id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16748 alphafold pae does not accept wild cards for file patterns matthias.vorlaender@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.3.1-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description alphafold pae does not accept wild cards for file patterns. While I can do: open AF_predictions/*model_1.cif and alphafold pae #1 file AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_full_data_1.json I cannot do alphafold pae #1 file AF_predictions/*data_1.json Invalid ""file"" argument: File 'AF_predictions/*data_1.json' does not exist Due to the stereotypical file naming of AF results, wild cards would be very useful to save a lot of typing and for scripting Log: Startup Messages --- note | available bundle cache has not been initialized yet > ui tool show CliX > alias map_missense runscript > /Users/matthias.vorlaender/Documents/ChimeraX_presets/map_missense.cxc $1 $2 > alias missense mutationscores define avg fromScore amiss setAttribute true > combine meancamera ortho > cofr centerOfView > volume defaultvalues limitVoxelCount false voxelLimitForPlane > 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true Saved volume settings > mousemode rightMode clip > mousemode alt rightMode ""contour level"" > mousemode alt leftMode ""translate selected models"" > mousemode shift leftMode ""rotate selected models"" > mousemode alt control leftMode ""pick blobs"" > alias cofron cofr centerofview showpivot 7,0.25 > alias cofroff cofr centerofview showpivot false > alias symclip cofr centerofview; clip near -$1 far $1 position cofr [Repeated 1 time(s)] > alias cootmode set bgColor black; surface cap false; surface style solid; > lighting flat; graphics silhouettes false; style stick; ~rib; color > ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style > solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70; > cofr centerofview; clip near -10 far 10 position cofr; color ~##num_residues > cornflower blue > alias cootmode_mesh surface cap false; surface style mesh; lighting flat; > graphics silhouettes false; style stick; ~rib; color ##num_residues gold; > color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size > ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far > 10 position cofr; color ~##num_residues #3d60ffff; transparency 50 > alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; > disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp > ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1 > alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp > @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius > 0.1 > alias map_sphere_15 volume unzone ##~num_residues; sel; close #10000; marker > #10000 position cofr; sel ~sel; volume zone ~##num_residues nearAtoms sel > minimalBounds true range 15; close #10000 > alias map_unsphere volume unzone ~##num_residues > alias map_sphere_15 volume unzone ##~num_residues; sel; close #10000; marker > #10000 position cofr; sel ~sel; volume zone ~##num_residues nearAtoms sel > minimalBounds true range 15; close #10000 > alias map_unsphere volume unzone ~##num_residues > alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5; > lighting soft > alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker > #10000 position cofr; sel ~sel; surface zone ~##num_residues nearAtoms sel > distance 0; close #10000 > alias showmaps surface unzone ~##num_residues > alias caps_off surface cap false > alias caps_on surface cap true > alias selbetween ks ri > alias helix setattr $1 res is_helix true > alias strand setattr $1 res is_strand true > alias coil setattr $1 res is_strand false; setattr $1 res is_helix false > alias rock_movie cofr showpivot false; movie record; rock y 30; wait 136; > movie encode ~/Desktop/rock_movie.mp4; stop > alias open_vseries ""open browse vseries true"" > alias cubic_map shape sphere radius $1 modelid #10000; volume onesmask > #10000 spacing 1 border -0.5 > buttonpanel Shortcuts rows 3 columns 5 > buttonpanel Shortcuts add