id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8470 KeyError formatting blast results chimerax-bug-report@… Zach Pearson "{{{ The following bug report has been submitted: Platform: macOS-12.3.1-arm64-arm-64bit ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > help help:quickstart > open /Users/jrutter/Downloads/AF-O75081-F1-model_v4.pdb AF-O75081-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for protein CBFA2T3 (O75081) [more info...] Chain information for AF-O75081-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | protein CBFA2T3 | MTG16_HUMAN > set bgColor white > lighting soft > lighting full > lighting simple > show cartoons [Repeated 1 time(s)] > hide cartoons > show cartoons > alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6 > color #1 #9fc7d7ff > style nucrib Expected a keyword > alias cylinders cartoon style protein modeh tube rad 2 sides 24 > sequence chain #1/A Alignment identifier is 1/A > open O75081 fromDatabase uniprot Summary of feedback from opening O75081 fetched from uniprot --- notes | Fetching compressed O75081 UniProt info from https://www.uniprot.org/uniprot/O75081.xml Alignment identifier is O75081 Associated AF-O75081-F1-model_v4.pdb chain A to O75081 with 0 mismatches Opened UniProt O75081 > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" sticks Using preset: Initial Styles / Sticks Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" cartoon Using preset: Initial Styles / Cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" ""space-filling (chain colors)"" Using preset: Initial Styles / Space-Filling (Chain Colors) Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""molecular surfaces"" ""atomic coloring (transparent)"" Using preset: Molecular Surfaces / Atomic Coloring (Transparent) Changed 4996 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color fromatoms targ s trans 70 > preset ""initial styles"" ""space-filling (single color)"" Using preset: Initial Styles / Space-Filling (Single Color) Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""molecular surfaces"" ""ghostly white"" Using preset: Molecular Surfaces / Ghostly White Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > preset ""molecular surfaces"" ""atomic coloring (transparent)"" Using preset: Molecular Surfaces / Atomic Coloring (Transparent) Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color fromatoms targ s trans 70 > preset ""molecular surfaces"" ""chain id coloring (opaque)"" Using preset: Molecular Surfaces / Chain ID Coloring (Opaque) Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color bychain targ s trans 0 > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > preset ""overall look"" interactive Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f lighting depthCue t > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > rainbow > open /Applications/BBEdit.app/ '/Applications/BBEdit.app/' has no suffix > mlp Map values for surface ""AF-O75081-F1-model_v4.pdb_A SES surface"": minimum -28.15, mean -5.205, maximum 23.3 To also show corresponding color key, enter the above mlp command and add key true > color bypolymer > color bychain > color byhetero > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for AF-O75081-F1-model_v4.pdb_A SES surface #1.1: minimum, -19.38, mean -0.23, maximum 13.98 To also show corresponding color key, enter the above coulombic command and add key true > mlp Map values for surface ""AF-O75081-F1-model_v4.pdb_A SES surface"": minimum -28.15, mean -5.205, maximum 23.3 To also show corresponding color key, enter the above mlp command and add key true > nucleotides atoms > style nucleic stick Changed 0 atom styles > style sphere Changed 4996 atom styles > mlp Map values for surface ""AF-O75081-F1-model_v4.pdb_A SES surface"": minimum -28.15, mean -5.205, maximum 23.3 To also show corresponding color key, enter the above mlp command and add key true > interfaces ~solvent 0 buried areas: > interfaces ~solvent 0 buried areas: > interfaces ~solvent 0 buried areas: > hbonds reveal true 345 hydrogen bonds found > style stick Changed 4996 atom styles Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A > interfaces ~solvent 0 buried areas: > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > ui tool show AlphaFold > select add #1 4996 atoms, 5127 bonds, 345 pseudobonds, 653 residues, 2 models selected > close > alphafold fetch alphafold fetch p29474 Expected a keyword > alphafold fetch O95071 Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json Fetching url https://alphafold.ebi.ac.uk/files/AF-O95071-F1-model_v4.cif failed: HTTP Error 404: Not Found > alphafold fetch P10242 Fetching compressed AlphaFold P10242 from