![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Last modified 7 months ago
#17285 accepted defect
Memory error in model.add_coordsets()
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | MD/Ensemble Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.10.dev202502060317 (2025-02-06 03:17:41 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10.dev202502060317 (2025-02-06)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/355SaurP12/355SaurP12_analysis.cxs"
Log from Thu Mar 13 14:29:48 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.10.dev202502060317 (2025-02-06)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/Proteins_models/308Ecol101PP_WLY86067.1.pdb"
308Ecol101PP_WLY86067.1.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) 308Ecol101PP_WLY86067.1
[more info...]
Chain information for 308Ecol101PP_WLY86067.1.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
Alignment identifier is 1/A
> select /A:162
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:162
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:3-11,39-50,60-80,84-90,93-113,115-122,126-135,137-141,143-155
842 atoms, 845 bonds, 106 residues, 1 model selected
> ui tool show "Render/Select by Attribute"
> select add #1
1288 atoms, 1309 bonds, 162 residues, 1 model selected
> ui tool show "Color Actions"
> open Z:/Documents/roboczy_rafal/BOOSTER/DeepGLycanSite/OUT/WLY86067.defattr
Line 1 in WLY86067.defattr is either not of the form 'name: value' or is
missing initial tab
error dialog finished
> open
> Z:/Documents/roboczy_rafal/BOOSTER/DeepGLycanSite/OUT/WLY86067_v2.defattr
Line 4 in WLY86067_v2.defattr is either not of the form 'name: value' or is
missing initial tab
error dialog finished
> open
> Z:/Documents/roboczy_rafal/BOOSTER/DeepGLycanSite/OUT/WLY86067_v2.defattr
Line 9 in WLY86067_v2.defattr is either not of the form 'name: value' or is
missing initial tab
error dialog finished
> open
> Z:/Documents/roboczy_rafal/BOOSTER/DeepGLycanSite/OUT/WLY86067_v2.defattr
Summary of feedback from opening
Z:/Documents/roboczy_rafal/BOOSTER/DeepGLycanSite/OUT/WLY86067_v2.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 162 residues using match mode: 1-to-1
> color byattribute WLY86067_v2 palete paecontacts
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color byattribute WLY86067_v2 palette ^rdylbu
No known/registered numeric attribute WLY86067_v2
> ui tool show "Render/Select by Attribute"
> color byattribute r:DeepGlycanSite_score target sabc palette
> 0.0433808,blue:0.378924,white:0.714466,red
1288 atoms, 162 residues, atom DeepGlycanSite_score range 0.0434 to 0.714
> show sel surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0433808,blue:0.378924,white:0.714466,red
1288 atoms, 162 residues, 1 surfaces, atom DeepGlycanSite_score range 0.0434
to 0.714
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0433808,blue:0.602072,white:0.714466,red
1288 atoms, 162 residues, 1 surfaces, atom DeepGlycanSite_score range 0.0434
to 0.714
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/308EcolP114/308Ecol101PP_WLY86067.1.pdb"
308Ecol101PP_WLY86067.1.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) 308Ecol101PP_WLY86067.1
[more info...]
Chain information for 308Ecol101PP_WLY86067.1.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/308EcolP114/OUT/WLY86067_v2.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/308EcolP114/OUT/WLY86067_v2.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 162 residues using match mode: 1-to-1
> ui tool show "Render/Select by Attribute"
> color byattribute r:DeepGlycanSite_score target sabc palette
> 0.0433808,blue:0.6,white:1,red
1288 atoms, 162 residues, atom DeepGlycanSite_score range 0.0434 to 0.714
> color byattribute r:DeepGlycanSite_score target sabc palette
> 0,blue:0.433859,white:0.714466,red
1288 atoms, 162 residues, atom DeepGlycanSite_score range 0.0434 to 0.714
> color byattribute r:DeepGlycanSite_score target sabc palette
> 0,blue:0.433859,white:0.714466,red
1288 atoms, 162 residues, atom DeepGlycanSite_score range 0.0434 to 0.714
> show surfaces
> ui tool show "Render/Select by Attribute"
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0433808,blue:0.378924,white:0.714466,red
1288 atoms, 162 residues, 1 surfaces, atom DeepGlycanSite_score range 0.0434
to 0.714
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0433808,blue:0.378924,white:0.714466,red
1288 atoms, 162 residues, 1 surfaces, atom DeepGlycanSite_score range 0.0434
to 0.714
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
1288 atoms, 162 residues, 1 surfaces, atom DeepGlycanSite_score range 0.0434
to 0.714
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/308EcolP114/OUT/308EcolP114_analysis.cxs"
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red colorkay: true
Expected a keyword
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red colourkay: true
Expected a keyword
> ui mousemode right "color key"
> key blue-white-red :min : :1
> key blue-white-red :0 : :1
> key blue-white-red :0 :0 :1
> key blue-white-red :0 :0. :1
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/308EcolP114/OUT/308EcolP114_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/BF13PseuP73/BF13PseuP73.pdb"
Chain information for BF13PseuP73.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/BF13PseuP73/out/BF13PseuP73.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/BF13PseuP73/out/BF13PseuP73.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 149 residues using match mode: 1-to-1
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
2334 atoms, 149 residues, 1 surfaces, atom DeepGlycanSite_score range 0.0428
to 0.728
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/BF13PseuP73/BF13PseuP73_analysis.cxs"
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY5:" "Operacja
ukończona pomyślnie."
