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Opened 10 months ago
Closed 6 months ago
#16547 closed defect (fixed)
Save X3D failure saving 2D labels
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | 1.10 |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | Eric Pettersen, Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.7.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Trying to save as x3d
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PPE3-peptidecomplex-
> apo-overlay.2.cxs format session
Log from Mon Dec 30 17:49:48 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PPE3-peptidecomplex-
> apo-overlay.2.cxs format session
Log from Sun Dec 29 22:24:38 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/apo-
> bound_PPEP3_1lettercode.transparencyup.2.cxs format session
Log from Wed Dec 18 14:27:06 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/apo-
> bound_PPEP3_1lettercode.cxs
Log from Tue Dec 17 18:26:58 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/overlay-apo-
> bound.cxs
Log from Tue Dec 17 14:25:57 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-
> pepcomplex.4b.cxs"
Log from Sat Dec 14 13:28:52 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-
> pepcomplex.4b.cxs"
Log from Sat Dec 14 13:01:30 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-
> pepcomplex.4b.cxs"
Log from Sat Dec 14 12:48:22 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-pepcomplex-
> wt.cxs"
Log from Sat Dec 14 00:29:48 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> toolshed show
> open "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/nohd-WT-zn.cif"
Summary of feedback from opening /Users/ubaumann/Sync/PPEP-Geo
Manuscript/Figures/nohd-WT-zn.cif
---
warnings | Atom H11 has no neighbors to form bonds with according to residue template for BCN /B:702
Atom H12 has no neighbors to form bonds with according to residue template for
BCN /B:702
notes | Fetching CCD BCN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/BCN/BCN.cif
Fetching CCD PEG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/PEG/PEG.cif
Chain information for nohd-WT-zn.cif #1
---
Chain | Description
A | No description available
B | No description available
50 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open /Users/ubaumann/Xtal/PPEP-geo/ESRF-20230721/Phenix-
> wt_m1macbook/PPEP-4-3-XDSnewest/Refine_39/PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb
Chain information for PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2
---
Chain | Description
A | No description available
B | No description available
50 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> hide #!1 models
> show #!1 models
> ui mousemode right pivot
> ui mousemode right zoom
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> dssp #2
Computing secondary structure
> dssp #2 minStrandLen 2
Computing secondary structure
> dssp #2 minStrandLen 3
Computing secondary structure
> dssp #2 minStrandLen 2
Computing secondary structure
> ui mousemode right pivot
> delete /B all
Expected a keyword
> delete /B attachedHyds
Missing "attachedHyds" keyword's argument
> delete /B ato
Expected a keyword
> delete /B atoms
Expected a keyword
> delete atoms /B
> delete :HOH
> hide atoms
> show :ZN,153,154,157,190,196,197,111 atoms
> hide :HOH
> show /A:BCN atoms
> delete elem H
Missing or invalid "atoms" argument: invalid atoms specifier
> delete atoms elem H
Expected a keyword
> delete atoms element H
Expected a keyword
> delete atoms H
> color :21-150 & strand forestgreen ribbons
> color :150-163 & helix darkorange ribbons
> color :164-235 & helix cornflowerblue ribbons
> color @C* slate gray atH
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color :21-149 & helix purple ribbons
> color coil gray ribbons
> color @C* slate gray atoms
> set bgColor white
> color coil silver ribbons
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/Ribbon-wt-3.cxs"
> color :164-235 & helix slateblue ribbons
> style :153,154,157,190,196,197,111 ball
Changed 140 atom styles
> color :BCN@C* lightgrey
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting full
> lighting soft
> lighting simple
> lighting full
> lighting shadows false
> color :ZN pink
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/Ribbon-wt-3.cxs"
> hide :196 atoms
> color :109-115 linnen ribb
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color :109-115 linen ribbons
> color :109-115 light cyan ribbons
> color 125:126 sea
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color :125,126 seagreen
> color seagreen :125,126 ribb
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/Ribbon-wt-3.cxs"
> label :153,154,157,190,197,111 text {0.name}{0.number} height 1.5
> label :153,154,157,190,197,111 text {0.name}{0.number} height 1.