https://alphafold.ebi.ac.uk/files/AF-P10242-F1-model_v4.cif Chain information for AlphaFold P10242 #1 --- Chain | Description | UniProt A | Transcriptional activator Myb | MYB_HUMAN > alphafold pae #1 uniprotId P10242 Fetching compressed AlphaFold PAE P10242 from https://alphafold.ebi.ac.uk/files/AF-P10242-F1-predicted_aligned_error_v4.json > trim true Unknown command: trim true > ui tool show AlphaFold > alphafold predict #1 Please cite ColabFold: Making protein folding accessible to all. Nature Methods (2022) if you use these predictions. > alphafold match #1 1 AlphaFold model found using UniProt identifier: P10242 (chain A) AlphaFold chains matching AlphaFold P10242 --- Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id A | MYB_HUMAN | P10242 | 0.00 | 640 | 640 | 100 Opened 1 AlphaFold model > alphafold search #1 Webservices job id: 529A6FQNOAT31LAL > close #2 > close > ui tool show AlphaFold [Repeated 1 time(s)] > ui tool show ViewDockX No suitable models found for ViewDockX No sequence chosen for AlphaFold match [Repeated 3 time(s)] > alphafold predict > MPAIMTMLADHAARQLLDFSQKLDINLLDNVVNCLYHGEGAQQRMAQEVLTHLKEHPDAWTRVDTILEFSQNMNTKYYGLQILENVIKTRWKILPRNQCEGIKKYVVGLIIKTSSDPTCVEKEKVYIGKLNMILVQILKQEWPKHWPTFISDIVGASRTSESLCQNNMVILKLLSEEVFDFSSGQITQVKSKHLKDSMCNEFSQIFQLCQFVMENSQNAPLVHATLETLLRFLNWIPLGYIFETKLISTLIYKFLNVPMFRNVSLKCLTEIAGVSVSQYEEQFVTLFTLTMMQLKQMLPLNTNIRLAYSNGKDDEQNFIQNLSLFLCTFLKEHDQLIEKRLNLRETLMEALHYMLLVSEVEETEIFKICLEYWNHLAAELYRESPFSTSASPLLSGSQHFDVPPRRQLYLPMLFKVRLLMVSRMAKPEEVLVVENDQGEVVREFMKDTDSINLYKNMRETLVYLTHLDYVDTERIMTEKLHNQVNGTEWSWKNLNTLCWAIGSISGAMHEEDEKRFLVTVIKDLLGLCEQKRGKDNKAIIASNIMYIVGQYPRFLRAHWKFLKTVVNKLFEFMHETHDGVQDMACDTFIKIAQKCRRHFVQVQVGEVMPFIDEILNNINTIICDLQPQQVHTFYEAVGYMIGAQTDQTVQEHLIEKYMLLPNQVWDSIIQQATKNVDILKDPETVKQLGSILKTNVRACKAVGHPFVIQLGRIYLDMLNVYKCLSENISAAIQANGEMVTKQPLIRSMRTVKRETLKLISGWVSRSNDPQMVAENFVPPLLDAVLIDYQRNVPAAREPEVLSTMAIIVNKLGGHITAEIPQIFDAVFECTLNMINKDFEEYPEHRTNFFLLLQAVNSHCFPAFLAIPPTQFKLVLDSIIWAFKHTMRNVADTGLQILFTLLQNVAQEEAAAQSFYQTYFCDILQHIFSVVTDTSHTAGLTMHASILAYMFNLVEEGKISTSLNPGNPVNNQIFLQEYVANLLKSAFPHLQDAQVKLFVTGLFSLNQDIPAFKEHLRDFLVQIKEFAGEDTSDLFLEEREIALRQADEEKHKRQMSVPGIFNPHEIPEEMCD,MSSSMWYIMQSIQSKYSLSERLIRTIAAIRSFPHDNVEDLIRGGADVNCTHGTLKPLHCACMVSDADCVELLLEKGAEVNALDGYNRTALHYAAEKDEACVEVLLEYGANPNALDGNRDTPLHWAAFKNNAECVRALLESGASVNALDYNNDTPLSWAAMKGNLESVSILLDYGAEVRVINLIGQTPISRLVALLVRGLGTEKEDSCFELLHRAVGHFELRKNGTMPREVARDPQLCEKLTVLCSAPGTLKTLARYAVRRSLGLQYLPDAVKGLPLPASLKEYLLLLE Running AlphaFold prediction [Repeated 2 time(s)]Traceback (most recent call last): File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 661, in customEvent func(*args, **kw) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/blastprotein/job.py"", line 97, in on_finish BlastProteinResults.from_job( File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/blastprotein/ui/results.py"", line 88, in from_job return cls( File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/blastprotein/ui/results.py"", line 84, in __init__ self._build_ui() File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/blastprotein/ui/results.py"", line 216, in _build_ui param_str = self._format_param_str() File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/blastprotein/ui/results.py"", line 191, in _format_param_str model_formatted = ''.join([str(self.session.models._models[(model_no,)]), chain]) KeyError: (1,) KeyError: (1,) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/blastprotein/ui/results.py"", line 191, in _format_param_str model_formatted = ''.join([str(self.session.models._models[(model_no,)]), chain]) See log for complete Python traceback. > open 4hat Summary of feedback from opening 4hat fetched from pdb --- notes | Fetching compressed mmCIF 4hat from http://files.rcsb.org/download/4hat.cif Fetching CCD GNP from http://ligand-expo.rcsb.org/reports/G/GNP/GNP.cif Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif Fetching CCD EDO from http://ligand-expo.rcsb.org/reports/E/EDO/EDO.cif Fetching CCD LMB from http://ligand-expo.rcsb.org/reports/L/LMB/LMB.cif Fetching CCD GOL from http://ligand-expo.rcsb.org/reports/G/GOL/GOL.cif Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif 4hat title: Crystal structure of CRM1 inhibitor Leptomycin B in complex with CRM1-Ran- RanBP1 [more info...] Chain information for 4hat #1 --- Chain | Description | UniProt A | GTP-binding nuclear protein Ran | RAN_HUMAN B | Ran-specific GTPase-activating protein 1 | YRB1_YEAST C | Exportin-1 | XPO1_YEAST Non-standard residues in 4hat #1 --- CL — chloride ion EDO — 1,2-ethanediol (ethylene glycol) GNP — phosphoaminophosphonic acid-guanylate ester GOL — glycerol (glycerin; propane-1,2,3-triol) LMB — Leptomycin B, bound form MG — magnesium ion > color byelement > color bychain