id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20605 glClear: invalid framebuffer operation drawing scene pujanajmera1@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.4-arm64-arm-64bit ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC) Description I simply kept the window open for a day and this error occurred. Last time I had something similar, I was suggested to upgrade to 1.12 but clearly this does not work Log: UCSF ChimeraX version: 1.12 (2026-06-12) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cred1/914_9FPG_run5_stripwat_conect.pdb /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cred1/625_9FPG_run5_stripwat_conect.pdb > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cred1/574_9FPG_run2_stripwat_conect.pdb /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cred1/432_9FPG_run1_stripwat_conect.pdb > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cred1/317_9FPG_run1_stripwat_conect.pdb /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cred1/244_9FPG_run4_stripwat_conect.pdb > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cred1/149_9FPG_run5_stripwat_conect.pdb /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cred1/317_9FPG_run1_esp_C.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cred1/432_9FPG_run1_esp_C.bild /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cred1/574_9FPG_run2_esp_C.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cred1/149_9FPG_run5_esp_C.bild /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cred1/914_9FPG_run5_esp_C.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cred1/244_9FPG_run4_esp_C.bild /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cred1/625_9FPG_run5_esp_C.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cred1/317_9FPG_run1_esp_B.bild /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cred1/432_9FPG_run1_esp_B.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cred1/574_9FPG_run2_esp_B.bild /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cred1/149_9FPG_run5_esp_B.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cred1/914_9FPG_run5_esp_B.bild /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cred1/244_9FPG_run4_esp_B.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cred1/625_9FPG_run5_esp_B.bild Chain information for 914_9FPG_run5_stripwat_conect.pdb #1 --- Chain | Description ? | No description available ? | No description available Chain information for 625_9FPG_run5_stripwat_conect.pdb #2 --- Chain | Description ? | No description available ? | No description available Chain information for 574_9FPG_run2_stripwat_conect.pdb #3 --- Chain | Description ? | No description available ? | No description available Chain information for 432_9FPG_run1_stripwat_conect.pdb #4 --- Chain | Description ? | No description available ? | No description available Chain information for 317_9FPG_run1_stripwat_conect.pdb #5 --- Chain | Description ? | No description available ? | No description available Chain information for 244_9FPG_run4_stripwat_conect.pdb #6 --- Chain | Description ? | No description available ? | No description available Chain information for 149_9FPG_run5_stripwat_conect.pdb #7 --- Chain | Description ? | No description available ? | No description available Computing secondary structure [Repeated 6 time(s)]Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1329 objects Opened BILD data containing 1330 objects > style stick Changed 132265 atom styles > rename #8 id #5 > rename #15 id #5 > rename #9 id #4 > rename #16 id #4 > rename #11 id #7 > rename #18 id #7 > rename #20 id #6 > rename #13 id #6 > rename #10 id #3 > rename #17 id #3 > rename #14 id #2 > rename #21 id #2 > rename #12 id #1 > rename #19 id #1 > open /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cint/830_9FPG-Cint_run4_stripwat_conect.pdb > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG-Cint/95_9FPG- > Cint_run5_stripwat_conect.pdb /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cint/578_9FPG-Cint_run1_stripwat_conect.pdb > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cint/552_9FPG-Cint_run1_stripwat_conect.pdb > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cint/475_9FPG-Cint_run4_stripwat_conect.pdb > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cint/133_9FPG-Cint_run4_stripwat_conect.pdb > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG-Cint/95_9FPG- > Cint_run5_esp_B.bild /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG- > ESP/9FPG-Cint/578_9FPG-Cint_run1_esp_B.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cint/830_9FPG-Cint_run4_esp_B.bild /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cint/552_9FPG-Cint_run1_esp_B.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cint/133_9FPG-Cint_run4_esp_B.bild /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cint/475_9FPG-Cint_run4_esp_B.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG-Cint/95_9FPG- > Cint_run5_esp_C.bild /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG- > ESP/9FPG-Cint/830_9FPG-Cint_run4_esp_C.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cint/552_9FPG-Cint_run1_esp_C.bild /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cint/475_9FPG-Cint_run4_esp_C.