> ui mousemode right label
> ui mousemode right "move label"
> label :153,154,157,190,197,111 text {0.name}{0.number} height 1.
> ui mousemode right "move label"
> label :153,154,157,190,197,111 text "text {0.residue.number}" height 1.
> label :153,154,157,190,197,111 text {0.residue.number} height 1.
[Repeated 1 time(s)]
> label :153,154,157,190,197,111 text {0.name}{0.number} height 1.
> label :BCN text {0.name} height 1
> 2dlabels text edge
> 2dlabels #3.1 xpos 0.493 ypos 0.618
> 2dlabels text S-loop
> 2dlabels #3.2 xpos 0.757 ypos 0.771
> 2dlabels #3.1 xpos 0.494 ypos 0.624
> 2dlabels #3.2 xpos 0.760 ypos 0.730
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting shadows false
> lighting shadows true
> 2dlabels text N
> 2dlabels #3.3 xpos 0.076 ypos 0.895
> 2dlabels #3.1 xpos 0.503 ypos 0.626
> 2dlabels #3.1 xpos 0.502 ypos 0.637
> 2dlabels #3.2 xpos 0.748 ypos 0.715
> 2dlabels #3.3 xpos 0.068 ypos 0.913
> 2dlabels text C
> 2dlabels #3.4 xpos 0.396 ypos 0.098
> 2dlabels #3.1 xpos 0.499 ypos 0.631
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon-
> ppep-3-wt-shadows.png" width 1567 height 1015 supersample 3
> view
> ui tool show "Side View"
> 2dlabels #3.3 xpos 0.069 ypos 0.946
> 2dlabels #3.4 xpos 0.425 ypos 0.124
> 2dlabels #3.1 xpos 0.514 ypos 0.678
> 2dlabels #3.3 xpos 0.051 ypos 0.910
> 2dlabels #3.4 xpos 0.411 ypos 0.067
> 2dlabels #3.1 xpos 0.501 ypos 0.638
> 2dlabels #3.1 xpos 0.498 ypos 0.635
> 2dlabels #3.4 xpos 0.410 ypos 0.096
> 2dlabels #3.3 xpos 0.053 ypos 0.906
> lighting shadows false
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/Ribbon-
> wt-3.labels.cxs"
> 2dlabels #3.2 xpos 0.737 ypos 0.725
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/Ribbon-
> wt-3.labels.cxs"
> show :161 atoms
> hide :161 atoms
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/Ribbon-
> wt-3.labels.cxs"
> label :30 text β1
> label :30 text β1 height 1
> label :31 text β1 height 1
> label :31 text β1 height 1.2
> ui mousemode right label
> label delete residues
> label :31 text β1 height 1.3
> label delete residues
> label :31 text β1 height 1.3
> ui mousemode right "move label"
> label :53 text β2 height 1.3
> label :90 text β3 height 1.3
> label :133 text β4 height 1.3
> label :70 text 𝛼2 height 1.3
> label :77 text 𝛼3 height 1.3
> ui mousemode right label
> label delete residues
> label :31 text β1 height 1.3
[Repeated 1 time(s)]
> ui mousemode right "move label"
> label :53 text β2 height 1.3
> label :90 text β3 height 1.3
> label :133 text β4 height 1.3
> label :71 text 𝛼2 height 1.3
> label :81 text 𝛼3 height 1.3
> label :BCN text {0.name} height 1
> label :153,154,157,190,197,111 text {0.name}{0.number} height 1.
