/Desktop/image38.png supersample 3

> save /Users/sdvorkin/Desktop/image39.png supersample 3

> show target c

> show :arg target a

> show :thr, tyr target a

> show #1 models

> hide #1 models

> show #!3 models

> show #!4 models

> show #!6 models

> show #!7 models

> hide #5 models

> hide #!2 models

> hide #5#!3-4,6-7 target m

> show #!2 models

> hide target a

> show :187 target a

> show #!3 models

> show #!4 models

> hide #!3 models

> hide #!4 models

> show :arg target a

> show :185 target a

> hide #!2 models

> show #!3 models

> show #!2 models

> show #!4 models

> show #5 models

> show #!6 models

> show #!7 models

> show #5 :183 target a

> save /Users/sdvorkin/Kinases/ERK2/Erk2_PDBs/Full_Sept082025.cxs

> hide #5#!4,6-7 target m

> hide :220-end target ac

> hide :1-60 target ac

> hide :75-145 target ac

> hide :153-160 target ac

> hide #2 :153-163 target ac

> hide #3 :151-160 target ac

> hide #!3 models

> color TPO red target a

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color :TPO red target a

> color :PTY red target a

> color :PTR red target a

> hide #!2 models

> show #!3 models

> color #3 :183, 185 coral target a

> show #3 :183, 185 target a

> show #!2 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> show # :195, 209, 198, 188, 184 target a

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #2 :195, 209, 198, 188, 184 target a

> show #3 :193, 207, 196, 186, 182 target a

> show #!3 models

> hide #!2 models

> save /Users/sdvorkin/Desktop/image40.png supersample 3

> show #!2 models

> hide #!3 models

> save /Users/sdvorkin/Desktop/image41.png supersample 3

> show #!3 models

> save /Users/sdvorkin/Desktop/image42.png supersample 3

> save /Users/sdvorkin/Desktop/image43.png supersample 3

[Repeated 1 time(s)]

> hide #!2 models

> save /Users/sdvorkin/Desktop/image44.png supersample 3

> show #!2 models

> hide #!3 models

> save /Users/sdvorkin/Desktop/image45.png supersample 3

> show #!3 models

> save /Users/sdvorkin/Kinases/ERK2/Erk2_PDBs/Aloop_2_Sept082025.cxs

——— End of log from Fri Sep 5 15:44:15 2025 ———

opened ChimeraX session  

> hide #!3 models

> show #2 target c

> hide #2 target a

> show #2: leu,val,met,ile target a

> color #2 grey target ac

> color #2: 209,198,333,199,108 magenta target a

> color #2: 338 , 335, 347, 256, 243, 240, 200, 157, 133, 90, 89, 86, 83, 74
> orange target a

> color #2: 84, 75, 69 red target a

> show #2: 168 target a

> color #2: 168 lime target a

> show #2: 185, 187 target a

> color #2: 185, 187 lime target a

> save /Users/sdvorkin/Desktop/image1.png supersample 3

> save /Users/sdvorkin/Desktop/image2.png supersample 3

> color #2: 76, 211 dodger blue target a

> save /Users/sdvorkin/Kinases/ERK2/Erk2_PDBs/4xCys_2p_CSPs_5v60.cxs

——— End of log from Mon Oct 27 14:42:46 2025 ———

opened ChimeraX session  

> color #2 light grey target ac

> show #2 :337, 336 target a

> color #2 :337, 336 cyan target a

> show #2 :71 target a

> color #2 :71 dodger blue target a

> color #2 :611 medium orchid target a

> color #2 :161 medium orchid target a

> show #2 :161 target a

> undo

[Repeated 1 time(s)]

> color #2 :346 medium orchid target a

> color #2 :352 medium orchid target a

> show #2 :352 target a

> color #2 :328-335 hot pink target c

> color #2 :335 lime target a

> show #!3 models

> show #3 :start-end target c

> color #3 light grey target ac

> hide #!2 models

> hide #2 target a

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> hide #3 target a

> show #3 :ile,val,met,thr,ala,leu

> renumber #3 start 6

523 residues renumbered  

> show #!2 models

> color #3 :335 lime target a

> color #3 :346 medium orchid target a

> color #3 :328-335 hot pink target c

> color #2,3 :333 lightblue orange target c

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #2,3 :333 orange target c

> color #2,3 :333 orange target a

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 150, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1178, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 58, 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 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 150, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1178, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 58, 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 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 150, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1178, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 58, 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 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 150, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1178, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 58, 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 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 2525, in res_hover  
_residue_mouse_hover(pick, session.logger)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 2518, in _residue_mouse_hover  
log.status("chain %s: %s" % (chain.chain_id, chain.description))  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/logger.py", line 459, in status  
StatusLogger.status(self, msg, **kw)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/logger.py", line 199, in status  
if l.status(msg, color, secondary) and getattr(l, "excludes_other_logs",
True):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 877, in status  
sbar.status(msg, color, secondary)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 150, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1178, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
Error processing trigger "mouse hover":  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1023, in <lambda>  
quit_action.triggered.connect(lambda *, s=self, sess=session:
s.file_quit_cb(sess))  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 672, in file_quit_cb  
session.ui.quit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 357, in quit  
log.status("Exiting ...", blank_after=0)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/logger.py", line 459, in status  
StatusLogger.status(self, msg, **kw)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/logger.py", line 199, in status  
if l.status(msg, color, secondary) and getattr(l, "excludes_other_logs",
True):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 877, in status  
sbar.status(msg, color, secondary)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 150, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1178, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 58, 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 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  

> save /Users/sdvorkin/ERK2_assignments.cxs

——— End of log from Tue Dec 9 08:36:39 2025 ———

> view name session-start

opened ChimeraX session  

> color #2,3 light grey target ac

> hide #!3 models

> color #2 :140, 74 hot pink target ac

> show #!3 models

> hide #!2 models

> color #2 :209, 74 hot pink target ac

> show #!2 models

> hide #!3 models

> color #2,3 light grey target ac

> color #2 :209, 74 hot pink target ac

> color #2 :209, 74, 140, 165 hot pink target ac

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.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-1.10.1.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-1.10.1.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-1.10.1.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-1.10.1.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-1.10.1.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-1.10.1.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-1.10.1.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-1.10.1.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-1.10.1.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-1.10.1.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-1.10.1.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-1.10.1.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-1.10.1.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-1.10.1.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: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac Studio
      Model Identifier: Mac13,1
      Model Number: MJMV3LL/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 13822.41.1
      OS Loader Version: 13822.41.1

Software:

    System Software Overview:

      System Version: macOS 26.1 (25B78)
      Kernel Version: Darwin 25.1.0
      Time since boot: 7 days, 14 hours, 28 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 24
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        DELL U3219Q:
          Resolution: 6720 x 3780
          UI Looks like: 3360 x 1890 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        DELL U3223QE:
          Resolution: 6720 x 3780
          UI Looks like: 3360 x 1890 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    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: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    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
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    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-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    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: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

[Tom Goddard]

macOS 26, two external Dell displays. Probably Qt 6.9 bug.