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cint/133_9FPG-Cint_run4_esp_C.bild /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cint/578_9FPG-Cint_run1_esp_C.bild Chain information for 830_9FPG-Cint_run4_stripwat_conect.pdb #8 --- Chain | Description ? | No description available ? | No description available Chain information for 95_9FPG-Cint_run5_stripwat_conect.pdb #9 --- Chain | Description ? | No description available ? | No description available Chain information for 578_9FPG-Cint_run1_stripwat_conect.pdb #10 --- Chain | Description ? | No description available ? | No description available Chain information for 552_9FPG-Cint_run1_stripwat_conect.pdb #11 --- Chain | Description ? | No description available ? | No description available Chain information for 475_9FPG-Cint_run4_stripwat_conect.pdb #12 --- Chain | Description ? | No description available ? | No description available Chain information for 133_9FPG-Cint_run4_stripwat_conect.pdb #13 --- Chain | Description ? | No description available ? | No description available Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1329 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1328 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Computing secondary structure [Repeated 5 time(s)] > style stick Changed 245635 atom styles > rename #14 id #9 > rename #20 id #9 > rename #16 id #8 > rename #21 id #8 > rename #22 id #11 > rename #17 id #11 > rename #15 id #10 > rename #25 id #10 > rename #24 id #13 > rename #18 id #13 > rename #19 id #12 > rename #23 id #12 > align #13@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.227 angstroms > align #12@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.120 angstroms > align #11@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.155 angstroms > align #10@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.362 angstroms > align #9@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.217 angstroms > align #8@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.211 angstroms > align #10@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.362 angstroms > align #9@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.217 angstroms > align #8@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.211 angstroms > align #7@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.059 angstroms > align #7@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.059 angstroms > align #6@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.046 angstroms > align #5@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.056 angstroms > align #4@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.031 angstroms > align #3@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.079 angstroms > align #2@CA toAtoms #1@CA RMSD between 1266 atom pairs is 0.907 angstroms > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!8 models > hide #!7 models > hide #!9 models > hide #!10 models > hide #!11 models > hide #!12 models > hide #!13 models > hide #1.2 models > show #1.2 models > hide #1.2 models > show #1.2 models > hide #1.2 models > show #1.2 models > hide #1.2 models > close #1.2 > hide #1.1 models > show #1.1 models > hide #1.1 models > show #1.1 models > hide #1.1 models > show #1.1 models > hide #1.3 models > hide #1.4 models > delete atoms sel > delete bonds sel > delete bonds > select clear > hide #!1 models > show #!2 models > close #1-2#3-13 > open /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cint/830_9FPG-Cint_run4_stripwat_conect.pdb Chain information for 830_9FPG-Cint_run4_stripwat_conect.pdb #1 --- Chain | Description ? | No description available ? | No description available Computing secondary structure > style stick Changed 18895 atom styles > style ball Changed 18895 atom styles > style stick Changed 18895 atom styles > close > open /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cint/830_9FPG-Cint_run4_stripwat_conect.pdb > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG-Cint/95_9FPG- > Cint_run5_stripwat_conect.pdb /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cint/578_9FPG-Cint_run1_stripwat_conect.pdb > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cint/552_9FPG-Cint_run1_stripwat_conect.pdb > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cint/475_9FPG-Cint_run4_stripwat_conect.pdb > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cint/133_9FPG-Cint_run4_stripwat_conect.pdb > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG-Cint/95_9FPG- > Cint_run5_esp_B.bild /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG- > ESP/9FPG-Cint/578_9FPG-Cint_run1_esp_B.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cint/830_9FPG-Cint_run4_esp_B.bild /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cint/552_9FPG-Cint_run1_esp_B.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cint/133_9FPG-Cint_run4_esp_B.bild /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cint/475_9FPG-Cint_run4_esp_B.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG-Cint/95_9FPG- > Cint_run5_esp_C.bild /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG- > ESP/9FPG-Cint/830_9FPG-Cint_run4_esp_C.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cint/552_9FPG-Cint_run1_esp_C.bild /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cint/475_9FPG-Cint_run4_esp_C.