Alignment identifier is 1/A Alignment identifier is 1/B Alignment identifier is 1/C > select > /C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051 7083 atoms, 7174 bonds, 877 residues, 1 model selected Destroying pre-existing alignment with identifier 1/C Alignment identifier is 1/C > graphics silhouettes false > graphics silhouettes true > lighting flat [Repeated 1 time(s)] > lighting full > lighting soft > lighting simple > lighting full > lighting simple > set bgColor black > ui tool show ""Side View"" > view orient Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic models, 0 maps. Hide dust shortcut requires a displayed map surface [Repeated 1 time(s)] > volume style surface No volumes specified > volume style mesh No volumes specified > color sel bychain > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel surfaces > show sel surfaces > hide sel surfaces > set bgColor white > select ligand 96 atoms, 92 bonds, 7 residues, 1 model selected > view sel > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > show sel atoms > hide sel atoms > show sel atoms > ui windowfill toggle [Repeated 2 time(s)] > ui tool show ""Selection Inspector"" > hbonds sel reveal true 67 hydrogen bonds found > ui tool show ""Show Sequence Viewer"" > sequence chain /C Alignment identifier is 1/C > select > /C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051 7083 atoms, 7174 bonds, 877 residues, 1 model selected > select /C:447 8 atoms, 7 bonds, 1 residue, 1 model selected > select /C:447-450 30 atoms, 29 bonds, 4 residues, 1 model selected > select /C:443-445,451-453 49 atoms, 47 bonds, 6 residues, 1 model selected > select > /C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051 7083 atoms, 7174 bonds, 877 residues, 1 model selected > select /C:447-450 30 atoms, 29 bonds, 4 residues, 1 model selected > select /C:454 9 atoms, 8 bonds, 1 residue, 1 model selected > select /C:454-458 45 atoms, 45 bonds, 5 residues, 1 model selected > select /C:443-445,451-453 49 atoms, 47 bonds, 6 residues, 1 model selected > select /C:454-458 45 atoms, 45 bonds, 5 residues, 1 model selected > select > /C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051 7083 atoms, 7174 bonds, 877 residues, 1 model selected > select /C:539 6 atoms, 5 bonds, 1 residue, 1 model selected > select /C:539 6 atoms, 5 bonds, 1 residue, 1 model selected > color (#!1 & sel) yellow > color (#!1 & sel) #ffd479ff > color (#!1 & sel) #f8dd74ff > color (#!1 & sel) #f8de74ff > color (#!1 & sel) #f8df71ff > color (#!1 & sel) #f8e06dff > color (#!1 & sel) #f8df6aff > color (#!1 & sel) #f8de66ff > color (#!1 & sel) #f8dc65ff > color (#!1 & sel) #f8dc63ff > color (#!1 & sel) #f8de60ff > color (#!1 & sel) #f8de5dff > color (#!1 & sel) #f8df5aff > color (#!1 & sel) #f8df58ff > color (#!1 & sel) #f8df57ff [Repeated 1 time(s)] > color (#!1 & sel) #f8e056ff [Repeated 2 time(s)] > color (#!1 & sel) #f8e055ff [Repeated 1 time(s)] > color (#!1 & sel) #f8e153ff > color (#!1 & sel) #f8e152ff > color (#!1 & sel) #f8e151ff > color (#!1 & sel) #f8e04fff > color (#!1 & sel) #f8df4cff > color (#!1 & sel) #f8e04aff > color (#!1 & sel) #f8e048ff > color (#!1 & sel) #f8e047ff > color (#!1 & sel) #f8df46ff > color (#!1 & sel) #f8dc43ff > color (#!1 & sel) #f8d940ff > color (#!1 & sel) #f8d840ff > color (#!1 & sel) #f8d73fff [Repeated 1 time(s)] > color (#!1 & sel) #f8d63eff > color (#!1 & sel) #f8d53dff > color (#!1 & sel) #f8d33cff > color (#!1 & sel) #f8d039ff > color (#!1 & sel) #f8cc36ff > color (#!1 & sel) #f8c732ff > color (#!1 & sel) #f8c42fff [Repeated 2 time(s)] > color (#!1 & sel) #f8c42eff > color (#!1 & sel) #f8c32aff > color (#!1 & sel) #f8c124ff > color (#!1 & sel) #f8bf20ff > color (#!1 & sel) #f8bd1dff > color (#!1 & sel) #f8bd1cff > color (#!1 & sel) #f8bc1cff > color (#!1 & sel) #f8bd1cff > color (#!1 & sel) #f8bf19ff > color (#!1 & sel) #f8c215ff > color (#!1 & sel) #f8c312ff > color (#!1 & sel) #f8c411ff > color (#!1 & sel) #f8c712ff > color (#!1 & sel) #f8cc14ff > color (#!1 & sel) #f8cf16ff > color (#!1 & sel) #f8d218ff [Repeated 1 time(s)] > color (#!1 & sel) #f8d318ff > color (#!1 & sel) #f8d418ff > color (#!1 & sel) #f8d517ff [Repeated 1 time(s)] > color (#!1 & sel) #f8d617ff > color (#!1 & sel) #f8d716ff > color (#!1 & sel) #f8d815ff > color (#!1 & sel) #f8d914ff [Repeated 1 time(s)] > color (#!1 & sel) #f8d913ff > color (#!1 & sel) #f8da12ff > color (#!1 & sel) #f8db11ff > color (#!1 & sel) #f8dc0fff [Repeated 2 time(s)] > color (#!1 & sel) #f8dd0eff > color (#!1 & sel) #f8de0dff > color (#!1 & sel) #f8df0dff > color (#!1 & sel) #f8df0cff [Repeated 1 time(s)] > color (#!1 & sel) #f8e00bff > color (#!1 & sel) #f8e00aff > color (#!1 & sel) #f8e109ff [Repeated 3 time(s)] > color (#!1 & sel) #f8dd02ff > color (#!1 & sel) #f8dc01ff > color (#!1 & sel) #f8d900ff > color (#!1 & sel) #f8d800ff > color (#!1 & sel) #f8d600ff > color (#!1 & sel) #f8d400ff > color (#!1 & sel) #f8d100ff > color (#!1 & sel) #f8cf00ff > color (#!1 & sel) #f8ce00ff > color (#!1 & sel) #f8d100ff > color (#!1 & sel) #f8d202ff [Repeated 2 time(s)] > color (#!1 & sel) #f8d302ff > color (#!1 & sel) #f8d301ff [Repeated 1 time(s)] > color (#!1 & sel) #f8d400ff > color (#!1 & sel) #f8d600ff > color (#!1 & sel) #f8d400ff > color (#!1 & sel) #f8d600ff > color (#!1 & sel) #f8d400ff > select ::name=""LMB"" 40 atoms, 39 bonds, 1 residue, 1 model selected > color sel byelement > view sel > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > select > /C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051 7083 atoms, 7174 bonds, 877 residues, 1 model selected > select /C:-1 4 atoms, 3 bonds, 1 residue, 1 model selected > select /C:-1-1052 8202 atoms, 8359 bonds, 1017 residues, 1 model selected > mlp sel Map values for surface ""4hat_C SES surface"": minimum -30.1, mean -4.745, maximum 24.83 To also show corresponding color key, enter the above mlp command and add key true > select /C:-1-1052 8202 atoms, 8359 bonds, 1017 residues, 1 model selected > select /C:-1-1052 8202 atoms, 8359 bonds, 1017 residues, 1 model selected > mlp sel Map values for surface ""4hat_C SES surface"": minimum -30.1, mean -4.745, maximum 24.83 To also show corresponding color key, enter the above mlp command and add key true > mlp sel Map values for surface ""4hat_C SES surface"": minimum -30.1, mean -4.745, maximum 24.83 To also show corresponding color key, enter the above mlp command and add key true > mlp sel Map values for surface ""4hat_C SES surface"": minimum -30.1, mean -4.745, maximum 24.83 To also show corresponding color key, enter the above mlp command and add key true > mlp sel Map values for surface ""4hat_C SES surface"": minimum -30.1, mean -4.745, maximum 24.83 To also show corresponding color key, enter the above mlp command and add key true > color sel bychain > preset ""initial styles"" cartoon Using preset: Initial Styles / Cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > color sel bychain > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 4hat_C SES surface #1.2: minimum, -20.99, mean -2.65, maximum 11.74 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""4hat_C SES surface"": minimum -30.1, mean -4.745, maximum 24.83 To also show corresponding color key, enter the above mlp command and add key true > transparency (#!1 & sel) 30 > transparency (#!1 & sel) 90 > transparency (#!1 & sel) 70 > color sel bychain > transparency (#!1 & sel) 70 > transparency (#!1 & sel) 50 > select sel :< 3 & sel :> 3 Nothing selected > select /C:-1-1052 8202 atoms, 8359 bonds, 1017 residues, 1 model selected > select /C:576 7 atoms, 6 bonds, 1 residue, 1 model selected > select /C:576-578 23 atoms, 22 bonds, 3 residues, 1 model selected > select > /C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051 7083 atoms, 7174 bonds, 877 residues, 1 model selected > select /C:595-596 11 atoms, 10 bonds, 2 residues, 1 model selected > select /C:595-596 11 atoms, 10 bonds, 2 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /C Destroying pre-existing alignment with identifier 1/C Alignment identifier is 1/C > select > /C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051 7083 atoms, 7174 bonds, 877 residues, 1 model selected > select /C 9410 atoms, 8415 bonds, 33 pseudobonds, 2170 residues, 2 models selected > select /C:576 7 atoms, 6 bonds, 1 residue, 1 model selected > select /C:576-577 15 atoms, 14 bonds, 2 residues, 1 model selected > select /C:577 8 atoms, 7 bonds, 1 residue, 1 model selected > select /C:576-577 15 atoms, 14 bonds, 2 residues, 1 model selected > open 4hat 4hat title: Crystal structure of CRM1 inhibitor Leptomycin B in complex with CRM1-Ran- RanBP1 [more info...] Chain information for 4hat #2 --- Chain | Description | UniProt A | GTP-binding nuclear protein Ran | RAN_HUMAN B | Ran-specific GTPase-activating protein 1 | YRB1_YEAST C | Exportin-1 | XPO1_YEAST Non-standard residues in 4hat #2 --- CL — chloride ion EDO — 1,2-ethanediol (ethylene glycol) GNP — phosphoaminophosphonic acid-guanylate ester GOL — glycerol (glycerin; propane-1,2,3-triol) LMB — Leptomycin B, bound form MG — magnesium ion > select ::name=""CYS"" 240 atoms, 200 bonds, 40 residues, 2 models selected > select #1/C:596-597 14 atoms, 13 bonds, 2 residues, 1 model selected > select #1/C:596-597 14 atoms, 13 bonds, 2 residues, 1 model selected > select #1/C:596 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:596 6 atoms, 5 bonds, 1 residue, 1 model selected > select ::name=""CYS"" 240 atoms, 200 bonds, 40 residues, 2 models selected > color (#!1-2 & sel) orange > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > color sel bychain [Repeated 1 time(s)] > select > #1/C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051 7083 atoms, 7174 bonds, 877 residues, 1 model selected > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > color sel bychain > select #1/C:-1-1052 8202 atoms, 8359 bonds, 1017 residues, 1 model selected > color sel bychain > select #1/C:606 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:606-607 15 atoms, 14 bonds, 2 residues, 1 model selected > select #1/C:606 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:606 6 atoms, 5 bonds, 1 residue, 1 model selected > select > #1/C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051 7083 atoms, 7174 bonds, 877 residues, 1 model selected > select #1/C:596 6 atoms, 5 bonds, 1 residue, 1 model selected > select ::name=""CYS"" 240 atoms, 200 bonds, 40 residues, 2 models selected > select #1/C:648 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:648 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:606 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:606 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:710 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:710-711 13 atoms, 12 bonds, 2 residues, 1 model selected > select #1/C:710 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:525-710 1507 atoms, 1534 bonds, 186 residues, 1 model selected > select #1/C:525 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/C:525 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/C:255 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:255 6 atoms, 5 bonds, 1 residue, 1 model selected > select ::name=""CYS"" 240 atoms, 200 bonds, 40 residues, 2 models selected > select #1/C:102 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:102 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:255 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:255 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:102 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:102 6 atoms, 5 bonds, 1 residue, 1 model selected > select ::name=""CYS"" 240 atoms, 200 bonds, 40 residues, 2 models selected > select #1/C:1022 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:1022 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:890 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:890 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:840 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:840 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:710 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:710 6 atoms, 5 bonds, 1 residue, 1 model selected > ui tool show Matchmaker > select #1/C:210 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/C:210-217 58 atoms, 57 bonds, 8 residues, 1 model selected > select #1/C:239 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:239-251 100 atoms, 101 bonds, 13 residues, 1 model selected > select #1/C:299 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/C:299-311 96 atoms, 97 bonds, 13 residues, 1 model selected > select #1/C:361-362 14 atoms, 13 bonds, 2 residues, 1 model selected > select #1/C:361-371 94 atoms, 97 bonds, 11 residues, 1 model selected > select #1/C:89-122 268 atoms, 269 bonds, 34 residues, 1 model selected > select #1/C:89-131 348 atoms, 352 bonds, 43 residues, 1 model selected > select #1/C:184-185 14 atoms, 13 bonds, 2 residues, 1 model selected > select #1/C:184-193 83 atoms, 83 bonds, 10 residues, 1 model selected > select #1/C:211-212 12 atoms, 11 bonds, 2 residues, 1 model selected > select #1/C:211-223 113 atoms, 116 bonds, 13 residues, 1 model selected > select #1/C:244 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/C:244-284 329 atoms, 332 bonds, 41 residues, 1 model selected > select #1/C:300 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/C:300-313 108 atoms, 109 bonds, 14 residues, 1 model selected > select #1/C:331 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/C:331-375 389 atoms, 397 bonds, 45 residues, 1 model selected > select #1/C:364 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/C:364-373 88 atoms, 91 bonds, 10 residues, 1 model selected > select #1/C:461 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/C:461-477 147 atoms, 149 bonds, 17 residues, 1 model selected > select #1/C:435-436 15 atoms, 14 bonds, 2 residues, 1 model selected > select #1/C:435-479 375 atoms, 379 bonds, 45 residues, 1 model selected > select #1/C:494-535 334 atoms, 341 bonds, 42 residues, 1 model selected > select #1/C:494-537 350 atoms, 357 bonds, 44 residues, 1 model selected > select > #1/C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051 7083 atoms, 7174 bonds, 877 residues, 1 model selected > select #1/C:539 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:539 6 atoms, 5 bonds, 1 residue, 1 model selected > color (#!1 & sel) yellow > label (#!1 & sel) attribute name > label (#!1 & sel) attribute label_specifier > label (#!1 & sel) text ""/{0.chain_id} {0.label_one_letter_code} > {0.number}{0.insertion_code}"" > label (#!1 & sel) text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > label (#!1 & sel) attribute label_one_letter_code > label (#!1 & sel) text ""{0.name} {0.number}{0.insertion_code}"" > label height 1 > label height 0.9 > label (#!1 & sel) atoms text C539 > color (#!1 & sel) yellow > ~label (#!1 & sel) residues > label (#!1 & sel) text default > ~label (#!1 & sel) residues [Repeated 1 time(s)] > label (#!1 & sel) attribute label_specifier > select #1/C#2/C 18820 atoms, 16830 bonds, 33 pseudobonds, 4340 residues, 3 models selected > ~label (#!1-2 & sel) residues > ~label (#!1-2 & sel) atoms > select #1/C:539 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:539 6 atoms, 5 bonds, 1 residue, 1 model selected > label (#!1 & sel) text ""{0.name} {0.number}{0.insertion_code}"" No visible Surface models selected > color sel bychain > undo > select #1/C:520 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:520-527 70 atoms, 70 bonds, 8 residues, 1 model selected > select #1/C:518 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/C:518-537 162 atoms, 162 bonds, 20 residues, 1 model selected > select #1/C:540 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/C:540-604 537 atoms, 549 bonds, 65 residues, 1 model selected > select #1/C:538 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/C:538-541 30 atoms, 29 bonds, 4 residues, 1 model selected > select > #1/C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051 7083 atoms, 7174 bonds, 877 residues, 1 model selected > select #1/C:557 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/C:557-575 171 atoms, 178 bonds, 19 residues, 1 model selected > select #1/C:546 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/C:546-584 329 atoms, 338 bonds, 39 residues, 1 model selected > select #1/C:520 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:520-584 539 atoms, 549 bonds, 65 residues, 1 model selected > label (#!1 & sel) text ""{0.name} {0.number}{0.insertion_code}"" QGestureManager::deliverEvent: could not find the target for gesture > undo > cartoon style (#!1 & sel) xsection oval modeHelix default > select ligand 192 atoms, 184 bonds, 14 residues, 2 models selected > mlp sel mlp: no amino acids specified > ~label sel residues > select #1/C:520 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:520-584 539 atoms, 549 bonds, 65 residues, 1 model selected > select #1/C:520-584 539 atoms, 549 bonds, 65 residues, 1 model selected > select #1/C:520-584 539 atoms, 549 bonds, 65 residues, 1 model selected > select #1/C:520-584 539 atoms, 549 bonds, 65 residues, 1 model selected > ~label (#!1 & sel) residues > select > #1/C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051 7083 atoms, 7174 bonds, 877 residues, 1 model selected > select #1/C:582 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/C:582 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > label (#!1 & sel) attribute label_specifier > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > ~label (#!1 & sel) residues > select > #1/C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051 7083 atoms, 7174 bonds, 877 residues, 1 model selected > select #1/C:539 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:539 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select ::name=""CL"" 8 atoms, 8 residues, 2 models selected > hide sel cartoons > select ::name=""EDO"" 24 atoms, 18 bonds, 6 residues, 2 models selected > hide sel cartoons > select ::name=""GNP"" 64 atoms, 68 bonds, 2 residues, 2 models selected > hide sel atoms > select ::name=""GOL"" 24 atoms, 20 bonds, 4 residues, 2 models selected > hide sel atoms > color bfactor sel 24 atoms, 4 residues, atom bfactor range 36.6 to 71.2 > select #1/C:520 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:520-584 539 atoms, 549 bonds, 65 residues, 1 model selected > show sel cartoons [Repeated 1 time(s)] > show sel atoms > hide sel atoms > undo [Repeated 1 time(s)] > preset ""initial styles"" cartoon Using preset: Initial Styles / Cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > undo [Repeated 4 time(s)] > hide sel atoms > color sel bychain > select 24862 atoms, 22366 bonds, 79 pseudobonds, 5628 residues, 5 models selected > color sel bychain > select ::name=""LMB"" 80 atoms, 78 bonds, 2 residues, 2 