> close session
QWindowsWindow::setMouseGrabEnabled: Not setting mouse grab for invisible
window QWidgetWindow/'ChainsWindow'
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/308EcolP114/308Ecol101PP_WLY86067.1.pdb"
308Ecol101PP_WLY86067.1.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) 308Ecol101PP_WLY86067.1
[more info...]
Chain information for 308Ecol101PP_WLY86067.1.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> open Z:/Documents/roboczy_rafal/BOOSTER/DeepGLycanSite/WLY86067.defattr
Line 7 in WLY86067.defattr is either not of the form 'name: value' or is
missing initial tab
error dialog finished
> open Z:/Documents/roboczy_rafal/BOOSTER/DeepGLycanSite/WLY86067.defattr
Summary of feedback from opening
Z:/Documents/roboczy_rafal/BOOSTER/DeepGLycanSite/WLY86067.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 162 residues using match mode: 1-to-1
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
1288 atoms, 162 residues, 1 surfaces, atom DeepGlycanSite_score range 0.0434
to 0.714
> key blue-white-red :0 :0.6 :1
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/BF16PseuP4/BF16PseuP4.pdb"
Chain information for BF16PseuP4.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/BF16PseuP4/BF16PseuP4.pdb"
Chain information for BF16PseuP4.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/BF16PseuP4/out/BF16PseuP4.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/BF16PseuP4/out/BF16PseuP4.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 174 residues using match mode: 1-to-1
> show surfaces
> key blue-white-red :0 :0.6 :1
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
2644 atoms, 174 residues, 1 surfaces, atom DeepGlycanSite_score range 0.0358
to 0.731
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/BF16PseuP4/BF16PseuP4_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/BF14PseuP43/BF14PseuP43.pdb"
Chain information for BF14PseuP43.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/BF14PseuP43/BF14PseuP43.pdb"
Chain information for BF14PseuP43.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/BF14PseuP43/out/BF14PseuP43.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/BF14PseuP43/out/BF14PseuP43.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 935 residues using match mode: 1-to-1
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
14192 atoms, 935 residues, 1 surfaces, atom DeepGlycanSite_score range 0.0372
to 0.82
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/BF14PseuP43/BF14PseuP43_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/216EcolP45/216EcolP45.pdb"
Chain information for 216EcolP45.pdb #1
---
Chain | Description
A B C | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45.defattr"
Selector (:1) on line 9 of 216EcolP45.defattr matched multiple residues
error dialog finished
> select /A
16387 atoms, 16603 bonds, 1064 residues, 1 model selected
> close session
> open
> Z:/Documents/roboczy_rafal/BOOSTER/DeepGLycanSite/216EcolP45/216EcolP45.pdb
Chain information for 216EcolP45.pdb #1
---
Chain | Description
A B C | No description available
Computing secondary structure
> split chains
Split 216EcolP45.pdb (#1) into 3 models
Chain information for 216EcolP45.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for 216EcolP45.pdb B #1.2
---
Chain | Description
B | No description available
Chain information for 216EcolP45.pdb C #1.3
---
Chain | Description
C | No description available
> close #1.2
> close #1.3
> concat chain
Unknown command: concat chain
> close session
> open
> Z:\Documents\roboczy_rafal\BOOSTER\DeepGLycanSite\216EcolP45\216EcolP45.pdb
> format pdb
Chain information for 216EcolP45.pdb #1
---
Chain | Description
A B C | No description available
Computing secondary structure
> changechains #1 B A
Proposed chainID change conflicts with existing residue /A MET 1
> changechains #1 A X
Chain IDs of 1064 residues changed
> changechains #1 B Y
Chain IDs of 1064 residues changed
> changechains #1 C Z
Chain IDs of 1064 residues changed
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/216EcolP45_changed_chains.pdb"
> relModel #1
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/216EcolP45_changed_chains.pdb"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/216EcolP45/216EcolP45_changed_chains.pdb
---
warnings | Ignored bad PDB record found on line 247
HELIA 1 1 ARG A 23 PHE A 25 1 3
Ignored bad PDB record found on line 248
HELIA 2 2 PRO A 36 LEU A 38 1 3
Ignored bad PDB record found on line 249
HELIA 3 3 ALA A 90 ALA A 145 1 56
Ignored bad PDB record found on line 250
HELIA 4 4 PRO A 195 GLA A 199 1 5
Ignored bad PDB record found on line 251
HELIA 5 5 ALA A 212 SER A 219 1 8
63 messages similar to the above omitted
PDB SEQRES record for chain A is incomplete. Ignoring input sequence records
as basis for sequence.
