id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18228 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.2-arm64-arm-64bit ChimeraX Version: 1.10.dev202504300222 (2025-04-30 02:22:20 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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unallocated=8.0G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 7408K 56 \nColorSync 768K 38 \nCoreAnimation 5696K 224 \nCoreGraphics 48K 3 \nCoreImage 96K 3 \nCoreUI image data 6320K 54 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 6.7G 222 \nMALLOC guard page 288K 18 \nMach message 96K 6 \nOpenGL GLSL 384K 4 \nSTACK GUARD 752K 47 \nStack 212.6M 48 \nStack Guard 56.0M 1 \nVM_ALLOCATE 569.4M 476 \nVM_ALLOCATE (reserved) 288.0M 3 reserved VM address space (unallocated)\n__AUTH 5285K 672 \n__AUTH_CONST 70.8M 920 \n__CTF 824 1 \n__DATA 36.4M 1055 \n__DATA_CONST 34.3M 1073 \n__DATA_DIRTY 2763K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 636.4M 147 \n__OBJC_RW 2373K 1 \n__TEXT 1.3G 1093 \n__TPRO_CONST 272K 2 \ndyld private memory 48K 2 \nmapped file 622.6M 83 \nowned unmapped memory 272.8M 1 \npage table in kernel 4674K 1 \nshared memory 3344K 32 \n=========== ======= ======= \nTOTAL 10.7G 6637 \nTOTAL, minus reserved VM space 10.4G 6637 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""22b27e153a84aa33d626967dae1c7cf4f5fc4aa3"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6761d0c9df60af01adb250fb"", ""factorPackIds"" : { }, ""deploymentId"" : 240000009 }, { ""rolloutId"" : ""6434420a89ec2e0a7a38bf5a"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== > alias analyse_af_screen_hit runscript > /Users/carlotta/ChimeraX/scripts/analyse_af_screen_hit.cxc $1 $2 > alias analyse_af3 runscript > /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction.cxc $1 $2 > alias analyse_auto-AF runscript > /Users/carlotta/ChimeraX/scripts/analyse_auto-alphafold_prediction.cxc $1 $2 > alias analyse_af3_prediction_ac_bc_only runscript > /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction_ac_bc_only.cxc $1 $2 > alias analyse_af3_prediction_modified runscript > /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction_modified.cxc $1 $2 > alias analyse_af3_prediction_modified_PAE runscript > /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction_modified_PAE.cxc $1 > $2 > alias analyse_af3_prediction_modified_5 runscript > /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction_modified_5.cxc $1 $2 > alias analyse_af3_prediction_CT runscript > /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction_CT.cxc $1 $2 UCSF ChimeraX version: 1.10.dev202504300222 (2025-04-30) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > cd /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255 Current working directory is: /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255 > analyse_af3_prediction_CT > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255 > fold_atg11_1_654_atg9_1_255_NEW > echo ""Usage: runscript analyse_af3_prediction.cxc > "" ""Usage: runscript analyse_af3_prediction.cxc "" > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_4*.cif Chain information for model_4.cif #1 --- Chain | Description A B | . C | . Computing secondary structure > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_4*.json > structure last-opened Opened AlphaFold PAE with values for 1563 residues and atoms > hide > show cartoons > alphafold contacts last-opened &/C name > model_4_af_contacts_fold_atg11_1_654_atg9_1_255_NEW distance 4.5 radius 1 Found 93 residue or atom pairs within distance 4.5 > select last-opened&pbonds 93 pseudobonds, 1 model selected > label sel pseudobonds text ""{0.atoms[0].residue.name} > {0.atoms[0].residue.number} to {0.atoms[1].residue.name} > {0.atoms[1].residue.number}"" > save > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt > format pseudobonds selectedOnly true Saved 93 pseudobonds to file /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt > echo ""AlphaFold contacts (derived from JSON file) saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt"" ""AlphaFold contacts (derived from JSON file) saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt"" > interfaces select last-opened&/C contacting last-opened&~/C bothSides true > areaCutoff 500 69 contacting residues > name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 sel > show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 > style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 ball Changed 576 atom styles > info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 > saveFile > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt > rainbow last-opened chains palette bupu > color byhetero > echo ""Interface residues saved in named selection > interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 and info saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt"" ""Interface residues saved in named selection interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 and info saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt"" > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_3*.cif Chain information for model_3.cif #2 --- Chain | Description A B | . C | . > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_3*.json > structure last-opened Opened AlphaFold PAE with values for 1563 residues and atoms > hide > show cartoons > alphafold contacts last-opened &/C distance 4.5 radius 1 Found 58 residue or atom pairs within distance 4.5 > select last-opened&pbonds 58 pseudobonds, 1 model selected > label sel pseudobonds text ""{0.atoms[0].residue.name} > {0.atoms[0].residue.number} to {0.atoms[1].residue.name} > {0.atoms[1].residue.number}"" > save > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt > format pseudobonds selectedOnly true Computing secondary structure Saved 58 pseudobonds to file /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt > echo ""AlphaFold contacts (derived from JSON file) saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt"" ""AlphaFold contacts (derived from JSON file) saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt"" > interfaces select last-opened&/C contacting last-opened&~/C bothSides true > areaCutoff 500 44 contacting residues > name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 sel > show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 > style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 ball Changed 378 atom styles > info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 > saveFile > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt > rainbow last-opened chains palette bupu > color byhetero > echo ""Interface residues saved in named selection > interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 and info saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt"" ""Interface residues saved in named selection interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 and info saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt"" > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_2*.cif Chain information for model_2.cif #3 --- Chain | Description A B | . C | . > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_2*.json > structure last-opened Opened AlphaFold PAE with values for 1563 residues and atoms > hide > show cartoons > alphafold contacts last-opened &/C distance 4.5 radius 1 Found 90 residue or atom pairs within distance 4.5 > select last-opened&pbonds 90 pseudobonds, 1 model selected > label sel pseudobonds text ""{0.atoms[0].residue.name} > {0.atoms[0].residue.number} to {0.atoms[1].residue.name} > {0.atoms[1].residue.number}"" > save > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt > format pseudobonds selectedOnly true Computing secondary structure Saved 90 pseudobonds to file /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt > echo ""AlphaFold contacts (derived from JSON file) saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt"" ""AlphaFold contacts (derived from JSON file) saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt"" > interfaces select last-opened&/C contacting last-opened&~/C bothSides true > areaCutoff 500 66 contacting residues > name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 sel > show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 > style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 ball Changed 553 atom styles > info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 > saveFile > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt > rainbow last-opened chains palette bupu > color byhetero > echo ""Interface residues saved in named selection > interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 and info saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt"" ""Interface residues saved in named selection interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 and info saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt"" > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_1*.cif Chain information for model_1.cif #4 --- Chain | Description A B | . C | . > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_1*.json > structure last-opened Opened AlphaFold PAE with values for 1563 residues and atoms > hide > show cartoons > alphafold contacts last-opened &/C distance 4.5 radius 1 Found 89 residue or atom pairs within distance 4.5 > select last-opened&pbonds 89 pseudobonds, 1 model selected > label sel pseudobonds text ""{0.atoms[0].residue.name} > {0.atoms[0].residue.number} to {0.atoms[1].residue.name} > {0.atoms[1].residue.number}"" > save > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt > format pseudobonds selectedOnly true Computing secondary structure Saved 89 pseudobonds to file /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt > echo ""AlphaFold contacts (derived from JSON file) saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt"" ""AlphaFold contacts (derived from JSON file) saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt"" > interfaces select last-opened&/C contacting last-opened&~/C bothSides true > areaCutoff 500 84 contacting residues > name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 sel > show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 > style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 ball Changed 713 atom styles > info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 > saveFile > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt > rainbow last-opened chains palette bupu > color byhetero > echo ""Interface residues saved in named selection > interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 and info saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt"" ""Interface residues saved in named selection interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 and info saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt"" > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_0*.cif Chain information for model_0.cif #5 --- Chain | Description A B | . C | . > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_0*.json > structure last-opened Opened AlphaFold PAE with values for 1563 residues and atoms > hide > show cartoons > alphafold contacts last-opened &/C distance 4.5 radius 1 Found 70 residue or atom pairs within distance 4.5 > select last-opened&pbonds 70 pseudobonds, 1 model selected > label sel pseudobonds text ""{0.atoms[0].residue.name} > {0.atoms[0].residue.number} to {0.atoms[1].residue.name} > {0.atoms[1].residue.number}"" > save > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt > format pseudobonds selectedOnly true Computing secondary structure Saved 70 pseudobonds to file /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt > echo ""AlphaFold contacts (derived from JSON file) saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt"" ""AlphaFold contacts (derived from JSON file) saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt"" > interfaces select last-opened&/C contacting last-opened&~/C bothSides true > areaCutoff 500 55 contacting residues > name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 sel > show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 > style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 ball Changed 466 atom styles > info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 > saveFile > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt > echo ""Interface residues saved in named selection > interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 and info saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt"" ""Interface residues saved in named selection interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 and info saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt"" > mmaker #*&~last-opened&/B to last-opened&/B 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 model_0.cif, chain B (#5) with model_4.cif, chain B (#1), sequence alignment score = 3359.5 RMSD between 420 pruned atom pairs is 0.942 angstroms; (across all 654 pairs: 4.670) Matchmaker model_0.cif, chain B (#5) with model_3.cif, chain B (#2), sequence alignment score = 3307.9 RMSD between 424 pruned atom pairs is 1.109 angstroms; (across all 654 pairs: 4.430) Matchmaker model_0.cif, chain B (#5) with model_2.cif, chain B (#3), sequence alignment score = 3366.1 RMSD between 501 pruned atom pairs is 1.013 angstroms; (across all 654 pairs: 5.032) Matchmaker model_0.cif, chain B (#5) with model_1.cif, chain B (#4), sequence alignment score = 3335.5 RMSD between 308 pruned atom pairs is 0.700 angstroms; (across all 654 pairs: 7.060) > mseries slider #1-5 title fold_atg11_1_654_atg9_1_255_NEW name > fold_atg11_1_654_atg9_1_255_NEW_slider > mseries #1-5 > echo ""Use the slider to go through the models!"" ""Use the slider to go through the models!"" > echo ""Pairwise contacts (based on the JSON fle) and all residues involved in > an interface (based on a buried surface are of 500 Angstrom or more) have > been saved in the input folder for each prediction"" ""Pairwise contacts (based on the JSON fle) and all residues involved in an interface (based on a buried surface are of 500 Angstrom or more) have been saved in the input folder for each prediction"" > echo ""You might want to increase stringency by calcualting the overlap > between all predictions"" ""You might want to increase stringency by calcualting the overlap between all predictions"" > key red:20 orange: yellow:10 cornflowerblue: blue:0 size .15,.03 pos .025,.1 > ticks true > 2dlabels text PAE xpos .075 ypos .15 > matchmaker #2-5/A to #1/A 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 model_4.cif, chain A (#1) with model_3.cif, chain A (#2), sequence alignment score = 3363.1 RMSD between 558 pruned atom pairs is 0.670 angstroms; (across all 654 pairs: 4.877) Matchmaker model_4.cif, chain A (#1) with model_2.cif, chain A (#3), sequence alignment score = 3357.7 RMSD between 474 pruned atom pairs is 0.870 angstroms; (across all 654 pairs: 5.548) Matchmaker model_4.cif, chain A (#1) with model_1.cif, chain A (#4), sequence alignment score = 3397.3 RMSD between 457 pruned atom pairs is 0.935 angstroms; (across all 654 pairs: 4.037) Matchmaker model_4.cif, chain A (#1) with model_0.cif, chain A (#5), sequence alignment score = 3363.1 RMSD between 432 pruned atom pairs is 0.896 angstroms; (across all 654 pairs: 4.891) > color sequential /a palette cornflower:teal > color sequential /c palette #f768a1:#7a0177 > color sequential /b palette lightgreen:seagreen > cartoon style protein thickness 2 width 3 > transparency 40 target s > lighting soft > graphics silhouettes true > select clear > hide #5.1.1 models > hide target a > analyse_af3_prediction_CT > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255 > fold_atg11_1_654_atg9_1_255_NEW > echo ""Usage: runscript analyse_af3_prediction.cxc > "" ""Usage: runscript analyse_af3_prediction.cxc "" > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_4*.cif Chain information for model_4.cif #8 --- Chain | Description A B | . C | . > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_4*.json > structure last-opened Opened AlphaFold PAE with values for 1563 residues and atoms > hide > show cartoons > alphafold contacts last-opened &/C name > model_4_af_contacts_fold_atg11_1_654_atg9_1_255_NEW distance 4.5 radius 1 > dashes 4 Found 93 residue or atom pairs within distance 4.5 > select last-opened&pbonds 93 pseudobonds, 1 model selected > label sel pseudobonds text ""{0.atoms[0].residue.name} > {0.atoms[0].residue.number} to {0.atoms[1].residue.name} > {0.atoms[1].residue.number}"" > save > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt > format pseudobonds selectedOnly true Computing secondary structure Saved 93 pseudobonds to file /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt > echo ""AlphaFold contacts (derived from JSON file) saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt"" ""AlphaFold contacts (derived from JSON file) saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt"" > interfaces select last-opened&/C contacting last-opened&~/C bothSides true > areaCutoff 500 69 contacting residues > name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 sel > show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 > style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 ball Changed 576 atom styles > info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 > saveFile > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt > rainbow last-opened chains palette bupu > color byhetero > echo ""Interface residues saved in named selection > interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 and info saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt"" ""Interface residues saved in named selection interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 and info saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt"" > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_3*.cif Chain information for model_3.cif #9 --- Chain | Description A B | . C | . > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_3*.json > structure last-opened Opened AlphaFold PAE with values for 1563 residues and atoms > hide > show cartoons > alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 4 Found 58 residue or atom pairs within distance 4.5 > select last-opened&pbonds 58 pseudobonds, 1 model selected > label sel pseudobonds text ""{0.atoms[0].residue.name} > {0.atoms[0].residue.number} to {0.atoms[1].residue.name} > {0.atoms[1].residue.number}"" > save > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt > format pseudobonds selectedOnly true Computing secondary structure Saved 58 pseudobonds to file /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt > echo ""AlphaFold contacts (derived from JSON file) saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt"" ""AlphaFold contacts (derived from JSON file) saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt"" > interfaces select last-opened&/C contacting last-opened&~/C bothSides true > areaCutoff 500 44 contacting residues > name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 sel > show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 > style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 ball Changed 378 atom styles > info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 > saveFile > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt > rainbow last-opened chains palette bupu > color byhetero > echo ""Interface residues saved in named selection > interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 and info saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt"" ""Interface residues saved in named selection interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 and info saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt"" > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_2*.cif Chain information for model_2.cif #10 --- Chain | Description A B | . C | . > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_2*.json > structure last-opened Opened AlphaFold PAE with values for 1563 residues and atoms > hide > show cartoons > alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 4 Found 90 residue or atom pairs within distance 4.5 > select last-opened&pbonds 90 pseudobonds, 1 model selected > label sel pseudobonds text ""{0.atoms[0].residue.name} > {0.atoms[0].residue.number} to {0.atoms[1].residue.name} > {0.atoms[1].residue.number}"" > save > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt > format pseudobonds selectedOnly true Computing secondary structure Saved 90 pseudobonds to file /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt > echo ""AlphaFold contacts (derived from JSON file) saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt"" ""AlphaFold contacts (derived from JSON file) saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt"" > interfaces select last-opened&/C contacting last-opened&~/C bothSides true > areaCutoff 500 66 contacting residues > name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 sel > show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 > style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 ball Changed 553 atom styles > info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 > saveFile > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt > rainbow last-opened chains palette bupu > color byhetero > echo ""Interface residues saved in named selection > interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 and info saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt"" ""Interface residues saved in named selection interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 and info saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt"" > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_1*.cif Chain information for model_1.cif #11 --- Chain | Description A B | . C | . > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_1*.json > structure last-opened Opened AlphaFold PAE with values for 1563 residues and atoms > hide > show cartoons > alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 4 Found 89 residue or atom pairs within distance 4.5 > select last-opened&pbonds 89 pseudobonds, 1 model selected > label sel pseudobonds text ""{0.atoms[0].residue.name} > {0.atoms[0].residue.number} to {0.atoms[1].residue.name} > {0.atoms[1].residue.number}"" > save > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt > format pseudobonds selectedOnly true Computing secondary structure Saved 89 pseudobonds to file /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt > echo ""AlphaFold contacts (derived from JSON file) saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt"" ""AlphaFold contacts (derived from JSON file) saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt"" > interfaces select last-opened&/C contacting last-opened&~/C bothSides true > areaCutoff 500 84 contacting residues > name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 sel > show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 > style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 ball Changed 713 atom styles > info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 > saveFile > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt > rainbow last-opened chains palette bupu > color byhetero > echo ""Interface residues saved in named selection > interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 and info saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt"" ""Interface residues saved in named selection interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 and info saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt"" > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_0*.cif Chain information for model_0.cif #12 --- Chain | Description A B | . C | . > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_0*.json > structure last-opened Opened AlphaFold PAE with values for 1563 residues and atoms > hide > show cartoons > alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 4 Found 70 residue or atom pairs within distance 4.5 > select last-opened&pbonds 70 pseudobonds, 1 model selected > label sel pseudobonds text ""{0.atoms[0].residue.name} > {0.atoms[0].residue.number} to {0.atoms[1].residue.name} > {0.atoms[1].residue.number}"" > save > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt > format pseudobonds selectedOnly true Computing secondary structure Saved 70 pseudobonds to file /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt > echo ""AlphaFold contacts (derived from JSON file) saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt"" ""AlphaFold contacts (derived from JSON file) saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt"" > interfaces select last-opened&/C contacting last-opened&~/C bothSides true > areaCutoff 500 55 contacting residues > name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 sel > show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 > style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 ball Changed 466 atom styles > info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 > saveFile > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt > echo ""Interface residues saved in named selection > interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 and info saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt"" ""Interface residues saved in named selection interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 and info saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt"" > mmaker #*&~last-opened&/B to last-opened&/B 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 model_0.cif, chain B (#12) with model_4.cif, chain B (#1), sequence alignment score = 3359.5 RMSD between 420 pruned atom pairs is 0.942 angstroms; (across all 654 pairs: 4.670) Matchmaker model_0.cif, chain B (#12) with model_3.cif, chain B (#2), sequence alignment score = 3307.9 RMSD between 424 pruned atom pairs is 1.109 angstroms; (across all 654 pairs: 4.430) Matchmaker model_0.cif, chain B (#12) with model_2.cif, chain B (#3), sequence alignment score = 3366.1 RMSD between 501 pruned atom pairs is 1.013 angstroms; (across all 654 pairs: 5.032) Matchmaker model_0.cif, chain B (#12) with model_1.cif, chain B (#4), sequence alignment score = 3335.5 RMSD between 308 pruned atom pairs is 0.700 angstroms; (across all 654 pairs: 7.060) Matchmaker model_0.cif, chain B (#12) with model_0.cif, chain B (#5), sequence alignment score = 3426.7 RMSD between 654 pruned atom pairs is 0.000 angstroms; (across all 654 pairs: 0.000) Matchmaker model_0.cif, chain B (#12) with model_4.cif, chain B (#8), sequence alignment score = 3359.5 RMSD between 420 pruned atom pairs is 0.942 angstroms; (across all 654 pairs: 4.670) Matchmaker model_0.cif, chain B (#12) with model_3.cif, chain B (#9), sequence alignment score = 3307.9 RMSD between 424 pruned atom pairs is 1.109 angstroms; (across all 654 pairs: 4.430) Matchmaker model_0.cif, chain B (#12) with model_2.cif, chain B (#10), sequence alignment score = 3366.1 RMSD between 501 pruned atom pairs is 1.013 angstroms; (across all 654 pairs: 5.032) Matchmaker model_0.cif, chain B (#12) with model_1.cif, chain B (#11), sequence alignment score = 