Vol_Viewer command ""tool show 'Volume Viewer'"" > buttonpanel Shortcuts add Model_Panel command ""tool show Models"" > buttonpanel Shortcuts add Log command ""tool show Log"" > buttonpanel Shortcuts add default_disp command default_mol_display > buttonpanel Shortcuts add map_sphere command map_sphere_15 > buttonpanel Shortcuts add map_unsphere command map_unsphere > buttonpanel Shortcuts add cofron command cofron > buttonpanel Shortcuts add cofroff command cofroff > buttonpanel Shortcuts add cootmode command cootmode > buttonpanel Shortcuts add mark_cofr command ""marker #20000 position cofr > radius 1"" > buttonpanel Shortcuts add hidemaps command hidemaps > buttonpanel Shortcuts add showmaps command showmaps > buttonpanel Shortcuts add reset_mouse command ""mousemode alt right contour ; > mousemode right clip ; mousemode alt left 'translate selected models' ; > mousemode shift left 'rotate selected models' ; mousemode alt control left > 'pick blobs'; help https://github.com/olibclarke/chimerax- > trimmings/blob/main/default_mousemodes.md"" > buttonpanel Shortcuts add view command view > buttonpanel Shortcuts add selbetween command ""ks ri"" UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > cd /Users/matthias.vorlaender/Library/CloudStorage/OneDrive- > VBC/HDYDI_ChimeraX Current working directory is: /Users/matthias.vorlaender/Library/CloudStorage/OneDrive-VBC/HDYDI_ChimeraX > alphafold interfaces ./Alphafold_missense_script 0 of 0 dimers have 10 or more confident residue interactions spanning <= 4 Angstroms with predicted aligned error <= 5 Angstroms. > alphafold interfaces ./AF_predictions 1 of 1 dimers have 10 or more confident residue interactions spanning <= 4 Angstroms with predicted aligned error <= 5 Angstroms. Sequences| Models| Confident pairs| #Res1| #Res2 | 2025_01_30_14_44_eif4a3_aly | 4 | 31 | 15 | 12 ---|---|---|---|--- Open best. Hide or show disordered loops (pLLDT <= 50). > open ./AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_model_3.cif Chain information for fold_2025_01_30_14_44_eif4a3_aly_model_3.cif #1 --- Chain | Description A | . B | . Computing secondary structure > rename last-opened 2025_01_30_14_44_eif4a3_aly > color last-opened bypolymer > select > /A:178,179,198,199,201,202,203,205,206,207,208,209,210,231,232/B:81,83,84,85,86,87,88,89,90,91,92,94 > & last-opened 248 atoms, 251 bonds, 27 residues, 1 model selected > alphafold pae last-opened file > ./AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_full_data_3.json plot > false > alphafold contacts last-opened & /A toAtoms last-opened & /B distance 4.0 > maxPae 5.0 Found 31 residue or atom pairs within distance 4 with pae <= 5 > wait 1 > tile 1 model tiled > label all models > open ./AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_model_3.cif Chain information for fold_2025_01_30_14_44_eif4a3_aly_model_3.cif #2 --- Chain | Description A | . B | . > rename last-opened 2025_01_30_14_44_eif4a3_aly > color last-opened bypolymer > select > /A:178,179,198,199,201,202,203,205,206,207,208,209,210,231,232/B:81,83,84,85,86,87,88,89,90,91,92,94 > & last-opened 248 atoms, 251 bonds, 27 residues, 1 model selected > alphafold pae last-opened file > ./AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_full_data_3.json > alphafold contacts last-opened & /A toAtoms last-opened & /B distance 4.0 > maxPae 5.0 Found 31 residue or atom pairs within distance 4 with pae <= 5 Computing secondary structure > open /Users/matthias.vorlaender/Library/CloudStorage/OneDrive- > VBC/HDYDI_ChimeraX/ChimeraX_tutorial_chimerax.html Opened ChimeraX_tutorial_chimerax.html > color #2/A:51 lime > color #2/A:227 magenta > color #2/B:97-196 lime > alphafold pae #2 colorDomains true > color #2/A:27-247 lime > color #2/B:82-94 magenta > name frozen interface sel > rainbow chains palette bupu > map_missense Q86V81 #1/B > echo Usage: runscript map_missense [uniprot-id-to-fetch-scores-from] [chain- > ID to apply mapping to] Usage: runscript map_missense [uniprot-id-to-fetch-scores-from] [chain-ID to