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cint/133_9FPG-Cint_run4_esp_C.bild /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cint/578_9FPG-Cint_run1_esp_C.bild Chain information for 830_9FPG-Cint_run4_stripwat_conect.pdb #1 --- Chain | Description ? | No description available ? | No description available Chain information for 95_9FPG-Cint_run5_stripwat_conect.pdb #2 --- Chain | Description ? | No description available ? | No description available Chain information for 578_9FPG-Cint_run1_stripwat_conect.pdb #3 --- Chain | Description ? | No description available ? | No description available Chain information for 552_9FPG-Cint_run1_stripwat_conect.pdb #4 --- Chain | Description ? | No description available ? | No description available Chain information for 475_9FPG-Cint_run4_stripwat_conect.pdb #5 --- Chain | Description ? | No description available ? | No description available Chain information for 133_9FPG-Cint_run4_stripwat_conect.pdb #6 --- Chain | Description ? | No description available ? | No description available Computing secondary structure [Repeated 5 time(s)]Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1329 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1328 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects > rename #7 id #2 > rename #13 id #2 > rename #9 id #1 > rename #14 id #1 > rename #10 id #4 > rename #15 id #4 > rename #18 id #3 > rename #8 id #3 > rename #11 id #6 > rename #17 id #6 > rename #12 id #5 > rename #16 id #5 > style stick Changed 113370 atom styles > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > show #!6 models > show #!5 models > show #!4 models > show #!3 models > show #!2 models > align #2@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.161 angstroms > align #3@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.327 angstroms > align #4@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.276 angstroms > align #5@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.024 angstroms > align #6@CA toAtoms #1@CA RMSD between 1266 atom pairs is 0.989 angstroms > hide #!2 models > hide #!3 models > hide #!4 models > show #!4 models > hide #!6 models > hide #!5 models > hide #!4 models > close #1.2 > close #2.2 > close #3.2 > close #4.2 > close #5.2 > close #6.2 > delete sel > select clear > delete atoms sel > delete bonds sel > hide #1.4 models > hide #1.3 models > show #1.3 models > show #1.4 models > hide #1.4 models > hide #1.3 models > show #1.3 models > show #1.4 models > hide #1.4 models > hide #1.3 models > show #1.3 models > show #1.4 models > hide #1.4 models > hide #1.3 models > show #1.3 models > show #1.4 models > hide #!1 models > show #!2 models > delete atoms sel > delete bonds sel > select clear > show #!3 models > hide #!2 models > select clear > delete atoms sel > delete bonds sel > select clear > show #!4 models > hide #!3 models > delete atoms sel > delete bonds sel > show #!5 models > hide #!4 models > select clear [Repeated 1 time(s)] > delete atoms sel > delete bonds sel > show #!6 models > hide #!5 models > delete atoms sel > delete bonds sel > delete atoms sel > delete bonds sel > select add #6.3 1 model selected > select add #6.4 2 models selected > view sel > show #!5 models > hide #!6 models > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > select ::name=""MET"" 3468 atoms, 3264 bonds, 204 residues, 6 models selected > select clear > select #5/?:851 17 atoms, 16 bonds, 1 residue, 1 model selected > show sel target ab > hide sel target a > select clear > select ::name=""ALA"" 9480 atoms, 8652 bonds, 948 residues, 6 models selected > hide (#!5 & sel) target a > select ::name=""ASN"" 4536 atoms, 4224 bonds, 324 residues, 6 models selected > hide (#!5 & sel) target a > select ::name=""GLN"" 3492 atoms, 3300 bonds, 204 residues, 6 models selected > hide (#!5 & sel) target a > select ::name=""MET"" 3468 atoms, 3264 bonds, 204 residues, 6 models selected > hide (#!5 & sel) target a > select clear > select ::name=""SER"" 3300 atoms, 3012 bonds, 300 residues, 6 models selected > hide (#!5 & sel) target a > select clear > select ::name=""ARG"" 7200 atoms, 6924 bonds, 300 residues, 6 models selected > hide (#!5 & sel) target a > select ::name=""ILE"" 9804 atoms, 9312 bonds, 516 residues, 6 models selected > hide (#!5 & sel) target a > select > ::name=""ALA""::name=""ARG""::name=""ASH""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLH""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HID""::name=""HIP""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 111348 atoms, 112068 bonds, 7440 residues, 6 models selected > hide (#!5 & sel) target a > select clear > show #!6 models > hide #!5 models > show #!5 models > show #!4 models > show #!3 models > show #!2 models > hide #!2 models > show #!1 models > show #!2 models > select > ::name=""ALA""::name=""ARG""::name=""ASH""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLH""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HID""::name=""HIP""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 111348 atoms, 112068 bonds, 7440 residues, 6 models selected > hide sel target a > select clear > open /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cred1/914_9FPG_run5_stripwat_conect.pdb /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cred1/625_9FPG_run5_stripwat_conect.pdb > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cred1/574_9FPG_run2_stripwat_conect.pdb /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cred1/432_9FPG_run1_stripwat_conect.pdb > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cred1/317_9FPG_run1_stripwat_conect.pdb /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cred1/244_9FPG_run4_stripwat_conect.pdb > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cred1/149_9FPG_run5_stripwat_conect.pdb /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cred1/317_9FPG_run1_esp_C.