3335.5 RMSD between 308 pruned atom pairs is 0.700 angstroms; (across all 654 pairs: 7.060) > mseries slider #1-5 title fold_atg11_1_654_atg9_1_255_NEW name > fold_atg11_1_654_atg9_1_255_NEW_slider > mseries #1-5 > echo ""Use the slider to go through the models!"" ""Use the slider to go through the models!"" > echo ""Pairwise contacts (based on the JSON fle) and all residues involved in > an interface (based on a buried surface are of 500 Angstrom or more) have > been saved in the input folder for each prediction"" ""Pairwise contacts (based on the JSON fle) and all residues involved in an interface (based on a buried surface are of 500 Angstrom or more) have been saved in the input folder for each prediction"" > echo ""You might want to increase stringency by calcualting the overlap > between all predictions"" ""You might want to increase stringency by calcualting the overlap between all predictions"" > key red:20 orange: yellow:10 cornflowerblue: blue:0 size .15,.03 pos .025,.1 > ticks true > 2dlabels text PAE xpos .075 ypos .15 > matchmaker #2-5/A to #1/A 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 model_4.cif, chain A (#1) with model_3.cif, chain A (#2), sequence alignment score = 3363.1 RMSD between 558 pruned atom pairs is 0.670 angstroms; (across all 654 pairs: 4.877) Matchmaker model_4.cif, chain A (#1) with model_2.cif, chain A (#3), sequence alignment score = 3357.7 RMSD between 474 pruned atom pairs is 0.870 angstroms; (across all 654 pairs: 5.548) Matchmaker model_4.cif, chain A (#1) with model_1.cif, chain A (#4), sequence alignment score = 3397.3 RMSD between 457 pruned atom pairs is 0.935 angstroms; (across all 654 pairs: 4.037) Matchmaker model_4.cif, chain A (#1) with model_0.cif, chain A (#5), sequence alignment score = 3363.1 RMSD between 432 pruned atom pairs is 0.896 angstroms; (across all 654 pairs: 4.891) > color sequential /a palette cornflower:teal > color sequential /c palette #f768a1:#7a0177 > color sequential /b palette lightgreen:seagreen > cartoon style protein thickness 2 width 3 > transparency 40 target s > lighting soft > graphics silhouettes true > hide #!5 models > hide #!5.1 models > hide #6 models > show #6 models > hide #!11 models > hide #!10 models > hide #!9 models > hide #!8 models > select clear > hide target a > hide #12.1.1 models > lighting soft > lighting simple > lighting full > lighting soft > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting simple > cartoon style protein thickness 1 width 2 > lighting soft > graphics silhouettes true > lighting flat > lighting shadows true intensity 0.5 > lighting soft > set bgColor gray > set bgColor black > lighting simple > lighting soft > graphics silhouettes false > hide #!12 models > hide #!12.1 models > show #!5 models > show #!5.1 models > hide #!5 models > hide #!5.1 models > analyse_af3_prediction_CT > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255 > fold_atg11_1_654_atg9_1_255_NEW > echo ""Usage: runscript analyse_af3_prediction.cxc > "" ""Usage: runscript analyse_af3_prediction.cxc "" > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_4*.cif Chain information for model_4.cif #13 --- Chain | Description A B | . C | . > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_4*.json > structure last-opened Opened AlphaFold PAE with values for 1563 residues and atoms > hide > show cartoons > alphafold contacts last-opened &/C name > model_4_af_contacts_fold_atg11_1_654_atg9_1_255_NEW distance 4.5 radius 1 > dashes 4 Found 93 residue or atom pairs within distance 4.5 > select last-opened&pbonds 93 pseudobonds, 1 model selected > label sel pseudobonds text ""{0.atoms[0].residue.name} > {0.atoms[0].residue.number} to {0.atoms[1].residue.name} > {0.atoms[1].residue.number}"" > save > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt > format pseudobonds selectedOnly true Computing secondary structure Saved 93 pseudobonds to file /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt > echo ""AlphaFold contacts (derived from JSON file) saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt"" ""AlphaFold contacts (derived from JSON file) saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt"" > interfaces select last-opened&/C contacting last-opened&~/C bothSides true > areaCutoff 500 69 contacting residues > name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 sel > show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 > style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 ball Changed 576 atom styles > info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 > saveFile > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt > rainbow last-opened chains palette bupu > color byhetero > echo ""Interface residues saved in named selection > interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 and info saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt"" ""Interface residues saved in named selection interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 and info saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt"" > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_3*.cif Chain information for model_3.cif #14 --- Chain | Description A B | . C | . > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_3*.json > structure last-opened Opened AlphaFold PAE with values for 1563 residues and atoms > hide > show cartoons > alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 4 Found 58 residue or atom pairs within distance 4.5 > select last-opened&pbonds 58 pseudobonds, 1 model selected > label sel pseudobonds text ""{0.atoms[0].residue.name} > {0.atoms[0].residue.number} to {0.atoms[1].residue.name} > {0.atoms[1].residue.number}"" > save > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt > format pseudobonds selectedOnly true Computing secondary structure Saved 58 pseudobonds to file /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt > echo ""AlphaFold contacts (derived from JSON file) saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt"" ""AlphaFold contacts (derived from JSON file) saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt"" > interfaces select last-opened&/C contacting last-opened&~/C bothSides true > areaCutoff 500 44 contacting residues > name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 sel > show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 > style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 ball Changed 378 atom styles > info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 > saveFile > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt > rainbow last-opened chains palette bupu > color byhetero > echo ""Interface residues saved in named selection > interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 and info saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt"" ""Interface residues saved in named selection interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 and info saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt"" > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_2*.cif Chain information for model_2.cif #15 --- Chain | Description A B | . C | . > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_2*.json > structure last-opened Opened AlphaFold PAE with values for 1563 residues and atoms > hide > show cartoons > alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 4 Found 90 residue or atom pairs within distance 4.5 > select last-opened&pbonds 90 pseudobonds, 1 model selected > label sel pseudobonds text ""{0.atoms[0].residue.name} > {0.atoms[0].residue.number} to {0.atoms[1].residue.name} > {0.atoms[1].residue.number}"" > save > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt > format pseudobonds selectedOnly true Computing secondary structure Saved 90 pseudobonds to file /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt > echo ""AlphaFold contacts (derived from JSON file) saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt"" ""AlphaFold contacts (derived from JSON file) saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt"" > interfaces select last-opened&/C contacting last-opened&~/C bothSides true > areaCutoff 500 66 contacting residues > name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 sel > show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 > style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 ball Changed 553 atom styles > info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 > saveFile > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt > rainbow last-opened chains palette bupu > color byhetero > echo ""Interface residues saved in named selection > interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 and info saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt"" ""Interface residues saved in named selection interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 and info saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt"" > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_1*.cif Chain information for model_1.cif #16 --- Chain | Description A B | . C | . > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_1*.json > structure last-opened Opened AlphaFold PAE with values for 1563 residues and atoms > hide > show cartoons > alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 4 Found 89 residue or atom pairs within distance 4.5 > select last-opened&pbonds 89 pseudobonds, 1 model selected > label sel pseudobonds text ""{0.atoms[0].residue.name} > {0.atoms[0].residue.number} to {0.atoms[1].residue.name} > {0.atoms[1].residue.number}"" > save > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt > format pseudobonds selectedOnly true Computing secondary structure Saved 89 pseudobonds to file /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt > echo ""AlphaFold contacts (derived from JSON file) saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt"" ""AlphaFold contacts (derived from JSON file) saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt"" > interfaces select last-opened&/C contacting last-opened&~/C bothSides true > areaCutoff 500 84 contacting residues > name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 sel > show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 > style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 ball Changed 713 atom styles > info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 > saveFile > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt > rainbow last-opened chains palette bupu > color byhetero > echo ""Interface residues saved in named selection > interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 and info saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt"" ""Interface residues saved in named selection interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 and info saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt"" > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_0*.cif Chain information for model_0.cif #17 --- Chain | Description A B | . C | . > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_0*.json > structure last-opened Opened AlphaFold PAE with values for 1563 residues and atoms > hide > show cartoons > alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 4 Found 70 residue or atom pairs within distance 4.5 > select last-opened&pbonds 70 pseudobonds, 1 model selected > label sel pseudobonds text ""{0.atoms[0].residue.name} > {0.atoms[0].residue.number} to {0.atoms[1].residue.name} > {0.atoms[1].residue.number}"" > save > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt > format pseudobonds selectedOnly true Computing secondary structure Saved 70 pseudobonds to file /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt > echo ""AlphaFold contacts (derived from JSON file) saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt"" ""AlphaFold contacts (derived from JSON file) saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt"" > interfaces select last-opened&/C contacting last-opened&~/C bothSides true > areaCutoff 500 55 contacting residues > name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 sel > show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 > style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 ball Changed 466 atom styles > info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 > saveFile > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt > echo ""Interface residues saved in named selection > interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 and info saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt"" ""Interface residues saved in named selection interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 and info saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt"" > mmaker #*&~last-opened&/B to last-opened&/B 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 model_0.cif, chain B (#17) with model_4.cif, chain B (#1), sequence alignment score = 3359.5 RMSD between 420 pruned atom pairs is 0.942 angstroms; (across all 654 pairs: 4.670) Matchmaker model_0.cif, chain B (#17) with model_3.cif, chain B (#2), sequence alignment score = 3307.9 RMSD between 424 pruned atom pairs is 1.109 angstroms; (across all 654 pairs: 4.430) Matchmaker model_0.cif, chain B (#17) with model_2.cif, chain B (#3), sequence alignment score = 3366.1 RMSD between 501 pruned atom pairs is 1.013 angstroms; (across all 654 pairs: 5.032) Matchmaker model_0.cif, chain B (#17) with model_1.cif, chain B (#4), sequence alignment score = 3335.5 RMSD between 308 pruned atom pairs is 0.700 angstroms; (across all 654 pairs: 7.060) Matchmaker model_0.cif, chain B (#17) with model_0.cif, chain B (#5), sequence alignment score = 3426.7 RMSD between 654 pruned atom pairs is 0.000 angstroms; (across all 654 pairs: 0.000) Matchmaker model_0.cif, chain B (#17) with model_4.cif, chain B (#8), sequence alignment score = 3359.5 RMSD between 420 pruned atom pairs is 0.942 angstroms; (across all 654 pairs: 4.670) Matchmaker model_0.cif, chain B (#17) with model_3.cif, chain B (#9), sequence alignment score = 3307.9 RMSD between 424 pruned atom pairs is 1.109 angstroms; (across all 654 pairs: 4.430) Matchmaker model_0.cif, chain B (#17) with model_2.cif, chain B (#10), sequence alignment score = 3366.1 RMSD between 501 pruned atom pairs is 1.013 angstroms; (across all 654 pairs: 5.032) Matchmaker model_0.cif, chain B (#17) with model_1.cif, chain B (#11), sequence alignment score = 3335.5 RMSD between 308 pruned atom pairs is 0.700 angstroms; (across all 654 pairs: 7.060) Matchmaker model_0.cif, chain B (#17) with model_0.cif, chain B (#12), sequence alignment score = 3426.7 RMSD between 654 pruned atom pairs is 0.000 angstroms; (across all 654 pairs: 0.000) Matchmaker model_0.cif, chain B (#17) with model_4.cif, chain B (#13), sequence alignment score = 3359.5 RMSD between 420 pruned atom pairs is 0.942 angstroms; (across all 654 pairs: 4.670) Matchmaker model_0.cif, chain B (#17) with model_3.cif, chain B (#14), sequence alignment score = 3307.9 RMSD between 424 pruned atom pairs is 1.109 angstroms; (across all 654 pairs: 4.430) Matchmaker model_0.cif, chain B (#17) with model_2.cif, chain B (#15), sequence alignment score = 3366.1 RMSD between 501 pruned atom pairs is 1.013 angstroms; (across all 654 pairs: 5.032) Matchmaker model_0.cif, chain B (#17) with model_1.cif, chain B (#16), sequence alignment score = 3335.5 RMSD between 308 pruned atom pairs is 0.700 angstroms; (across all 654 pairs: 7.060) > mseries slider #1-5 title fold_atg11_1_654_atg9_1_255_NEW name > fold_atg11_1_654_atg9_1_255_NEW_slider > mseries #1-5 > echo ""Use the slider to go through the models!"" ""Use the slider to go through the models!"" > echo ""Pairwise contacts (based on the JSON fle) and all residues involved in > an interface (based on a buried surface are of 500 Angstrom or more) have > been saved in the input folder for each prediction"" ""Pairwise contacts (based on the JSON fle) and all residues involved in an interface (based on a buried surface are of 500 Angstrom or more) have been saved in the input folder for each prediction"" > echo ""You might want to increase stringency by calcualting the overlap > between all predictions"" ""You might want to increase stringency by calcualting the overlap between all predictions"" > key red:20 orange: yellow:10 cornflowerblue: blue:0 size .15,.03 pos .025,.1 > ticks true > 2dlabels text PAE xpos .075 ypos .15 > matchmaker #2-5/A to #1/A 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 model_4.cif, chain A (#1) with model_3.cif, chain A (#2), sequence alignment score = 3363.1 RMSD between 558 pruned atom pairs is 0.670 angstroms; (across all 654 pairs: 4.877) Matchmaker model_4.cif, chain A (#1) with model_2.cif, chain A (#3), sequence alignment score = 3357.7 RMSD between 474 pruned atom pairs is 0.870 angstroms; (across all 654 pairs: 5.548) Matchmaker model_4.cif, chain A (#1) with model_1.cif, chain A (#4), sequence alignment score = 3397.3 RMSD between 457 pruned atom pairs is 0.935 angstroms; (across all 654 pairs: 4.037) Matchmaker model_4.cif, chain A (#1) with model_0.cif, chain A (#5), sequence alignment score = 3363.1 RMSD between 432 pruned atom pairs is 0.896 angstroms; (across all 654 pairs: 4.891) > color sequential /a palette cornflower:teal > color sequential /c palette #f768a1:#7a0177 > color sequential /b palette lightgreen:seagreen > cartoon style protein thickness 2 width 3 > transparency 40 target s > lighting soft > graphics silhouettes true > hide #!5 models > show #!5 models > hide #!5 models > hide #!13 models > hide #!14 models > hide #!15 models > hide #!16 models > close all > analyse_af3_prediction_CT > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255 > fold_atg11_1_654_atg9_1_255_NEW > echo ""Usage: runscript analyse_af3_prediction.cxc > "" ""Usage: runscript analyse_af3_prediction.cxc "" > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_4*.cif Chain information for model_4.cif #1 --- Chain | Description A B | . C | . Computing secondary structure > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_4*.json > structure last-opened Opened AlphaFold PAE with values for 1563 