Opened 9 months ago

Last modified 9 months ago

#16748 assigned enhancement

alphafold pae does not accept wild cards for file patterns

Reported by: matthias.vorlaender@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc: pett
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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
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Change History (7)

comment:1 by pett, 9 months ago

Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → alphafold pae does not accept wild cards for file patterns
Type: defect → enhancement

comment:2 by Tom Goddard, 9 months ago

Cc: pett added

ChimeraX command file argument handling in general doesn't support wildcards * except for the open command. I'm not sure why.

Eric can you comment on why OpenFileNamesArg and OpenFileNameArg don't support globbing? I would think this would always be desirable for the OpenFileNamesArg and in this bug report even though it is specifying a single file the globbing is still useful to avoid typing horrendous long file names. Do you think it would it cause problems if those two arg parsers handled globbing? I'm not sure if the open command code which does its own globbing would need to be changed.

comment:3 by pett, 9 months ago

The OpenFileNamesArg does not directly glob because the open command needs to be able to hand off the unprocessed file argument to commands that want to do their own processing/globbing, such as the processing of the file argument for image stacks -- which makes some substitutions into the string before globbing.

That said, the open command subclasses from OpenFileNamesArg, so it would be possible to put control over globbing into a class variable of OpenFileNamesArg (glob? noglob?), which the open command would then be able to suppress.

comment:4 by pett, 9 months ago

Just as a short-term tip: you can drag and drop files from the system file browser into the command line, and the path to the file will be inserted into the command line.

comment:5 by Tom Goddard, 9 months ago

Matthias, there is actually an easy solution for your problem. You can open PAE files using the open command

open *data_0.json structure #1

This is the same as using the "alphafold pae", just two ways of doing the same thing.

comment:6 by matthias.vorlaender@…, 9 months ago 

That's Great, thanks a lot! it makes writing a little wrapper script for af related analysis easier compared to drag and drop :)

Thanks for the fantastic support once again!

Best,
Matthias

Sent from Outlook for Android<https://aka.ms/AAb9ysg>
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, January 31, 2025 11:25:58 PM
To: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at>
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #16748: alphafold pae does not accept wild cards for file patterns

#16748: alphafold pae does not accept wild cards for file patterns
--------------------------------------------+-------------------------
          Reporter:  matthias.vorlaender@…  |      Owner:  Tom Goddard
              Type:  enhancement            |     Status:  assigned
          Priority:  normal                 |  Milestone:
         Component:  Input/Output           |    Version:
        Resolution:                         |   Keywords:
        Blocked By:                         |   Blocking:
Notify when closed:                         |   Platform:  all
           Project:  ChimeraX               |
--------------------------------------------+-------------------------
Comment (by Tom Goddard):

 Matthias, there is actually an easy solution for your problem.  You can
 open PAE files using the open command

    open *data_0.json structure #1

 This is the same as using the "alphafold pae", just two ways of doing the
 same thing.
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/16748#comment:5>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:7 by Tom Goddard, 9 months ago

I think it makes better sense to open the PAE data using the "open" command since that is the command for opening all kinds of data. So I'm going to put off messing with more general file name wildcard support (e.g. the "alphafold pae" file option) until someone else makes a case for it. There are too many higher priority ChimeraX problems to work on.

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