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cred1/432_9FPG_run1_esp_C.bild /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cred1/574_9FPG_run2_esp_C.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cred1/149_9FPG_run5_esp_C.bild /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cred1/914_9FPG_run5_esp_C.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cred1/244_9FPG_run4_esp_C.bild /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cred1/625_9FPG_run5_esp_C.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cred1/317_9FPG_run1_esp_B.bild /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cred1/432_9FPG_run1_esp_B.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cred1/574_9FPG_run2_esp_B.bild /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cred1/149_9FPG_run5_esp_B.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cred1/914_9FPG_run5_esp_B.bild /Users/pujanajmera/Downloads/9FPG- > chargetransfer/9FPG-ESP/9FPG-Cred1/244_9FPG_run4_esp_B.bild > /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cred1/625_9FPG_run5_esp_B.bild Chain information for 914_9FPG_run5_stripwat_conect.pdb #7 --- Chain | Description ? | No description available ? | No description available Chain information for 625_9FPG_run5_stripwat_conect.pdb #8 --- Chain | Description ? | No description available ? | No description available Chain information for 574_9FPG_run2_stripwat_conect.pdb #9 --- Chain | Description ? | No description available ? | No description available Chain information for 432_9FPG_run1_stripwat_conect.pdb #10 --- Chain | Description ? | No description available ? | No description available Chain information for 317_9FPG_run1_stripwat_conect.pdb #11 --- Chain | Description ? | No description available ? | No description available Chain information for 244_9FPG_run4_stripwat_conect.pdb #12 --- Chain | Description ? | No description available ? | No description available Chain information for 149_9FPG_run5_stripwat_conect.pdb #13 --- Chain | Description ? | No description available ? | No description available Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1330 objects Opened BILD data containing 1329 objects Opened BILD data containing 1330 objects Computing secondary structure [Repeated 6 time(s)] > rename #14 id #11 > rename #21 id #11 > rename #19 id #12 > rename #26 id #12 > rename #17 id #13 > rename #24 id #13 > rename #15 id #10 > rename #22 id #10 > rename #16 id #9 > rename #23 id #9 > rename #20 id #8 > rename #27 id #8 > rename #18 id #7 > rename #25 id #7 > align #7@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.211 angstroms > align #8@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.206 angstroms > align #9@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.224 angstroms > align #10@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.172 angstroms > align #11@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.303 angstroms > align #12@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.154 angstroms > align #13@CA toAtoms #1@CA RMSD between 1266 atom pairs is 1.146 angstroms > select clear > style stick Changed 245635 atom styles > select > ::name=""ALA""::name=""ARG""::name=""ASH""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLH""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HID""::name=""HIP""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 241254 atoms, 242814 bonds, 16120 residues, 13 models selected > hide sel target a > select clear > select add #1.3 1 model selected > select add #1.4 2 models selected > view sel > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!8 models > hide #!9 models > hide #!10 models > hide #!11 models > hide #!12 models > hide #!13 models > close #7.2 > delete atoms sel > delete bonds sel > select clear > hide #!7 models > show #!8 models > delete atoms sel > delete bonds sel > close #8.2 > hide #!8 models > show #!9 models > close #9.2 > delete atoms sel > delete bonds sel > show #!10 models > hide #!9 models > close #10.2 > delete bonds sel [Repeated 1 time(s)] > hide #!10 models > show #!11 models > close #11.2 > delete bonds sel [Repeated 1 time(s)] > hide #!11 models > show #!12 models > delete bonds sel > close #12.2 > delete bonds sel > hide #!12 models > show #!13 models > close #13.2 > delete bonds sel [Repeated 2 time(s)] > hide #!13 models > show #!1 models > view #1-13 clip false > undo > show #!1-13 target m > viewname esp Unknown command: viewname esp > view name esp > select clear > view #1 clip false > view name esp > select add #1.3 1 model selected > select add #1.4 2 models selected > view sel > hide #!1 models > hide #1.4 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6-13 target m > show #!1 models > hide #!1 models > show #!1 models > show #1.4 models > view sel > hide #!1 models > view sel > show #!1 models > show #1#!2-13 target m > transparency 75 target cartoon Invalid ""target"" argument: Character 't' is not an allowed target, must be one of acrsbmpfl > transparency 75 target c > select clear > hide #!2-13 target m > undo [Repeated 4 time(s)] > redo > transparency 0 target c > style #!1 ball Changed 18895 atom styles > style #!1 stick Changed 18895 atom styles > style #!1 sphere Changed 18895 atom styles > style #!1 stick Changed 18895 atom styles > open /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cint/830_9FPG-Cint_run4_esp_B_test.bild Opened BILD data containing 1330 objects > hide #1.3 models > hide #14 models > show #1.3 models > hide #1.3 models > show #14 models > transparency 75 target c > transparency 80 target c > style #!1 ball Changed 18895 atom styles > show #1.3 models > hide #14 models > show #14 models > open /Users/pujanajmera/Downloads/9FPG-chargetransfer/9FPG-ESP/9FPG- > Cint/830_9FPG-Cint_run4_esp_C_test.bild Opened BILD data containing 1328 objects > hide #14 models > hide #1.3 models > hide #1.4 models > hide #15 models > show #15 models > hide #15 models > show #1.4 models > show #15 models > hide #15 models > hide #1.4 models > show #15 models > hide #15 models > style #!1 stick Changed 18895 atom styles > show #15 models > hide #15 models > show #1.4 models > hide #1.4 models > show #15 models > show #1.4 models > hide #15 models > transparency 0 target c > style #!1 ball Changed 18895 atom styles > transparency 75 target c > hide #1.4 models > show #15 models > style #!1 stick Changed 18895 atom styles > hide #15 models > select #1/?:651@FE 1 atom, 1 residue, 1 model selected > select add #1/?:650@S 2 atoms, 2 residues, 1 model selected > select add #1/?:646@NI 3 atoms, 3 residues, 1 model selected > select add #1/?:649@S 4 atoms, 4 residues, 1 model selected > bond sel Created 5 bonds > select #1/?:649@S 1 atom, 1 residue, 1 model selected > select add #1/?:651@FE 2 atoms, 2 residues, 1 model selected > transparency 0 target c > select clear > delete atoms sel > delete bonds sel > select clear > transparency 75 target c > select #1/?:651@FE 1 atom, 1 residue, 1 model selected > select add #1/?:649@S 2 atoms, 2 residues, 1 model selected > bond sel Created 1 bond > select clear > select #1/?:649@S 1 atom, 1 residue, 1 model selected > select add #1/?:646@NI 2 atoms, 2 residues, 1 model selected > bond sel Created 1 bond > select #1/?:646@NI 1 atom, 1 residue, 1 model selected > select add #1/?:650@S 2 atoms, 2 residues, 1 model selected > bond sel Created 1 bond > select #1/?:650@S 1 atom, 1 residue, 1 model selected > select add #1/?:651@FE 2 atoms, 2 residues, 1 model selected > bond sel Created 1 bond > select #1/?:651@FE 1 atom, 1 residue, 1 model selected > select add #1/?:648@S 2 atoms, 2 residues, 1 model selected > bond sel Created 1 bond > select #1/?:648@S 1 atom, 1 residue, 1 model selected > select add #1/?:652@FE 2 atoms, 2 residues, 1 model selected > bond sel Created 1 bond > select #1/?:652@FE 1 atom, 1 residue, 1 model selected > select add #1/?:650@S 2 atoms, 2 residues, 1 model selected > bond sel Created 1 bond > select #1/?:653@FE 1 atom, 1 residue, 1 model selected > select add #1/?:648@S 2 atoms, 2 residues, 1 model selected > bond sel Created 1 bond > bond Missing or invalid ""atoms"" argument: empty atom specifier > bond :648,653 Created 12 bonds > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > select clear > bond :648,651 Created 12 bonds > bond :648,652 Created 12 bonds > bond :650,652 Created 12 bonds > bond :650,651 Created 12 bonds > bond :650,646 Created 12 bonds > bond :649,653 Created 13 bonds > bond :649,646 Created 12 bonds > bond :649,651 Created 12 bonds > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #2.4 models > hide #2.3 models > hide #!1 models > show #!1 models > hide #!2 models > bond :647,653 Created 13 bonds > bond :647,652 Created 13 bonds > bond :647,646 Created 1 bond > hide #!1 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > delete atoms sel > delete bonds sel > select clear > hide #!5 models > show #!1 models > bond #1:651,443 Created 1 bond > bond :651,443 Created 12 bonds > bond #1:652,473 Created 1 bond > bond :652,473 Created 12 bonds An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command ""graphics restart"" after changing the settings that caused the error. GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) Traceback (most recent call last): File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/updateloop.py"", line 84, in draw_new_frame view.draw(check_for_changes = False) File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 188, in draw self._draw_scene(camera, drawings) File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 239, in _draw_scene camera.draw_background(vnum, r) File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/camera.py"", line 195, in draw_background render.draw_background() File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1267, 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,) ) Unsupported scale factor (0.000000) detected on Display0 [Repeated 7 time(s)] > graphics restart An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command ""graphics restart"" after changing the settings that caused the error. GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) Traceback (most recent call last): File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/updateloop.py"", line 84, in draw_new_frame view.draw(check_for_changes = False) File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 188, in draw self._draw_scene(camera, drawings) File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 239, in _draw_scene camera.draw_background(vnum, r) File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/camera.py"", line 195, in draw_background render.draw_background() File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1267, 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 version: 4.1 Metal - 90.5 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.10.2, Qt 6.10.0 Qt runtime version: 6.10.