Chain information for 216EcolP45_changed_chains.pdb #1
---
Chain | Description
A | No description available
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45.defattr"
Selector (:1) on line 9 of 216EcolP45.defattr matched multiple residues
error dialog finished
Alignment identifier is 1/A
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45.defattr"
Selector (:1) on line 9 of 216EcolP45.defattr matched multiple residues
error dialog finished
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/216EcolP45_changed_chains.pdb"
Chain information for 216EcolP45_changed_chains.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45.defattr"
Selector (:1) on line 9 of 216EcolP45.defattr matched multiple residues
error dialog finished
> renumber #1
0 residues renumbered
Alignment identifier is 1/A
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/216EcolP45_changed_chains_2.pdb"
> relModel #1
> select /A:1064
69 atoms, 66 bonds, 3 residues, 1 model selected
> select /A:1064
69 atoms, 66 bonds, 3 residues, 1 model selected
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45.defattr"
Selector (:1) on line 9 of 216EcolP45.defattr matched multiple residues
error dialog finished
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/216EcolP45_changed_chains.pdb"
Chain information for 216EcolP45_changed_chains.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> split chains
Did not split 216EcolP45_changed_chains.pdb, has only one piece
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45.defattr"
Selector (:1) on line 9 of 216EcolP45.defattr matched multiple residues
error dialog finished
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/216EcolP45/216EcolP45.pdb"
Chain information for 216EcolP45.pdb #1
---
Chain | Description
A B C | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45.defattr"
Selector (:1) on line 9 of 216EcolP45.defattr matched multiple residues
error dialog finished
> split chains
Split 216EcolP45.pdb (#1) into 3 models
Chain information for 216EcolP45.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for 216EcolP45.pdb B #1.2
---
Chain | Description
B | No description available
Chain information for 216EcolP45.pdb C #1.3
---
Chain | Description
C | No description available
> close #1.3
> close #1.2
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45.defattr"
Selector (:1065) on line 1073 of 216EcolP45.defattr matched nothing
error dialog finished
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45_A.defattr"
Illegal control value ('') for recipient given on line 8 of
216EcolP45_A.defattr; legal values are: atoms, structures, bonds, molecules,
residues, pseudobonds, or chains
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45_A.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45_A.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 1064 residues using match mode: 1-to-1
error dialog finished
error dialog finished
error dialog finished
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
No atoms specified
> color byattribute r:DeepGlycanSite_score #!1.1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
16387 atoms, 1064 residues, 1 surfaces, atom DeepGlycanSite_score range 0.0397
to 0.748
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/216EcolP45/216EcolP45.pdb"
Chain information for 216EcolP45.pdb #1
---
Chain | Description
A B C | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45_A.defattr"
Selector (:1) on line 9 of 216EcolP45_A.defattr matched multiple residues
error dialog finished
> color byattribute r:DeepGlycanSite_score #!1.1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
No atoms specified
> split chains
Split 216EcolP45.pdb (#1) into 3 models
Chain information for 216EcolP45.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for 216EcolP45.pdb B #1.2
---
Chain | Description
B | No description available
Chain information for 216EcolP45.pdb C #1.3
---
Chain | Description
C | No description available
> color byattribute r:DeepGlycanSite_score #!1.1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
All 'DeepGlycanSite_score' values are None
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45_A.defattr"
Selector (:1) on line 9 of 216EcolP45_A.defattr matched multiple residues
error dialog finished
> color byattribute r:DeepGlycanSite_score #!1.1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
All 'DeepGlycanSite_score' values are None
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
No atoms specified
> color byattribute r:DeepGlycanSite_score #!1.2 target sabc palette
> 0.0,blue:0.6,white:1.0,red
All 'DeepGlycanSite_score' values are None
> hide #1.2 models
> hide #1.3 models
> color byattribute r:DeepGlycanSite_score #!1.1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
All 'DeepGlycanSite_score' values are None
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45_A.defattr"
Selector (:1) on line 9 of 216EcolP45_A.defattr matched multiple residues
error dialog finished
> color byattribute r:DeepGlycanSite_score #!1.1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
All 'DeepGlycanSite_score' values are None
> close #1.3
> close #1.2
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45_A.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45_A.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 1064 residues using match mode: 1-to-1
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1.1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
16387 atoms, 1064 residues, 1 surfaces, atom DeepGlycanSite_score range 0.0397