residues and atoms > hide > show cartoons > alphafold contacts last-opened &/C name > model_4_af_contacts_fold_atg11_1_654_atg9_1_255_NEW distance 4.5 radius 1 > dashes 10 Found 93 residue or atom pairs within distance 4.5 > select last-opened&pbonds 93 pseudobonds, 1 model selected > label sel pseudobonds text ""{0.atoms[0].residue.name} > {0.atoms[0].residue.number} to {0.atoms[1].residue.name} > {0.atoms[1].residue.number}"" > save > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt > format pseudobonds selectedOnly true Saved 93 pseudobonds to file /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt > echo ""AlphaFold contacts (derived from JSON file) saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt"" ""AlphaFold contacts (derived from JSON file) saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt"" > interfaces select last-opened&/C contacting last-opened&~/C bothSides true > areaCutoff 500 69 contacting residues > name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 sel > show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 > style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 ball Changed 576 atom styles > info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 > saveFile > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt > rainbow last-opened chains palette bupu > color byhetero > echo ""Interface residues saved in named selection > interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 and info saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt"" ""Interface residues saved in named selection interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 and info saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt"" > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_3*.cif Chain information for model_3.cif #2 --- Chain | Description A B | . C | . > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_3*.json > structure last-opened Opened AlphaFold PAE with values for 1563 residues and atoms > hide > show cartoons > alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 10 Found 58 residue or atom pairs within distance 4.5 > select last-opened&pbonds 58 pseudobonds, 1 model selected > label sel pseudobonds text ""{0.atoms[0].residue.name} > {0.atoms[0].residue.number} to {0.atoms[1].residue.name} > {0.atoms[1].residue.number}"" > save > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt > format pseudobonds selectedOnly true Computing secondary structure Saved 58 pseudobonds to file /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt > echo ""AlphaFold contacts (derived from JSON file) saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt"" ""AlphaFold contacts (derived from JSON file) saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt"" > interfaces select last-opened&/C contacting last-opened&~/C bothSides true > areaCutoff 500 44 contacting residues > name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 sel > show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 > style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 ball Changed 378 atom styles > info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 > saveFile > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt > rainbow last-opened chains palette bupu > color byhetero > echo ""Interface residues saved in named selection > interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 and info saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt"" ""Interface residues saved in named selection interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 and info saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt"" > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_2*.cif Chain information for model_2.cif #3 --- Chain | Description A B | . C | . > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_2*.json > structure last-opened Opened AlphaFold PAE with values for 1563 residues and atoms > hide > show cartoons > alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 10 Found 90 residue or atom pairs within distance 4.5 > select last-opened&pbonds 90 pseudobonds, 1 model selected > label sel pseudobonds text ""{0.atoms[0].residue.name} > {0.atoms[0].residue.number} to {0.atoms[1].residue.name} > {0.atoms[1].residue.number}"" > save > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt > format pseudobonds selectedOnly true Computing secondary structure Saved 90 pseudobonds to file /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt > echo ""AlphaFold contacts (derived from JSON file) saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt"" ""AlphaFold contacts (derived from JSON file) saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt"" > interfaces select last-opened&/C contacting last-opened&~/C bothSides true > areaCutoff 500 66 contacting residues > name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 sel > show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 > style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 ball Changed 553 atom styles > info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 > saveFile > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt > rainbow last-opened chains palette bupu > color byhetero > echo ""Interface residues saved in named selection > interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 and info saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt"" ""Interface residues saved in named selection interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 and info saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt"" > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_1*.cif Chain information for model_1.cif #4 --- Chain | Description A B | . C | . > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_1*.json > structure last-opened Opened AlphaFold PAE with values for 1563 residues and atoms > hide > show cartoons > alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 10 Found 89 residue or atom pairs within distance 4.5 > select last-opened&pbonds 89 pseudobonds, 1 model selected > label sel pseudobonds text ""{0.atoms[0].residue.name} > {0.atoms[0].residue.number} to {0.atoms[1].residue.name} > {0.atoms[1].residue.number}"" > save > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt > format pseudobonds selectedOnly true Computing secondary structure Saved 89 pseudobonds to file /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt > echo ""AlphaFold contacts (derived from JSON file) saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt"" ""AlphaFold contacts (derived from JSON file) saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt"" > interfaces select last-opened&/C contacting last-opened&~/C bothSides true > areaCutoff 500 84 contacting residues > name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 sel > show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 > style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 ball Changed 713 atom styles > info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 > saveFile > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt > rainbow last-opened chains palette bupu > color byhetero > echo ""Interface residues saved in named selection > interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 and info saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt"" ""Interface residues saved in named selection interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 and info saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt"" > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_0*.cif Chain information for model_0.cif #5 --- Chain | Description A B | . C | . > open > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_0*.json > structure last-opened Opened AlphaFold PAE with values for 1563 residues and atoms > hide > show cartoons > alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 10 Found 70 residue or atom pairs within distance 4.5 > select last-opened&pbonds 70 pseudobonds, 1 model selected > label sel pseudobonds text ""{0.atoms[0].residue.name} > {0.atoms[0].residue.number} to {0.atoms[1].residue.name} > {0.atoms[1].residue.number}"" > save > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt > format pseudobonds selectedOnly true Computing secondary structure Saved 70 pseudobonds to file /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt > echo ""AlphaFold contacts (derived from JSON file) saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt"" ""AlphaFold contacts (derived from JSON file) saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt"" > interfaces select last-opened&/C contacting last-opened&~/C bothSides true > areaCutoff 500 55 contacting residues > name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 sel > show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 > style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 ball Changed 466 atom styles > info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 > saveFile > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt > echo ""Interface residues saved in named selection > interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 and info saved to > /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt"" ""Interface residues saved in named selection interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 and info saved to /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt"" > mmaker #*&~last-opened&/B to last-opened&/B 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 model_0.cif, chain B (#5) with model_4.cif, chain B (#1), sequence alignment score = 3359.5 RMSD between 420 pruned atom pairs is 0.942 angstroms; (across all 654 pairs: 4.670) Matchmaker model_0.cif, chain B (#5) with model_3.cif, chain B (#2), sequence alignment score = 3307.9 RMSD between 424 pruned atom pairs is 1.109 angstroms; (across all 654 pairs: 4.430) Matchmaker model_0.cif, chain B (#5) with model_2.cif, chain B (#3), sequence alignment score = 3366.1 RMSD between 501 pruned atom pairs is 1.013 angstroms; (across all 654 pairs: 5.032) Matchmaker model_0.cif, chain B (#5) with model_1.cif, chain B (#4), sequence alignment score = 3335.5 RMSD between 308 pruned atom pairs is 0.700 angstroms; (across all 654 pairs: 7.060) > mseries slider #1-5 title fold_atg11_1_654_atg9_1_255_NEW name > fold_atg11_1_654_atg9_1_255_NEW_slider > mseries #1-5 > echo ""Use the slider to go through the models!"" ""Use the slider to go through the models!"" > echo ""Pairwise contacts (based on the JSON fle) and all residues involved in > an interface (based on a buried surface are of 500 Angstrom or more) have > been saved in the input folder for each prediction"" ""Pairwise contacts (based on the JSON fle) and all residues involved in an interface (based on a buried surface are of 500 Angstrom or more) have been saved in the input folder for each prediction"" > echo ""You might want to increase stringency by calcualting the overlap > between all predictions"" ""You might want to increase stringency by calcualting the overlap between all predictions"" > key red:20 orange: yellow:10 cornflowerblue: blue:0 size .15,.03 pos .025,.1 > ticks true > 2dlabels text PAE xpos .075 ypos .15 > matchmaker #2-5/A to #1/A 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 model_4.cif, chain A (#1) with model_3.cif, chain A (#2), sequence alignment score = 3363.1 RMSD between 558 pruned atom pairs is 0.670 angstroms; (across all 654 pairs: 4.877) Matchmaker model_4.cif, chain A (#1) with model_2.cif, chain A (#3), sequence alignment score = 3357.7 RMSD between 474 pruned atom pairs is 0.870 angstroms; (across all 654 pairs: 5.548) Matchmaker model_4.cif, chain A (#1) with model_1.cif, chain A (#4), sequence alignment score = 3397.3 RMSD between 457 pruned atom pairs is 0.935 angstroms; (across all 654 pairs: 4.037) Matchmaker model_4.cif, chain A (#1) with model_0.cif, chain A (#5), sequence alignment score = 3363.1 RMSD between 432 pruned atom pairs is 0.896 angstroms; (across all 654 pairs: 4.891) > color sequential /a palette cornflower:teal > color sequential /c palette #f768a1:#7a0177 > color sequential /b palette lightgreen:seagreen > cartoon style protein thickness 2 width 3 > transparency 40 target s > lighting soft > graphics silhouettes true > hide #5.1.1 models > select up 3662 atoms, 3717 bonds, 455 residues, 1 model selected > select down 466 atoms, 55 residues, 1 model selected > select clear > hide target a > set bgColor white > lighting simple > lighting soft > lighting gentle > lighting shadows true intensity 0.5 > graphics silhouettes false > graphics silhouettes true > cartoon style protein thickness 1 width 2 > lighting soft > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > graphics silhouettes false > graphics silhouettes true > lighting full > lighting soft > cartoon style protein thickness 2 width 3 > ui mousemode right rotate > view > ui tool show ""Side View"" > ui mousemode right zoom > ui mousemode right ""translate selected models"" > show target s > transparency 70 target s > transparency 40 target s > transparency 70 target s > hide #!5.1 models > lighting soft > lighting gentle > lighting soft > lighting simple > lighting soft > lighting flat > graphics silhouettes false > ui mousemode right translate > ui mousemode right zoom > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting soft > graphics silhouettes true > lighting simple > graphics silhouettes false > lighting full > lighting soft > lighting gentle > ui mousemode right rotate > show #!4 models > hide #!4.1 models > show #!3 models > hide #!3.1 models > hide #3.2 models > hide #3.3 models > hide #3.4 models > hide #4.2 models > hide #4.3 models > hide #4.4 models > hide #5.2 models > hide #5.3 models > hide #5.4 models > hide #!5 models > hide #!3 models > show #!3 models > hide #!4 models > graphics silhouettes true > show #!4 models > show #!5 models > lighting simple > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > graphics silhouettes false > lighting soft > graphics silhouettes true > hide #6 models > hide #!7 models > save superimposed.png supersample 4 transparentBackground true width 4000 > height 2000 > view name super > view super > hide #!3 models > hide #!4 models > show surfaces > hide surfaces /c Expected ',' or a keyword > hide /c target s > transparency 40 target s > transparency 0 target s > view super > lighting soft > lighting gentle > lighting full > lighting simple > lighting soft > graphics silhouettes false > cartoon style protein thickness 2 width 3 > hide #4.2 models > hide #4.3 models > show #4.3 models > show #4.2 models > hide #5.4 models > show #5.4 models > hide #5.3 models > show #5.3 models > hide #5.3 models > hide #3.2 models > hide #3.3 models > hide #3.4 models > hide #!4 models > hide #4.2 models > hide #4.3 models > hide #4.4 models > hide #!5 models > show #!5 models > show #5.3 models > show #3.3 models > hide #3.3 models > hide #!3 models > hide #5.2 models > hide #5.3 models > show #!4 models > show #!3 models > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > show #5.3 models > show #5.2 models > hide #!4 models > hide #!3 models > save model_0_NEW.png supersample 4 transparentBackground true width 4000 > height 2000 > hide #!5 models > hide #5.2 models > hide #5.3 models > hide #5.4 models > show #!4 models > show #4.2 models > show #4.3 models > view super > save model_1_NEW.png supersample 4 transparentBackground true width 4000 > height 2000 > hide #!4 models > hide #4.2 models > hide #4.3 models > show #!3 models > show #3.2 models > show #3.3 models > save model_2_NEW.png supersample 4 transparentBackground true width 4000 > height 2000 > ui mousemode right zoom > ui mousemode right translate > ui mousemode right zoom > save model_2_NEW.png supersample 4 transparentBackground true width 4000 > height 4000 > hide #!3 models > hide #3.2 models > hide #3.3 models > show #!4 models > show #4.2 models > show #4.3 models > ui mousemode right translate > ui mousemode right zoom > ui mousemode right translate > save model_1_NEW.png supersample 4 transparentBackground true width 4000 > height 4000 > hide #!4 models > hide #4.2 models > hide #4.3 models > show #!5 models > show #5.2 models > show #5.3 models > ui mousemode right zoom > ui mousemode right translate > hide /a target c > transparency 40 target s > transparency 0 target s > ui mousemode right zoom > ui mousemode right translate > ui mousemode right zoom > ui mousemode right translate > save model_0_NEW.png supersample 4 transparentBackground true width 4000 > height 4000 > color > color list No custom colors. 248 builtin colors: alice blue , aliceblue , antique white , antiquewhite , aqua , aquamarine , azure , beige , bisque , black , blanched almond , blanchedalmond , blue , blue violet , blueviolet , brown , burly wood , burlywood , cadet blue , cadetblue , chartreuse , chocolate , coral , cornflower blue , cornflowerblue , cornsilk , crimson , cyan , dark blue , dark cyan , dark goldenrod , dark gray , dark green , dark grey , dark khaki , dark magenta , dark olive green , dark orange , dark orchid , dark red , dark salmon , dark sea green , dark seagreen , dark slate blue , dark slate gray , dark slate grey , dark turquoise , dark violet , darkblue , darkcyan , darkgoldenrod , darkgray , darkgreen , darkgrey , darkkhaki , darkmagenta , darkolivegreen , darkorange , darkorchid , darkred , darksalmon , darkseagreen , darkslateblue , darkslategray , darkslategrey , darkturquoise , darkviolet , deep pink , deep sky blue , deep skyblue , deeppink , deepskyblue , dim gray , dim grey , dimgray , dimgrey , dodger blue , dodgerblue , fire brick , firebrick , floral white , floralwhite , forest green , forestgreen , fuchsia , gainsboro , ghost white , ghostwhite , gold , goldenrod , gray , green , green yellow , greenyellow , grey , honeydew , hot pink , hotpink , indian red , indianred , indigo , ivory , khaki , lavender , lavender blush , lavenderblush , lawn green , lawngreen , lemon chiffon , lemonchiffon , light blue , light coral , light cyan , light goldenrod yellow , light gray , light green , light grey , light pink , light salmon , light sea green , light seagreen , light sky blue , light skyblue , light slate gray , light slate grey , light steel blue , light yellow , lightblue , lightcoral , lightcyan , lightgoldenrodyellow , lightgray , lightgreen , lightgrey , lightpink , lightsalmon , lightseagreen , lightskyblue , lightslategray , lightslategrey , lightsteelblue , lightyellow , lime , lime green , limegreen , linen , magenta , maroon , medium aquamarine , medium blue , medium orchid , medium purple , medium sea green , medium seagreen , medium slate blue , medium spring green , medium turquoise , medium violet red , mediumaquamarine , mediumblue , mediumorchid , mediumpurple , mediumseagreen , mediumslateblue , mediumspringgreen , mediumturquoise , mediumvioletred , midnight blue , midnightblue , mint cream , mintcream , misty rose , mistyrose , moccasin , navajo white , navajowhite , navy , old lace , oldlace , olive , olive drab , olivedrab , orange , orange red , orangered , orchid , pale goldenrod , pale green , pale turquoise , pale violet red , palegoldenrod , palegreen , paleturquoise , palevioletred , papaya whip , papayawhip , peach puff , peachpuff , peru , pink , plum , powder blue , powderblue , purple , rebecca purple , rebeccapurple , red , rosy brown , rosybrown , royal blue , royalblue , saddle brown , saddlebrown , salmon , sandy brown , sandybrown , sea green , seagreen , seashell , sienna , silver , sky blue , skyblue , slate blue , slate gray , slate grey , slateblue , slategray , slategrey , snow , spring green , springgreen , steel blue , steelblue , tan , teal , thistle , tomato , transparent , turquoise , violet , wheat , white , white smoke , whitesmoke , yellow , yellow green , and yellowgreen . > color #5.2-3#!5 #f050acff > color #5.2-3#!5 #ff40ffff > undo > color #5.2-3#!5 #f050aeff > undo > color list No custom colors. 248 builtin colors: alice blue , aliceblue , antique white , antiquewhite , aqua , aquamarine , azure , beige , bisque , black , blanched almond , blanchedalmond , blue , blue violet , blueviolet , brown , burly wood , burlywood , cadet blue , cadetblue , chartreuse , chocolate , coral , cornflower blue , cornflowerblue , cornsilk , crimson , cyan , dark blue , dark cyan , dark goldenrod , dark gray , dark green , dark grey , dark khaki , dark magenta , dark olive green , dark orange , dark orchid , dark red , dark salmon , dark sea green , dark seagreen , dark slate blue , dark slate gray , dark slate grey , dark turquoise , dark violet , darkblue , darkcyan , darkgoldenrod , darkgray , darkgreen , darkgrey , darkkhaki , darkmagenta , darkolivegreen , darkorange , darkorchid , darkred , darksalmon , darkseagreen , darkslateblue , darkslategray , darkslategrey , darkturquoise , darkviolet , deep pink , deep sky blue , deep skyblue , deeppink , deepskyblue , dim gray , dim grey , dimgray , dimgrey , dodger blue , dodgerblue , fire brick , firebrick , floral white , floralwhite , forest green , forestgreen , fuchsia , gainsboro , ghost white , ghostwhite , gold , goldenrod , gray , green , green yellow , greenyellow , grey , honeydew , hot pink , hotpink , indian red , indianred , indigo , ivory , khaki , lavender , lavender blush , lavenderblush , lawn green , lawngreen , lemon chiffon , lemonchiffon , light blue , light coral , light cyan , light goldenrod yellow , light gray , light green , light grey , light pink , light salmon , light sea green , light seagreen , light sky blue , light skyblue , light slate gray , light slate grey , light steel blue , light yellow , lightblue , lightcoral , lightcyan , lightgoldenrodyellow , lightgray , lightgreen , lightgrey , lightpink , lightsalmon , lightseagreen , lightskyblue , lightslategray , lightslategrey , lightsteelblue , lightyellow , lime , lime green , limegreen , linen , magenta , maroon , medium aquamarine , medium blue , medium orchid , medium purple , medium sea green , medium seagreen , medium slate blue , medium spring green , medium turquoise , medium violet red , mediumaquamarine , mediumblue , mediumorchid , mediumpurple , mediumseagreen , mediumslateblue , mediumspringgreen , mediumturquoise , mediumvioletred , midnight blue , midnightblue , mint cream , mintcream , misty rose , mistyrose , moccasin , navajo white , navajowhite , navy , old lace , oldlace , olive , olive drab , olivedrab , orange , orange red , orangered , orchid , pale goldenrod , pale green , pale turquoise , pale violet red , palegoldenrod , palegreen , paleturquoise , palevioletred , papaya whip , papayawhip , peach puff , peachpuff , peru , pink , plum , powder blue , powderblue , purple , rebecca purple , rebeccapurple , red , rosy brown , rosybrown , royal blue , royalblue , saddle brown , saddlebrown , salmon , sandy brown , sandybrown , sea green , seagreen , seashell , sienna , silver , sky blue , skyblue , slate blue , slate gray , slate grey , slateblue , slategray , slategrey , snow , spring green , springgreen , steel blue , steelblue , tan , teal , thistle , tomato , transparent , turquoise , violet , wheat , white , white smoke , whitesmoke , yellow , yellow green , and yellowgreen . > color > color show Illegal color name: """" > color #5.2-3#!5 #6fdf88ff > undo > color #5.2-3#!5 #0edf01ff > undo > color #5.2-3#!5 #3aa2d6ff > undo > color #5.2-3#!5 #6fdf88ff > color #5.2-3#!5 #3aa2d6ff > color #5.2-3#!5 #64c87aff > color #5.2-3#!5 #3aa2d6ff > color #5.2-3#!5 #0edf01ff > color #5.2-3#!5 #39a1d4ff ===== Log before crash end ===== Log: > alias analyse_af_screen_hit runscript > /Users/carlotta/ChimeraX/scripts/analyse_af_screen_hit.cxc $1 $2 > alias analyse_af3 runscript > /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction.cxc $1 $2 > alias analyse_auto-AF runscript > /Users/carlotta/ChimeraX/scripts/analyse_auto-alphafold_prediction.cxc $1 $2 > alias analyse_af3_prediction_ac_bc_only runscript > /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction_ac_bc_only.cxc $1 $2 > alias analyse_af3_prediction_modified runscript > /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction_modified.cxc $1 $2 > alias analyse_af3_prediction_modified_PAE runscript > /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction_modified_PAE.cxc $1 > $2 > alias analyse_af3_prediction_modified_5 runscript > /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction_modified_5.cxc $1 $2 > alias analyse_af3_prediction_CT runscript > /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction_CT.cxc $1 $2 UCSF ChimeraX version: 1.10.dev202504300222 (2025-04-30) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M2 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: 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: MacBook Pro Model Identifier: Mac14,10 Model Number: Z178000G3D/A Chip: Apple M2 Pro Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 32 GB System Firmware Version: 11881.61.3 OS Loader Version: 11881.61.3 Software: System Software Overview: System Version: macOS 15.2 (24C101) Kernel Version: Darwin 24.2.0 Time since boot: 25 days, 16 hours, 8 minutes Graphics/Displays: Apple M2 Pro: Chipset Model: Apple M2 Pro Type: GPU Bus: Built-In Total Number of Cores: 19 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.3.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.3.1 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.1 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.3 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.5 ChimeraX-AtomicLibrary: 14.1.17 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: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 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: 1.2.6 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.dev202504300222 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: 1.6.1 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: 2.2.1 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: 2.7.9 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: 1.1.1 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: 1.2.0 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: 1.45.1 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.8.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.57.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.13.0 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: 8.1.6 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.14 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.4.4 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 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: 4.3.7 pluggy: 1.5.0 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 pyelftools: 0.32 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: 8.3.5 pytest-cov: 6.1.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 26.4.0 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: 2.2.0 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: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.13.2 tzdata: 2025.2 urllib3: 2.4.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Window Toolkit duplicate all ChimeraX