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Model Number: MKGP3LL/A Chip: Apple M1 Pro Total Number of Cores: 8 (6 Performance and 2 Efficiency) Memory: 16 GB System Firmware Version: 18000.101.7 OS Loader Version: 18000.101.7 Software: System Software Overview: System Version: macOS 26.4 (25E246) Kernel Version: Darwin 25.4.0 Time since boot: 17 days, 18 hours, 4 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: accessible-pygments: 0.0.5 aiohappyeyeballs: 2.6.2 aiohttp: 3.13.4 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.13.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 26.1.0 babel: 2.18.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 4.4.3 bs4: 0.0.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.7 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.2 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.2 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: 1.67.1 ChimeraX-AtomicLibrary: 14.4 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: 1.4.1 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.4 ChimeraX-Cluster: 1.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.1 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.12 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: 1.2.2 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: 2.5.3 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: 1.8.2 ChimeraX-Label: 1.5 ChimeraX-LightingGUI: 1.0 ChimeraX-ListInfo: 1.3.1 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.3 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-MatchAlign: 1.2 ChimeraX-MatchMaker: 2.4.1 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.2.0 ChimeraX-MDcrds: 2.19 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.9 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.23 ChimeraX-ModelPanel: 1.6.1 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: 1.0.1 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: 1.15.4 ChimeraX-OpenFold: 1.0 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.13 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: 1.6 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.8.2 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: 3.5.12 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.18 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-SNFG: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.3 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: 2.5.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.4 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.50.8 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.6.2 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: 8.4.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.14.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.2.4 debugpy: 1.8.21 decorator: 5.3.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.63.0 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.16.0 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.18 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 2.0.0 iniconfig: 2.3.0 ipykernel: 7.1.0 ipython: 9.9.0 ipython_pygments_lexers: 1.1.1 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.8.0 jupyter_core: 5.9.1 kiwisolver: 1.5.0 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: 0.2.2 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.1 narwhals: 2.22.1 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: 8.4.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.7 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: 4.10.0 plotly: 6.8.0 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.5.2 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: 2.13.4 pydantic-settings: 2.14.1 pydantic_core: 2.46.4 pydata-sphinx-theme: 0.18.0 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.5.1 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: 6.10.2 PyQt6-Qt6: 6.10.2 PyQt6-WebEngine-commercial: 6.10.0 PyQt6-WebEngine-Qt6: 6.10.2 PyQt6_sip: 13.10.3 pytest: 9.0.3 pytest-cov: 7.1.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.2 python-multipart: 0.0.32 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 rpds-py: 2026.5.1 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.1.1 sortedcontainers: 2.4.0 soupsieve: 2.8.4 Sphinx: 9.0.4 sphinx-autodoc-typehints: 3.6.1 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: 3.4.4 stack-data: 0.6.3 starlette: 1.3.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 3.2.1 threadpoolctl: 3.6.0 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.7 tqdm: 4.68.2 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 Unidecode: 1.4.0 urllib3: 2.7.0 uvicorn: 0.49.0 wcwidth: 0.8.1 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 yarl: 1.24.2 }}} " defect closed normal Graphics duplicate all ChimeraX