apply mapping to] > alphafold fetch Q86V81 Chain information for AlphaFold Q86V81 #3 --- Chain | Description | UniProt A | THO complex subunit 4 | THOC4_HUMAN 1-257 Color AlphaFold Q86V81 by residue attribute pLDDT_score > open Q86V81 fromDatabase alpha_missense format amiss Summary of feedback from opening Q86V81 fetched from alpha_missense --- note | Plotted 4883 scores having range 0.0438 to 1 for amiss Fetched AlphaMissense scores Q86V81 for 257 residues > mutationscores structure #1/B mutationSet Q86V81 > mutationscores label #1/B amiss height 3 mutationSet Q86V81 Added 257 residue labels to chain 2025_01_30_14_44_eif4a3_aly #1/B for amiss (0.0438 - 1), no mutation scores for 0 residues > mutationscores define avg fromScoreName amiss setAttribute true combine mean > mutationSet Q86V81 Defined score avg having range 0.232 to 1 for 257 residues using 4883 mutations Set attribute avg for 257 residues of chain 2025_01_30_14_44_eif4a3_aly #1/B > color byattribute r:avg #1/B target csab palette bluered range full 1888 atoms, 257 residues, atom avg range 0.232 to 1 > cartoon byattribute r:avg #1/B 668 residues, residue avg range 0.232 to 1 > hide #!2 [Repeated 1 time(s)] > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > ~label ~interface > hide #!2 models > hide #3 models > ui mousemode right translate > show #!2 models > hide #!2 models > ~label ~interface > map_missense Q86V81 #1/B > echo Usage: runscript map_missense [uniprot-id-to-fetch-scores-from] [chain- > ID to apply mapping to] Usage: runscript map_missense [uniprot-id-to-fetch-scores-from] [chain-ID to apply mapping to] > alphafold fetch Q86V81 Chain information for AlphaFold Q86V81 #4 --- Chain | Description | UniProt A | THO complex subunit 4 | THOC4_HUMAN 1-257 Color AlphaFold Q86V81 by residue attribute pLDDT_score > open Q86V81 fromDatabase alpha_missense format amiss Summary of feedback from opening Q86V81 fetched from alpha_missense --- note | Plotted 9766 scores having range 0.0438 to 1 for amiss Fetched AlphaMissense scores Q86V81 for 257 residues > mutationscores structure #1/B mutationSet Q86V81 > mutationscores label #1/B amiss height 3 mutationSet Q86V81 Added 257 residue labels to chain 2025_01_30_14_44_eif4a3_aly #1/B for amiss (0.0438 - 1), no mutation scores for 0 residues > mutationscores define avg fromScoreName amiss setAttribute true combine mean > mutationSet Q86V81 Defined score avg having range 0.232 to 1 for 257 residues using 9766 mutations Set attribute avg for 257 residues of chain 2025_01_30_14_44_eif4a3_aly #1/B > color byattribute r:avg #1/B target csab palette bluered range full 1888 atoms, 257 residues, atom avg range 0.232 to 1 > cartoon byattribute r:avg #1/B 668 residues, residue avg range 0.232 to 1 > hide #4 models > close #3-4 > name frozen interface sel > select interfaces Expected an objects specifier or a keyword > select interface 248 atoms, 251 bonds, 31 pseudobonds, 27 residues, 2 models selected > ~label ~interface > label interface > hide #2.1 models > hide #2.2 models > 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 ~worm 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 > view interface No displayed objects specified. > close > alphafold interfaces AF_predictions 1 of 1 dimers have 10 or more confident residue interactions spanning <= 4 Angstroms with predicted aligned error <= 5 Angstroms. Sequences| Models| Confident pairs| #Res1| #Res2 | 2025_01_30_14_44_eif4a3_aly | 4 | 31 | 15 | 12 ---|---|---|---|--- Open best. Hide or show disordered loops (pLLDT <= 50). > open AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_model_3.cif Chain information for fold_2025_01_30_14_44_eif4a3_aly_model_3.cif #1 --- Chain | Description A | . B | . Computing secondary structure > rename last-opened 2025_01_30_14_44_eif4a3_aly > color last-opened bypolymer > select > /A:178,179,198,199,201,202,203,205,206,207,208,209,210,231,232/B:81,83,84,85,86,87,88,89,90,91,92,94 > & last-opened 248 atoms, 251 bonds, 27 residues, 1 model selected > alphafold pae last-opened file > AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_full_data_3.json > alphafold contacts last-opened & /A toAtoms last-opened & /B distance 4.0 > maxPae 5.0 Found 31 residue or atom pairs within distance 4 with pae <= 5 > name frozen interface sel > rainbow chains palette bupu > map_missense Q86V81 #1/B > echo Usage: runscript map_missense [uniprot-id-to-fetch-scores-from] [chain- > ID to apply mapping to] Usage: runscript map_missense [uniprot-id-to-fetch-scores-from] [chain-ID to apply mapping to] > alphafold fetch Q86V81 Chain information for AlphaFold Q86V81 #2 --- Chain | Description | UniProt A | THO complex subunit 4 | THOC4_HUMAN 1-257 Color AlphaFold Q86V81 by residue attribute pLDDT_score > open Q86V81 fromDatabase alpha_missense format amiss Summary of feedback from opening Q86V81 fetched from alpha_missense --- note | Plotted 14649 scores having range 0.0438 to 1 for amiss Fetched AlphaMissense scores Q86V81 for 257 residues > mutationscores structure #1/B mutationSet Q86V81 > mutationscores label #1/B amiss height 3 mutationSet Q86V81 Added 257 residue labels to chain 2025_01_30_14_44_eif4a3_aly #1/B for amiss (0.0438 - 1), no mutation scores for 0 residues > mutationscores define avg fromScoreName amiss setAttribute true combine mean > mutationSet Q86V81 Defined score avg having range 0.232 to 1 for 257 residues using 14649 mutations Set attribute avg for 257 residues of chain 2025_01_30_14_44_eif4a3_aly #1/B > color byattribute r:avg #1/B target csab palette bluered range full 1888 atoms, 257 residues, atom avg range 0.232 to 1 > cartoon byattribute r:avg #1/B 668 residues, residue avg range 0.232 to 1 > hide #!2 > hide #2 models > ~label ~interface > 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 ~worm 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 > show interface atoms > view interface > colour byhetero > open AF_predictions/*.cif Chain information for fold_2025_01_30_14_44_eif4a3_aly_model_0.cif #3 --- Chain | Description A | . B | . Chain information for fold_2025_01_30_14_44_eif4a3_aly_model_1.cif #4 --- Chain | Description A | . B | . Chain information for fold_2025_01_30_14_44_eif4a3_aly_model_2.cif #5 --- Chain | Description A | . B | . Chain information for fold_2025_01_30_14_44_eif4a3_aly_model_3.cif #6 --- Chain | Description A | . B | . Chain information for fold_2025_01_30_14_44_eif4a3_aly_model_4.cif #7 --- Chain | Description A | . B | . Computing secondary structure [Repeated 4 time(s)] > mcopy #1 toAtoms #3-7 > hide #!1 > name RecA2 /A:47-240 > mmaker #3-7&RecA2 to #1&RecA2 Computing secondary structure [Repeated 5 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2025_01_30_14_44_eif4a3_aly, chain A (#1) with fold_2025_01_30_14_44_eif4a3_aly_model_0.cif, chain A (#3), sequence alignment score = 979.9 RMSD between 194 pruned atom pairs is 0.352 angstroms; (across all 194 pairs: 0.352) Matchmaker 2025_01_30_14_44_eif4a3_aly, chain A (#1) with fold_2025_01_30_14_44_eif4a3_aly_model_1.cif, chain A (#4), sequence alignment score = 979.3 RMSD between 194 pruned atom pairs is 0.293 angstroms; (across all 194 pairs: 0.293) Matchmaker 2025_01_30_14_44_eif4a3_aly, chain A (#1) with fold_2025_01_30_14_44_eif4a3_aly_model_2.cif, chain A (#5), sequence alignment score = 982.9 RMSD between 194 pruned atom pairs is 0.216 angstroms; (across all 194 pairs: 0.216) Matchmaker 2025_01_30_14_44_eif4a3_aly, chain A (#1) with fold_2025_01_30_14_44_eif4a3_aly_model_3.cif, chain A (#6), sequence alignment score = 992.5 RMSD between 194 pruned atom pairs is 0.000 angstroms; (across all 194 pairs: 0.000) Matchmaker 2025_01_30_14_44_eif4a3_aly, chain A (#1) with fold_2025_01_30_14_44_eif4a3_aly_model_4.cif, chain A (#7), sequence alignment score = 985.9 RMSD between 194 pruned atom pairs is 0.200 angstroms; (across all 194 pairs: 0.200) > view > mseries slider #3-7 > hide #!1 models > select RecA2 10579 atoms, 10728 bonds, 1358 residues, 7 models selected > select clear > select#1/B:lys Unknown command: select#1/B:lys > name frozen