to 0.748
> key blue-white-red :0 :0.6 :1
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/216EcolP45/216EcolP45.pdb"
Chain information for 216EcolP45.pdb #3
---
Chain | Description
A B C | No description available
Computing secondary structure
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/216EcolP45/216EcolP45.pdb"
Chain information for 216EcolP45.pdb #1
---
Chain | Description
A B C | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45.defattr"
Selector (:1) on line 9 of 216EcolP45.defattr matched multiple residues
error dialog finished
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45_A.defattr"
Illegal control value ('chain') for recipient given on line 8 of
216EcolP45_A.defattr; legal values are: atoms, structures, bonds, molecules,
residues, pseudobonds, or chains
error dialog finished
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45_A.defattr"
Data line 9 in 216EcolP45_A.defattr not of the form: <tab> atomspec <tab>
value
error dialog finished
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45_A.defattr"
Line 10 in 216EcolP45_A.defattr is either not of the form 'name: value' or is
missing initial tab
error dialog finished
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45_A.defattr"
Data line 9 in 216EcolP45_A.defattr not of the form: <tab> atomspec <tab>
value
error dialog finished
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45_A.defattr"
Line 8 in 216EcolP45_A.defattr is either not of the form 'name: value' or is
missing initial tab
error dialog finished
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45_A.defattr"
Line 8 in 216EcolP45_A.defattr is either not of the form 'name: value' or is
missing initial tab
error dialog finished
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45_A.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/216EcolP45/out/216EcolP45_A.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 3192 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1.1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
No atoms specified
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
49161 atoms, 3192 residues, 3 surfaces, atom DeepGlycanSite_score range 0.0397
to 0.748
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/216EcolP45/216EcolP45_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/351SaurP13/351SaurP13.pdb"
Chain information for 351SaurP13.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/351SaurP13/out/351SaurP13.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/351SaurP13/out/351SaurP13.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 249 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
3891 atoms, 249 residues, 1 surfaces, atom DeepGlycanSite_score range 0.038 to
0.684
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/351SaurP13/351SaurP13_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/351SaurP14/351SaurP14.pdb"
Chain information for 351SaurP14.pdb #1
---
Chain | Description
A B C | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/351SaurP14/out/351SaurP14.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/351SaurP14/out/351SaurP14.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 1941 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
31059 atoms, 1941 residues, 3 surfaces, atom DeepGlycanSite_score range 0.0374
to 0.691
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/351SaurP14/351SaurP14_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/351SaurP9/351SaurP9.pdb"
Chain information for 351SaurP9.pdb #1
---
Chain | Description
A B C | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/351SaurP9/out/351SaurP9.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/351SaurP9/out/351SaurP9.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 1455 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
22293 atoms, 1455 residues, 3 surfaces, atom DeepGlycanSite_score range 0.041
to 0.678
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/351SaurP9/351SaurP9_analysis.cxs"
QWindowsWindow::setMouseGrabEnabled: Not setting mouse grab for invisible
window QWidgetWindow/'ChainsWindow'
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/357SaurP108/357SaurP108.pdb"
Chain information for 357SaurP108.pdb #1
---
Chain | Description
A B C | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/357SaurP108/out/357SaurP108.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/357SaurP108/out/357SaurP108.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 1920 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
30327 atoms, 1920 residues, 3 surfaces, atom DeepGlycanSite_score range 0.0334
to 0.746
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/357SaurP108/357SaurP108_analysis.cxs"
> transparency 70
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/357SaurP117/357SaurP117.pdb"
Chain information for 357SaurP117.pdb #1
---
Chain | Description
A B C | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/357SaurP117/out/357SaurP117.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/357SaurP117/out/357SaurP117.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 2544 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
20262 atoms, 2544 residues, 3 surfaces, atom DeepGlycanSite_score range 0.0349
to 0.762
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/357SaurP117/357SaurP117_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/308EcolP79/308EcolP79.pdb"
308EcolP79.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org)
OR062945.1_prot_WLY86034.1_79 [more info...]