models selected > color sel byelement > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset ""initial styles"" cartoon Using preset: Initial Styles / Cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > undo [Repeated 4 time(s)] > redo [Repeated 2 time(s)] > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > select #1/C:520 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:520-584 539 atoms, 549 bonds, 65 residues, 1 model selected > rainbow sel > color sel byhetero [Repeated 1 time(s)] > color sel bychain > color sel bynucleotide > color bfactor sel 539 atoms, 65 residues, 1 surfaces, atom bfactor range 17 to 97.2 > hbonds sel reveal true 390 hydrogen bonds found > ~hbonds > select ::name=""HOH"" 2910 atoms, 2910 residues, 2 models selected > hide sel atoms > select #1/C:520 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:520-584 539 atoms, 549 bonds, 65 residues, 1 model selected > color sel bychain > show (#!1 & sel-residues & sidechain) target ab > hide sel atoms [Repeated 2 time(s)] > select #1/C:539 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:539 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > show sel atoms > color (#!1 & sel) orange > select ::name=""LMB"" 80 atoms, 78 bonds, 2 residues, 2 models selected > color sel byhetero > color sel byelement > select > #1/C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051 7083 atoms, 7174 bonds, 877 residues, 1 model selected > surface (#!1 & sel) > select #1/C:-1-1052 8202 atoms, 8359 bonds, 1017 residues, 1 model selected > surface (#!1 & sel) > transparency (#!1 & sel) 50 > transparency (#!1 & sel) 80 > open ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/UCSF > ChimeraX-YewujI/download.png"" Image mode RGBA is not supported (L, P, I;16, I;16B, I;16L, I;16S, F, F;32BF, I, RGB) > alphafold fetch Missing or invalid ""uniprotId"" argument: Expected a text string > O14980 Unknown command: O14980 > alphafold fetch O14980 Fetching compressed AlphaFold O14980 from https://alphafold.ebi.ac.uk/files/AF-O14980-F1-model_v4.cif Chain information for AlphaFold O14980 #3 --- Chain | Description | UniProt A | Exportin-1 | XPO1_HUMAN > ui tool show Matchmaker > matchmaker #3 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 4hat, chain C (#2) with AlphaFold O14980, chain A (#3), sequence alignment score = 3127.6 RMSD between 763 pruned atom pairs is 1.151 angstroms; (across all 1006 pairs: 3.662) > surface hidePatches (#!1 & sel) > color sel bychain [Repeated 1 time(s)] > select 33531 atoms, 31217 bonds, 12 pseudobonds, 6699 residues, 7 models selected > color sel bychain [Repeated 1 time(s)] > ui tool show ""Model Panel"" > hide #!1 models > select subtract #1 21100 atoms, 20034 bonds, 6 pseudobonds, 3885 residues, 4 models selected > color #3 #942193ff > color #3 #8e668dff > color #3 #00fdffff > color #3 #73fdffff > color #3 #c2f6fdff > color #3 #c7ebfdff > color #3 #c9fdc7ff > color #3 #eddcfdff > color #3 #dab2fdff > color #3 #fdaec3ff > color #3 #fdd4a5ff > color #3 #d5affdff > color #3 #c0a4fdff > color #3 #c7aafdff > color #3 #c2a5f7ff > close #1 > ui tool show ""Show Sequence Viewer"" > sequence chain #2/C Alignment identifier is 2/C > select #2/C:596 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms [Repeated 1 time(s)] > hide sel atoms > select > #2/C:-1-6,12-44,46-58,60-130,136-145,148-168,175-204,207-221,226-231,233-261,268-290,296-304,307-331,333-351,355-374,416-434,458-496,501-515,520-542,544-584,588-612,620-634,637-653,657-686,688-714,717-777,779-823,826-846,852-876,878-894,897-919,921-945,948-968,986-1003,1007-1021,1024-1039,1045-1051 7083 atoms, 7174 bonds, 877 residues, 1 model selected > select #2/C:539 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > color sel yellow > select ::name=""LMB"" 40 atoms, 39 bonds, 1 residue, 1 model selected > color sel byelement > hbonds sel reveal true 12 hydrogen bonds found > hide #3 models > color :sti & C salmon > color :LMB salmon > color :sti & LMB salmon Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > select :sti Nothing selected > select :LMB 40 atoms, 39 bonds, 1 residue, 1 model selected > view sel > hide~ sel Unknown command: hide~ sel > hide~sel Unknown command: hide~sel > hide ~sel > hbonds :LMB reveal true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 2 4hat 3 AlphaFold O14980 12 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 4hat #2/C LYS 525 NZ 4hat #2/C LMB 1101 O5 no hydrogen 3.160 N/A 4hat #2/C LYS 525 NZ 4hat #2/C LMB 1101 O6 no hydrogen 3.505 N/A 4hat #2/C LYS 548 NZ 4hat #2/C LMB 1101 O1 no hydrogen 2.696 N/A 4hat #2/C LMB 1101 O4 4hat #2/C HOH 2126 O no hydrogen 2.648 N/A 4hat #2/C HOH 1892 O 4hat #2/C LMB 1101 O3 no hydrogen 2.793 N/A 4hat #2/C HOH 1892 O 4hat #2/C LMB 1101 O6 no hydrogen 3.091 N/A 4hat #2/C HOH 2126 O 4hat #2/C LMB 1101 O4 no hydrogen 2.648 N/A 4hat #2/C HOH 2300 O 4hat #2/C LMB 1101 O1 no hydrogen 3.399 N/A 4hat #2/C HOH 2300 O 4hat #2/C LMB 1101 O1' no hydrogen 2.950 N/A 4hat #2/C HOH 2307 O 4hat #2/C LMB 1101 O6 no hydrogen 3.304 N/A 4hat #2/C HOH 2308 O 4hat #2/C LMB 1101 O5 no hydrogen 2.503 N/A AlphaFold O14980 #3/A LYS 537 NZ 4hat #2/C LMB 1101 O1 no hydrogen 2.456 N/A 12 hydrogen bonds found > save ""/Users/jrutter/Dropbox (MIT)/Ebert > Lab/Ebert_computational/XPO1_LMB.cxs"" Traceback (most recent call last): File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/blastprotein/ui/results.py"", line 150, in take_snapshot , 'table_session': self.table.session_info() AttributeError: 'BlastProteinResults' object has no attribute 'table' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> : Error while saving session data for 'tools' -> -> ValueError: error processing: 'tools' -> -> : Error while saving session data for 'tools' -> -> File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/blastprotein/ui/results.py"", line 150, in take_snapshot , 'table_session': self.table.session_info() AttributeError: 'BlastProteinResults' object has no attribute 'table' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> : Error while saving session data for 'tools' -> -> ValueError: error processing: 'tools' -> -> : Error while saving session data for 'tools' -> -> File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > ui tool show Log > ui tool show ""Command Line Interface"" > alphafold predict > MPAIMTMLADHAARQLLDFSQKLDINLLDNVVNCLYHGEGAQQRMAQEVLTHLKEHPDAWTRVDTILEFSQNMNTKYYGLQILENVIKTRWKILPRNQCEGIKKYVVGLIIKTSSDPTCVEKEKVYIGKLNMILVQILKQEWPKHWPTFISDIVGASRTSESLCQNNMVILKLLSEEVFDFSSGQITQVKSKHLKDSMCNEFSQIFQLCQFVMENSQNAPLVHATLETLLRFLNWIPLGYIFETKLISTLIYKFLNVPMFRNVSLKCLTEIAGVSVSQYEEQFVTLFTLTMMQLKQMLPLNTNIRLAYSNGKDDEQNFIQNLSLFLCTFLKEHDQLIEKRLNLRETLMEALHYMLLVSEVEETEIFKICLEYWNHLAAELYRESPFSTSASPLLSGSQHFDVPPRRQLYLPMLFKVRLLMVSRMAKPEEVLVVENDQGEVVREFMKDTDSINLYKNMRETLVYLTHLDYVDTERIMTEKLHNQVNGTEWSWKNLNTLCWAIGSISGAMHEEDEKRFLVTVIKDLLGLCEQKRGKDNKAIIASNIMYIVGQYPRFLRAHWKFLKTVVNKLFEFMHETHDGVQDMACDTFIKIAQKCRRHFVQVQVGEVMPFIDEILNNINTIICDLQPQQVHTFYEAVGYMIGAQTDQTVQEHLIEKYMLLPNQVWDSIIQQATKNVDILKDPETVKQLGSILKTNVRACKAVGHPFVIQLGRIYLDMLNVYKCLSENISAAIQANGEMVTKQPLIRSMRTVKRETLKLISGWVSRSNDPQMVAENFVPPLLDAVLIDYQRNVPAAREPEVLSTMAIIVNKLGGHITAEIPQIFDAVFECTLNMINKDFEEYPEHRTNFFLLLQAVNSHCFPAFLAIPPTQFKLVLDSIIWAFKHTMRNVADTGLQILFTLLQNVAQEEAAAQSFYQTYFCDILQHIFSVVTDTSHTAGLTMHASILAYMFNLVEEGKISTSLNPGNPVNNQIFLQEYVANLLKSAFPHLQDAQVKLFVTGLFSLNQDIPAFKEHLRDFLVQIKEFAGEDTSDLFLEEREIALRQADEEKHKRQMSVPGIFNPHEIPEEMCD,MSSSMWYIMQSIQSKYSLSERLIRTIAAIRSFPHDNVEDLIRGGADVNCTHGTLKPLHCACMVSDADCVELLLEKGAEVNALDGYNRTALHYAAEKDEACVEVLLEYGANPNALDGNRDTPLHWAAFKNNAECVRALLESGASVNALDYNNDTPLSWAAMKGNLESVSILLDYGAEVRVINLIGQTPISRLVALLVRGLGTEKEDSCFELLHRAVGHFELRKNGTMPREVARDPQLCEKLTVLCSAPGTLKTLARYAVRRSLGLQYLPDAVKGLPLPASLKEYLLLLE Running AlphaFold prediction > save ""/Users/jrutter/Dropbox (MIT)/Ebert > Lab/Ebert_computational/ChimeraX/XPO1.cxs"" Traceback (most recent call last): File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/blastprotein/ui/results.py"", line 150, in take_snapshot , 'table_session': self.table.session_info() AttributeError: 'BlastProteinResults' object has no attribute 'table' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> : Error while saving session data for 'tools' -> -> ValueError: error processing: 'tools' -> -> : Error while saving session data for 'tools' -> -> File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/blastprotein/ui/results.py"", line 150, in take_snapshot , 'table_session': self.table.session_info() AttributeError: 'BlastProteinResults' object has no attribute 'table' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> : Error while saving session data for 'tools' -> -> ValueError: error processing: 'tools' -> -> : Error while saving session data for 'tools' -> -> File ""/private/var/folders/q_/_54tqhsx2l55p935l4k82d280000gn/T/AppTranslocation/AD45645C-C953-4216-9730-58DE5BABC190/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir10,1 Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 7459.101.3 OS Loader Version: 7459.101.3 Software: System Software Overview: System Version: macOS 12.3.1 (21E258) Kernel Version: Darwin 21.4.0 Time since boot: 9 days 13:50 Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.6 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 setuptools-scm: 7.0.5 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 typing-extensions: 4.4.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.11.0 }}} " defect closed normal Sequence fixed all ChimeraX