leucines :leu > color leucines yellow > name list RecA2 /A:47-240 interface [248 atoms, 502 bonds] leucines [2624 atoms, 2321 bonds, 7 models] > alias list 23 alias: ca_and_sidechains, ca_trace, caps_off, caps_on, cofroff, cofron, coil, cootmode, cootmode_mesh, cubic_map, default_mol_display, helix, hidemaps, map_missense, map_sphere_15, map_unsphere, missense, open_vseries, rock_movie, selbetween, showmaps, strand, and symclip > close all > open 6id1 6id1 title: Cryo-EM structure of a human intron lariat spliceosome after Prp43 loaded (ILS2 complex) at 2.9 angstrom resolution [more info...] Chain information for 6id1 #1 --- Chain | Description | UniProt A | Pre-mRNA-processing-splicing factor 8 | PRP8_HUMAN 1-2335 B | U5snRNA | C | 116 kDa U5 small nuclear ribonucleoprotein component | U5S1_HUMAN 1-972 E | U5 small nuclear ribonucleoprotein 40 kDa protein | SNR40_HUMAN 1-357 F | U6snRNA | G | pre-mRNA | H | U2snRNA | I | Pre-mRNA-splicing factor SYF1 | SYF1_HUMAN 1-855 J | Crooked neck-like protein 1 | CRNL1_HUMAN 1-848 K | Pre-mRNA-splicing factor SPF27 | SPF27_HUMAN 1-225 L | Cell division cycle 5-like protein | CDC5L_HUMAN 1-802 M | Pre-mRNA-splicing factor SYF2 | SYF2_HUMAN 1-243 N | Protein BUD31 homolog | BUD31_HUMAN 1-144 O | Pre-mRNA-splicing factor RBM22 | RBM22_HUMAN 1-420 P | Spliceosome-associated protein CWC15 homolog | CWC15_HUMAN 1-229 Q | RNA helicase aquarius | AQR_HUMAN 1-1485 R | SNW domain-containing protein 1 | SNW1_HUMAN 1-536 S | Peptidyl-prolyl cis-trans isomerase-like 1 | PPIL1_HUMAN 1-166 T | Pleiotropic regulator 1 | PLRG1_HUMAN 1-514 U | CWF19-like protein 2 | C19L2_HUMAN 1-894 V | Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 | DHX15_HUMAN 1-795 W | Pre-mRNA-processing factor 17 | PRP17_HUMAN 1-579 a h | Small nuclear ribonucleoprotein Sm D3 | SMD3_HUMAN 1-126 b i | Small nuclear ribonucleoprotein-associated protein | Q66K91_HUMAN 1-231 c j | Small nuclear ribonucleoprotein Sm D1 | SMD1_HUMAN 1-119 d k | Small nuclear ribonucleoprotein Sm D2 | SMD2_HUMAN 1-118 e l | Small nuclear ribonucleoprotein E | RUXE_HUMAN 1-92 f m | Small nuclear ribonucleoprotein F | RUXF_HUMAN 1-86 g n | Small nuclear ribonucleoprotein G | RUXG_HUMAN 1-76 o | U2 small nuclear ribonucleoprotein A' | RU2A_HUMAN 1-255 p | U2 small nuclear ribonucleoprotein B'' | RU2B_HUMAN 1-225 q r s t | Pre-mRNA-processing factor 19 | PRP19_HUMAN 1-504 y | Peptidyl-prolyl cis-trans isomerase E | PPIE_HUMAN 1-301 Non-standard residues in 6id1 #1 --- GTP — guanosine-5'-triphosphate IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol 1,2,3,4,5,6-hexakisphosphate) MG — magnesium ion ZN — zinc ion > open 8ro1 8ro1 title: Structure of the C. elegans Intron Lariat Spliceosome double-primed for disassembly (ILS'') [more info...] Chain information for 8ro1 #2 --- Chain | Description | UniProt 2 | U2 snRNA | 5 | U5 snRNA | 6 | U6 snRNA | A | Pre-mRNA-splicing factor 8 homolog | PRP8_CAEEL 1-2329 C | Tr-type G domain-containing protein | Q23463_CAEEL 1-974 D | Protein isy-1 | ISY1_CAEEL 1-267 DX | Pre-mRNA-splicing factor ATP-dependent RNA helicase ddx-15 | DHX15_CAEEL 1-739 E | WD_REPEATS_REGION domain-containing protein | Q19211_CAEEL 1-331 I | Pre-mRNA-splicing factor SYF1 | P91175_CAEEL 1-855 IN | Intron lariat RNA | J | TPR_REGION domain-containing protein | O16376_CAEEL 1-744 K | Pre-mRNA-splicing factor SPF27 | Q22417_CAEEL 1-238 L | Cell division cycle 5-like protein | G5EFC4_CAEEL 1-755 L1 | CWF19-like protein 1 homolog | C19L1_CAEEL 1-533 L2 | CWF19-like protein 2 homolog | C19L2_CAEEL 1-460 M | Pre-mRNA-splicing factor syf-2 | SYF2_CAEEL 1-234 N | Protein BUD31 homolog | BUD31_CAEEL 1-147 O | Pre-mRNA-splicing factor RBM22 | Q22412_CAEEL 1-408 P | Spliceosome-associated protein CWC15 homolog | CWC15_CAEEL 1-230 PX | GCF C-terminal domain-containing protein | G5ECH1_CAEEL 1-809 Q | Intron-binding protein aquarius | Q9U1Q7_CAEEL 1-1467 R | Uncharacterized protein T27F2.1 | YGH1_CAEEL 1-535 S | Peptidyl-prolyl cis-trans isomerase | Q18445_CAEEL 1-169 T | WD_REPEATS_REGION