Chain information for 308EcolP79.pdb #1
---
Chain | Description
A C E | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/308EcolP79/out/308EcolP79.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/308EcolP79/out/308EcolP79.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 1716 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
13269 atoms, 1716 residues, 3 surfaces, atom DeepGlycanSite_score range 0.039
to 0.719
> key blue-white-red :0 :0.6 :1
QWindowsWindow::setMouseGrabEnabled: Not setting mouse grab for invisible
window QWidgetWindow/'ChainsWindow'
> transparency 50
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/308EcolP79/308EcolP79_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/308EcolP77/308EcolP77.pdb"
308EcolP77.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org)
OR062945.1_prot_WLY86032.1_77 [more info...]
Chain information for 308EcolP77.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/308EcolP77/out/308EcolP77.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/308EcolP77/out/308EcolP77.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 97 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
721 atoms, 97 residues, 1 surfaces, atom DeepGlycanSite_score range 0.0374 to
0.81
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/308EcolP77/308EcolP77_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/236EcolP145/236EcolP145.pdb"
236EcolP145.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org)
PP434423.1_prot_WWT49718.1_145 [more info...]
Chain information for 236EcolP145.pdb #1
---
Chain | Description
A C E | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/236EcolP145/out/236EcolP145.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/236EcolP145/out/236EcolP145.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 1710 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
13179 atoms, 1710 residues, 3 surfaces, atom DeepGlycanSite_score range 0.0385
to 0.696
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/236EcolP145/236EcolP145_analyisis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/236EcolP147/236EcolP147.pdb"
236EcolP147.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org)
PP434423.1_prot_WWT49720.1_147 [more info...]
Chain information for 236EcolP147.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/236EcolP147/out/236EcolP147.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/236EcolP147/out/236EcolP147.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 97 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
717 atoms, 97 residues, 1 surfaces, atom DeepGlycanSite_score range 0.0319 to
0.875
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/236EcolP147/236EcolP147_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/60AhydP26/60AhydP26.pdb"
60AhydP26.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org)
NC_055747.1_prot_YP_010095754.1_26 [more info...]
Chain information for 60AhydP26.pdb #1
---
Chain | Description
A C E | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/60AhydP26/out/60AhydP26.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/60AhydP26/out/60AhydP26.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 1737 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
13413 atoms, 1737 residues, 3 surfaces, atom DeepGlycanSite_score range 0.0354
to 0.709
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/60AhydP26/60AhydP26_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/60AhydP24/60AhydP24.pdb"
60AhydP24.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org)
NC_055747.1_prot_YP_010095752.1_24 [more info...]
Chain information for 60AhydP24.pdb #1
---
Chain | Description
D | No description available
Non-standard residues in 60AhydP24.pdb #1
---
FE — (FE)
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/60AhydP24/out/60AhydP24.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/60AhydP24/out/60AhydP24.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 96 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
719 atoms, 96 residues, 1 surfaces, atom DeepGlycanSite_score range 0.0643 to
0.271
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/60AhydP24/60AhydP24_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/39APmirP167/39APmirP167.pdb"
39APmirP167.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) 39A_VJPZATXW_CDS_0167 [more
info...]
Chain information for 39APmirP167.pdb #1
---
Chain | Description
A C E | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/39APmirP167/out/39APmirP167.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/39APmirP167/out/39APmirP167.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 1713 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
13395 atoms, 1713 residues, 3 surfaces, atom DeepGlycanSite_score range 0.0384
to 0.72
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/39APmirP167/39APmirP167_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/39APmirP204/39APmirP204.pdb"
39APmirP204.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) >VJPZATXW_CDS_0204 [more
info...]
Chain information for 39APmirP204.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/39APmirP204/out/39APmirP204.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/39APmirP204/out/39APmirP204.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 115 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
943 atoms, 118 residues, 1 surfaces, atom DeepGlycanSite_score range 0.0352 to
0.851
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/39APmirP204/39APmirP204_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/347EcolP198/347EcolP198.pdb"
Chain information for 347EcolP198.pdb #1
---
Chain | Description
A B C | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/347EcolP198/out/347EcolP198.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/347EcolP198/out/347EcolP198.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 3051 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
23223 atoms, 3051 residues, 3 surfaces, atom DeepGlycanSite_score range 0.0369
to 0.795
> transparency 50
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/347EcolP198/347EcolP198_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/347EcolP200/347EcolP200.pdb"
Chain information for 347EcolP200.pdb #1
---
Chain | Description
A B C | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/347EcolP200/out/347EcolP200.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/347EcolP200/out/347EcolP200.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 2673 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
19803 atoms, 2673 residues, 3 surfaces, atom DeepGlycanSite_score range 0.0349
to 0.717
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/347EcolP200/347EcolP200_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/223EcolP49/223EcolP49.pdb"
Chain information for 223EcolP49.pdb #1
---
Chain | Description
A B C | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/223EcolP49/out/223EcolP49.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/223EcolP49/out/223EcolP49.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 1626 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
12450 atoms, 1626 residues, 3 surfaces, atom DeepGlycanSite_score range 0.0364
to 0.685
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/223EcolP49/223EcolP49_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/223EcolP50/223EcolP50.pdb"
Chain information for 223EcolP50.pdb #1
---
Chain | Description
A B C | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/223EcolP50/out/223EcolP50.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/223EcolP50/out/223EcolP50.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 1656 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
12600 atoms, 1656 residues, 3 surfaces, atom DeepGlycanSite_score range 0.0356
to 0.735
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/223EcolP50/223EcolP50_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/212EcolP5/212EcolP5.pdb"
Chain information for 212EcolP5.pdb #1
---
Chain | Description
A B C | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/212EcolP5/out/212EcolP5.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/212EcolP5/out/212EcolP5.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 2433 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
19149 atoms, 2433 residues, 3 surfaces, atom DeepGlycanSite_score range 0.0347
to 0.737
> show surfaces
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/212EcolP5/212EcolP5_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/201EcolP52/201EcolP52.pdb"
Chain information for 201EcolP52.pdb #1
---
Chain | Description
A B C | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/201EcolP52/out/201EcolP52.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/201EcolP52/out/201EcolP52.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 1512 residues using match mode: any
> show surfaces
[Repeated 1 time(s)]
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
11298 atoms, 1512 residues, 3 surfaces, atom DeepGlycanSite_score range 0.0357
to 0.709
> key blue-white-red :0 :0.6 :1
QWindowsWindow::setMouseGrabEnabled: Not setting mouse grab for invisible
window QWidgetWindow/'ChainsWindow'
[Repeated 2 time(s)]
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/201EcolP52/201EcolP52_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/202EcolP4/202EcolP4.pdb"
Chain information for 202EcolP4.pdb #1
---
Chain | Description
A B C | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/202EcolP4/out/202EcolP4.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/202EcolP4/out/202EcolP4.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 2268 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
17382 atoms, 2268 residues, 3 surfaces, atom DeepGlycanSite_score range 0.0375
to 0.689
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/202EcolP4/202EcolP4_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/211EcolP4/211EcolP4.pdb"
Chain information for 211EcolP4.pdb #1
---
Chain | Description
A B C | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/211EcolP4/out/211EcolP4.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/211EcolP4/out/211EcolP4.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 2526 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
18753 atoms, 2526 residues, 3 surfaces, atom DeepGlycanSite_score range 0.0369
to 0.685
> key blue-white-red :0 :0.6 :1
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/208EcolP53/208EcolP53.pdb"
Chain information for 208EcolP53.pdb #1
---
Chain | Description
A B C | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/208EcolP53/out/208EcolP53.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/208EcolP53/out/208EcolP53.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 2037 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
15201 atoms, 2037 residues, 3 surfaces, atom DeepGlycanSite_score range 0.0373
to 0.733
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/208EcolP53/208EcolP53_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/213EcolP13/213EcolP13.pdb"
Chain information for 213EcolP13.pdb #1
---
Chain | Description
A B C | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/213EcolP13/out/213EcolP13.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/213EcolP13/out/213EcolP13.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 2112 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
15642 atoms, 2112 residues, 3 surfaces, atom DeepGlycanSite_score range 0.0347
to 0.714
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/213EcolP13/213EcolP13_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/5SentP34/5SentP34.pdb"
5SentP34.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org)
MT653144.1_prot_QNI21770.1_34 [more info...]
Chain information for 5SentP34.pdb #1
---
Chain | Description
A | No description available
B C | No description available
Non-standard residues in 5SentP34.pdb #1
---
CA — (CA)
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/5SentP34/out/5SentP34.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/5SentP34/out/5SentP34.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 2034 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
15281 atoms, 2034 residues, 3 surfaces, atom DeepGlycanSite_score range 0.0358
to 0.659
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/5SentP34/5SentP34_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/236EcolP124/236EcolP124.pdb"
236EcolP124.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) 236Ecol005PP_WWT49697.1
[more info...]