domain-containing protein | G5EEL2_CAEEL 1-494 TF | Septin and tuftelin-interacting protein 1 homolog | TFP11_CAEEL 1-830 W | WD_REPEATS_REGION domain-containing protein | O44729_CAEEL 1-567 X | Replication stress response regulator SDE2 | G5EC45_CAEEL 1-500 Z | Coiled-coil domain-containing protein 12 | Q95XJ1_CAEEL 84-152 a h | Small nuclear ribonucleoprotein Sm D3 | SMD3_CAEEL 1-136 b i | Probable small nuclear ribonucleoprotein-associated protein B | RSMB_CAEEL 1-160 c j | Small nuclear ribonucleoprotein Sm D1 | E3LR34_CAERE 1-127 d k | Probable small nuclear ribonucleoprotein Sm D2 | SMD2_CAEEL 1-118 e l | Probable small nuclear ribonucleoprotein E | RUXE_CAEEL 1-90 f m | Probable small nuclear ribonucleoprotein F | RUXF_CAEEL 1-85 g n | Probable small nuclear ribonucleoprotein G | RUXG_CAEEL 1-77 o | Probable U2 small nuclear ribonucleoprotein A' | RU2A_CAEEL 1-253 p | RRM domain-containing protein | Q21323_CAEEL 1-217 q r s t | Pre-mRNA-processing factor 19 | PRP19_CAEEL 1-492 y | Peptidyl-prolyl cis-trans isomerase E | Q9U2S6_CAEEL 10-88 Non-standard residues in 8ro1 #2 --- GTP — guanosine-5'-triphosphate IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol 1,2,3,4,5,6-hexakisphosphate) MG — magnesium ion ZN — zinc ion > description Unknown command: description > name PRP8 //description='Pre-mRNA-processing-splicing factor 8' > |//description='Pre-mRNA-processing-splicing factor 8 hiomolo' > select PRP8 16477 atoms, 16926 bonds, 1 pseudobond, 1981 residues, 2 models selected > hide > show PRP8 cartoons > view > hide #!2 models > show #!2 models > hide #!1 models > hide #!2 models > show #!2 models > show #!1 models > hide #!2 models > show #!2 models > name PRP8 //description='Pre-mRNA-processing-splicing factor 8' > |//description='Pre-mRNA-processing-splicing factor 8 homolo' > show PRP8 cartoons > view > name PRP8 //description='Pre-mRNA-processing-splicing factor 8' > |//description='Pre-mRNA-processing-splicing factor 8 homolog' > show PRP8 cartoons > view > hide #!2 models > hide #!1 models > show #!2 models > hide #!2 models > show #!2 models > name PRP8 //description='Pre-mRNA-processing-splicing factor 8' | //description='Pre-mRNA-splicing factor 8 homolog' > show PRP8 cartoons > show #!1 models > select up 16513 atoms, 16962 bonds, 1 pseudobond, 1982 residues, 2 models selected > select up 79882 atoms, 81847 bonds, 65 pseudobonds, 11135 residues, 2 models selected > name U2 //description='U2*snRNA' > show U2 cartoons Unsupported scale factor (0.000000) detected on Display1 [Repeated 13 time(s)] > close all > open /Users/matthias.vorlaender/Library/CloudStorage/OneDrive- > VBC/HDYDI_ChimeraX/AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_model_2.cif Chain information for fold_2025_01_30_14_44_eif4a3_aly_model_2.cif #1 --- Chain | Description A | . B | . Computing secondary structure > alphafold pae No structure or PAE file specified. > alphafold pae No structure or PAE file specified. > Incomplete command: alphafold > alphafold pae #1 file > AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_model_2.cif AlphaFold predicted aligned error (PAE) files must be in JSON (*.json) or numpy (*.npy) or pickle (*.pkl) format, AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_model_2.cif unrecognized format > alphafold pae #1 file > AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_full_data_2.json > alphafold pae #1 file > AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_summary_confidences_2.json JSON file ""AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_summary_confidences_2.json"" is not AlphaFold predicted aligned error data, expected a top level list > alphafold pae > #1AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_summary_confidences_2.json Expected an atomic structure specifier or a keyword > alphafold pae #1 > AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_summary_confidences_2.json Expected a keyword > alphafold pae #1 file > AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_full_data_2.json > close all > paea echo `alphafold pae #1 file > AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_full_data_1.json` Unknown command: alphafold paea echo `alphafold pae #1 file AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_full_data_1.json` > alias af_contacts `alphafold contacts #1/A toAtoms #1/B,C,D distance 4.0 > maxPae 5.0` > af_contacts > `alphafold contacts #1/A toAtoms #1/B,C,D distance 4.0 maxPae 5.0` Unknown command: `alphafold contacts #1/A toAtoms #1/B,C,D distance 4.0 maxPae 5.0` > alias af_pae echo alphafold pae #1 file > AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_full_data_1.json > alias af_contacts echo alphafold contacts #1/A toAtoms #1/B,C,D distance 4.0 > maxPae 5.0 > alias af_pae echo alphafold pae #1 file > AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_full_data_1.json #this > associated pae with the model# > alias af_contacts echo alphafold contacts #1/A toAtoms #1/B,C,D distance 4.0 > maxPae 5.0 #this generates the contact maps from the PAE > alias af_pae echo alphafold pae #1 file > AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_full_data_1.json #this > associated pae with the model# > alias af_contacts echo alphafold contacts #1/A toAtoms #1/B,C,D distance 4.0 > maxPae 5.0 #this generates the contact maps from the PAE > alias af_pae echo alphafold pae #1 file > AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_full_data_1.json ""this > associated pae with the model"" > alias af_contacts echo alphafold contacts #1/A toAtoms #1/B,C,D distance 4.0 > maxPae 5.0 ""this generates the contact maps from the PAE"" > af_pae alphafold pae #1 file AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_full_data_1.json ""this associated pae with the model"" > open AF_predictions/*model_$1.[cif|pdb} Unrecognized file suffix '.[cif|pdb}' > open AF_predictions/*model_$1.[cif|pdb] Unrecognized file suffix '.[cif|pdb]' > open AF_predictions/*model_$1.{cif,pdb} Unrecognized file suffix '.{cif,pdb}' > open AF_predictions/*model_*.{cif,pdb} Unrecognized file suffix '.{cif,pdb}' > open AF_predictions/*model_*.{cif|pdb} Unrecognized file suffix '.{cif|pdb}' > open AF_predictions/*model_*.[cif|pdb] Unrecognized file suffix '.[cif|pdb]' > open > /Users/matthias.vorlaender/Downloads/ChimeraX/AlphaFold/AF-Q95XJ1-F1-model_v4.cif > format mmcif Chain information for AF-Q95XJ1-F1-model_v4.cif #1 --- Chain | Description | UniProt A | Uncharacterized protein | Q95XJ1_CAEEL 1-169 Color AF-Q95XJ1-F1-model_v4.cif by residue attribute pLDDT_score > close all > af_pae alphafold pae #1 file AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_full_data_1.json ""this associated pae with the model"" > open AF_predictions/*model_1.cif Chain information for fold_2025_01_30_14_44_eif4a3_aly_model_1.cif #1 --- Chain | Description A | . B | . Computing secondary structure > alpahfold pae #1 file AF_predictions/*data_4.json Unknown command: alpahfold pae #1 file AF_predictions/*data_4.json > alphafold pae #1 file AF_predictions/*data_4.json Invalid ""file"" argument: File 'AF_predictions/*data_4.json' does not exist > alphafold pae #1 file AF_predictions/*data_4*json Invalid ""file"" argument: File 'AF_predictions/*data_4*json' does not exist > close > alphafold pae #1 file AF_predictions/*data_1*json Expected an atomic structure specifier or a keyword > open AF_predictions/*model_1.cif Chain information for fold_2025_01_30_14_44_eif4a3_aly_model_1.cif #1 --- Chain | Description A | . B | . Computing secondary structure > alphafold pae #1 file AF_predictions/*data_1*json Invalid ""file"" argument: File 'AF_predictions/*data_1*json' does not exist > af_pae alphafold pae #1 file AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_full_data_1.json ""this associated pae with the model"" > alphafold pae #1 file > AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_full_data_1.json > alphafold pae #1 file AF_predictions/f*data_1.json Invalid ""file"" argument: File 'AF_predictions/f*data_1.json' does not exist > alphafold pae #1 file