Chain information for 236EcolP124.pdb #1
---
Chain | Description
A | No description available
Non-standard residues in 236EcolP124.pdb #1
---
HED — (HED)
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/236EcolP124/out/236EcolP124.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/236EcolP124/out/236EcolP124.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 163 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
1299 atoms, 163 residues, 1 surfaces, atom DeepGlycanSite_score range 0.0429
to 0.737
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/236EcolP124/236EcolP124_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/60AhydP191/60AhydP191.pdb"
60AhydP191.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) 60AhydR15PP_YP_010095919.1
[more info...]
Chain information for 60AhydP191.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/60AhydP191/out/60AhydP191.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/60AhydP191/out/60AhydP191.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 163 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
1282 atoms, 163 residues, 1 surfaces, atom DeepGlycanSite_score range 0.0382
to 0.784
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/60AhydP191/60AhydP191_analysis.cxs"
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/355SaurP12/355SaurP12.pdb"
355SaurP12.pdb title:
Esmfold V1 prediction for input [more info...]
Chain information for 355SaurP12.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/355SaurP12/out/355SaurP12.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04
Bioinformatics_data/DeepGLycanSite/355SaurP12/out/355SaurP12.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 169 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
1434 atoms, 169 residues, 1 surfaces, atom DeepGlycanSite_score range 0.0349
to 0.815
> key blue-white-red :0 :0.6 :1
> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/DeepGLycanSite/355SaurP12/355SaurP12_analysis.cxs"
——— End of log from Thu Mar 13 14:29:48 2025 ———
> view name session-start
opened ChimeraX session
> close session
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/6His-
> tbs-351SaurP13-Linker_2-351SaurP14/6His-
> tbs-351SaurP13-Linker_2-351SaurP14.pdb"
Chain information for 6His-tbs-351SaurP13-Linker_2-351SaurP14.pdb #1
---
Chain | Description
A B C | No description available
Computing secondary structure
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/DeepGLycanSite/6His-
> tbs-351SaurP13-Linker_2-351SaurP14/out/6His-
> tbs-351SaurP13-Linker_2-351SaurP14.defattr"
Summary of feedback from opening C:/Users/rmatusiak/PROTEON PHARMACEUTICALS
S.A/Projekt Booster - Dokumenty/04 Bioinformatics_data/DeepGLycanSite/6His-
tbs-351SaurP13-Linker_2-351SaurP14/out/6His-
tbs-351SaurP13-Linker_2-351SaurP14.defattr
---
note | Assigned attribute 'DeepGlycanSite_score' to 2511 residues using match mode: any
> show surfaces
> color byattribute r:DeepGlycanSite_score #!1 target sabc palette
> 0.0,blue:0.6,white:1.0,red
39015 atoms, 2511 residues, 3 surfaces, atom DeepGlycanSite_score range 0.0381
to 0.688
> key blue-white-red :0 :0.6 :1
> ui tool show "Molecular Dynamics Viewer"
Please register the custom scheme 'kmd' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 316, in interceptRequest
self._callback(info)
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\ui\htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\ui\gui.py", line 447, in thread_safe
func(*args, **kw)
File "C:\Users\rmatusiak\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 57, in handle_scheme
self.openFile()
File "C:\Users\rmatusiak\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 239, in openFile
self.atomStruct.atoms.coords = self.atomLocation[0]
~~~~~~~~~~~~~~~~~^^^
IndexError: list index out of range
IndexError: list index out of range
File "C:\Users\rmatusiak\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 239, in openFile
self.atomStruct.atoms.coords = self.atomLocation[0]
~~~~~~~~~~~~~~~~~^^^
See log for complete Python traceback.
error dialog finished
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 316, in interceptRequest
self._callback(info)
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\ui\htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\ui\gui.py", line 447, in thread_safe
func(*args, **kw)
File "C:\Users\rmatusiak\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 57, in handle_scheme
self.openFile()
File "C:\Users\rmatusiak\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 239, in openFile
self.atomStruct.atoms.coords = self.atomLocation[0]
~~~~~~~~~~~~~~~~~^^^
IndexError: list index out of range
IndexError: list index out of range
File "C:\Users\rmatusiak\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\com\kdiller\dynamics\viewer\gui.py", line 239, in openFile
self.atomStruct.atoms.coords = self.atomLocation[0]
~~~~~~~~~~~~~~~~~^^^
See log for complete Python traceback.
error dialog finished
> toolshed show
QWindowsWindow::setGeometry: Unable to set geometry 844x886+858+307 (frame:
860x925+850+276) on QWidgetWindow/"QDockWidgetClassWindow" on "LQ156M1JW03".
Resulting geometry: 850x903+855+293 (frame: 866x942+847+262) margins: 8, 31,
8, 8 minimum size: 840x882 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=524303, y=524326), mintrack=POINT(x=856, y=921)))
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/gromacs/6His-
> tbs-351Saur13-linker_2-351Saur14/20250304/out_20250304/part_md_center_part.xtc"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 339, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3215, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3215, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 215, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\md_crds\\__init__.py", line 118, in open
num_coords = read_coords(session, data, structure_model, md_type,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\md_crds\read_coords.py", line 40, in read_coords
coords = array(coords_list, dtype=float64)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 87.2 GiB for an
array with shape (100001, 39015, 3) and data type float64
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 87.2 GiB for an
array with shape (100001, 39015, 3) and data type float64
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\md_crds\read_coords.py", line 40, in read_coords
coords = array(coords_list, dtype=float64)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
error dialog finished
> save Z:/Documents/roboczy_rafal/BOOSTER/DeepGLycanSite/6His-
> tbs-351SaurP13-Linker_2-351SaurP14/analysis.cxs
> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/gromacs/6His-
> tbs-351Saur13-linker_2-351Saur14/20250304/out_20250304/md_center_part_dt10.xtc"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 339, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3215, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3215, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 215, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\md_crds\\__init__.py", line 118, in open
num_coords = read_coords(session, data, structure_model, md_type,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\md_crds\read_coords.py", line 80, in read_coords
model.add_coordsets(coords, replace=replace)
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1759, in add_coordsets
f(self._c_pointer, replace, pointer(xyzs), *xyzs.shape[:2])
MemoryError: not enough memory
MemoryError: not enough memory
File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1759, in add_coordsets
f(self._c_pointer, replace, pointer(xyzs), *xyzs.shape[:2])
See log for complete Python traceback.
error dialog finished
QWindowsWindow::setGeometry: Unable to set geometry 600x487+980+507 (frame:
616x526+972+476) on QWidgetWindow/"QDockWidgetClassWindow" on "LQ156M1JW03".
Resulting geometry: 606x504+977+493 (frame: 622x543+969+462) margins: 8, 31,
8, 8 minimum size: 600x333 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=524303, y=524326), mintrack=POINT(x=616, y=372)))
OpenGL version: 3.3.0 NVIDIA 572.70
OpenGL renderer: NVIDIA GeForce RTX 3080 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: pl_PL.cp1250
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: GIGABYTE
Model: AORUS 15P YD
OS: Microsoft Windows 10 Pro for Workstations (Build 19045)
Memory: 34,089,021,440
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: pl-PL
Installed Packages:
alabaster: 1.0.0
anyio: 4.8.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.2.0
babel: 2.17.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2025.1.31
cftime: 1.6.4.post1
charset-normalizer: 3.4.1
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.18.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.2
ChimeraX-AtomicLibrary: 14.1.13
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.dev202502060317
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: 1.2.7
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-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.5.1
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: 2.1.7
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.7
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-ProfileGrids: 1.0.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.16
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.1
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: 1.43
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
comtypes: 1.4.5
contourpy: 1.3.1
coverage: 7.6.10
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.12
decorator: 5.1.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.15.4
fonttools: 4.55.8
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
iniconfig: 2.0.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.5
joblib: 1.4.2
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.8
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
MolecularDynamicsViewer: 1.6
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
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
plotly: 5.24.1
pluggy: 1.5.0
prompt_toolkit: 3.0.50
psutil: 6.0.0
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: 3.3.5
pynndescent: 0.5.13
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.1
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
pytest: 8.3.4
pytest-cov: 6.0.0
python-dateutil: 2.9.0.post0
pytz: 2025.1
pywin32: 306
pyzmq: 26.2.1
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.1
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
tables: 3.10.2
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
tornado: 6.4.2
tqdm: 4.67.1
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2025.1
umap-learn: 0.5.7
urllib3: 2.3.0
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
Change History (1)
comment:1 by , 7 months ago
| Component: | Unassigned → MD/Ensemble Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Memory error in model.add_coordsets() |
Note:
See TracTickets
for help on using tickets.
AFAIK, the coordinates have already been read in, so add_coordsets() shouldn't use much additional memory...