AF_predictions/*data_1.json Invalid ""file"" argument: File 'AF_predictions/*data_1.json' does not exist > alphafold pae #1 file AF_predictions/*data_1.json Invalid ""file"" argument: File 'AF_predictions/*data_1.json' does not exist > close all > open AF_predictions/*model_1.cif Chain information for fold_2025_01_30_14_44_eif4a3_aly_model_1.cif #1 --- Chain | Description A | . B | . Computing secondary structure > alphafold pae #1 file > AF_predictions/fold_2025_01_30_14_44_eif4a3_aly_full_data_1.json > alphafold pae #1 file AF_predictions/fold*data_1.json Invalid ""file"" argument: File 'AF_predictions/fold*data_1.json' does not exist > alphafold pae #1 file AF_predictions/*data_1.json Invalid ""file"" argument: File 'AF_predictions/*data_1.json' does not exist > alphafold pae #1 file AF_predictions/*data_1.json Invalid ""file"" argument: File 'AF_predictions/*data_1.json' does not exist > alphafold pae #1 file AF_predictions/*data_1.json Invalid ""file"" argument: File 'AF_predictions/*data_1.json' does not exist OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,6 Model Number: Z1AU002HPD/A Chip: Apple M3 Pro Total Number of Cores: 11 (5 performance and 6 efficiency) Memory: 18 GB System Firmware Version: 10151.81.1 OS Loader Version: 10151.81.1 Software: System Software Overview: System Version: macOS 14.3.1 (23D60) Kernel Version: Darwin 23.3.0 Time since boot: 15 days, 20 hours, 24 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal HP Z32: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 30.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.12.3 biopython: 1.83 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 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: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.23.0 ChimeraX-clix: 0.1.9 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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 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-ISOLDE: 1.8.dev0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 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 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.3.7 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 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: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 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-StarMap: 1.2.15 ChimeraX-StdCommands: 1.18.1 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 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: 1.41 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: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 DiffFit: 0.6.2 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 fsspec: 2024.10.0 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 jedi: 0.19.1 Jinja2: 3.1.4 joblib: 1.4.2 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 llvmlite: 0.44.0 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.10.0 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 more-itertools: 10.3.0 mpmath: 1.3.0 mrcfile: 1.5.0 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numba: 0.61.0 numexpr: 2.10.2 numpy: 2.2.2 numpy: 1.26.4 openvr: 1.26.701 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 platformdirs: 4.2.2 plotly: 5.24.1 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pyKVFinder: 0.7.2 pynmrstar: 3.3.4 pynndescent: 0.5.13 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 pyqtgraph: 0.13.7 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scikit-learn: 1.6.1 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 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: 0.6.3 sympy: 1.13.3 tables: 3.10.1 tcia_utils: 1.5.1 tenacity: 9.0.0 threadpoolctl: 3.5.0 tifffile: 2024.7.24 tinyarray: 1.2.4 toml: 0.10.2 tomli: 2.0.1 torch: 2.2.1 tornado: 6.4.2 tqdm: 4.67.1 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 typing_extensions: 4.12.2 tzdata: 2024.2 umap-learn: 0.5.7 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " enhancement assigned normal Input/Output Eric Pettersen all ChimeraX