> label :158 text 𝛼4 height 1.3
> label :200 text 𝛼7 height 1.3
> label :133 text β5 height 1.3
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/Ribbon-
> wt-3.labels-v2.cxs"
> 2dlabels #3.1 xpos 0.496 ypos 0.620
> label :125 text β4 height 1.3
> 2dlabels #3.1 xpos 0.502 ypos 0.624
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/Ribbon-
> wt-3.labels-v2.cxs"
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon-
> ppep-3-wt-shadows.png" width 3134 height 2030 supersample 3
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/Ribbon-
> wt-3.labels-v3.cxs"
> label :178 text 𝛼5 height 1.3
> label :189 text 𝛼6 height 1.3
> label :226 text 𝛼9 height 1.3
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/Ribbon-
> wt-3.labels-v3.cxs"
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon-
> ppep-3-wt-shadows.png" width 3134 height 2030 supersample 4
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/Ribbon-
> wt-3.labels-v4.cxs"
> open /Users/ubaumann/Xtal/PPEP-geo/ESRF-20240430/FW30-4/Phenix-
> FW30-4_M1Macbook/Refine_3/chain_A_E.pdb
Chain information for chain_A_E.pdb #4
---
Chain | Description
A | No description available
E | No description available
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> mmaker #4 to #2
Computing secondary structure
[Repeated 1 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 PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb, chain A (#2)
with chain_A_E.pdb, chain A (#4), sequence alignment score = 1080.2
RMSD between 177 pruned atom pairs is 0.531 angstroms; (across all 208 pairs:
1.506)
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-pepcomplex-
> wt.cxs"
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/complex-to-wt.pdb"
> models #4
> hide #!2 models
> hide #!3 models
> dssp #4 minStrandLen 2
Computing secondary structure
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-pepcomplex-
> wt.cxs"
——— End of log from Sat Dec 14 00:29:48 2024 ———
opened ChimeraX session
> show #!2 models
> hide #4 models
> show #!3 models
> 2dlabels #3.4 xpos 0.376 ypos 0.085
> 2dlabels #3.3 xpos 0.090 ypos 0.883
> 2dlabels #3.1 xpos 0.503 ypos 0.617
> 2dlabels #3.1 xpos 0.491 ypos 0.629
> 2dlabels #3.2 xpos 0.731 ypos 0.753
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-pepcomplex-
> wt.v2.cxs"
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon-
> ppep-3-wt.v2.png" width 1567 height 1015 supersample 3
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon-
> ppep-3-wt.v2.png" width 3134 height 2030 supersample 3
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-pepcomplex-
> wt.v2.cxs"
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon-
> ppep-3-wt.v2.png" width 1567 height 1015 supersample 3
> hide #!2 models
> hide #!3 models
> show #4 models
> open "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/draw-complex_v2.cxc"
> dssp #4 minStrandLen 2
> hide atoms
> show :ZN,153,154,157,190,197,111 atoms
> show #4/E atoms
> style #4/E ball
Changed 110 atom styles
> hide :HOH
> show /A:BCN atoms
> delete atoms H
> color :21-149 & helix purple ribbons
> color :21-150 & strand forestgreen ribbons
> color :150-163 & helix darkorange ribbons
> color :164-235 & helix slateblue ribbons
> color #2:BCN@C* lightgrey
> color :125,126 seagreen ribbons
> color :ZN pink
> color coil silver ribbons
> color :109-115 light cyan ribbons
> style :153,154,157,190,196,197,111 ball
Changed 205 atom styles
> label :153,154,157,190,197,111 text {0.name}{0.number} height 1.
> label :BCN text {0.name} height 1
> label :31 text β1 height 1.3
> label :53 text β2 height 1.3
> label :90 text β3 height 1.3
> label :125 text β4 height 1.3
> label :133 text β5 height 1.3
> label :178 text 𝛼5 height 1.3
> label :189 text 𝛼6 height 1.3
> label :226 text 𝛼9 height 1.3
> label :200 text 𝛼7 height 1.3
> label #4:158 text 𝛼4 height 1.3
> color #4/A@C* slate gray atoms
> color #4/E@C* cyan atoms
executed draw-complex_v2.cxc
> transparency 50 #4 rib
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency #4 50 ribbons
> hide #!4 models
> show #!2 models
> ui mousemode right zoom
> ui mousemode right "move label"
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-pepcomplex-
> wt.v3.cxs"
[Repeated 1 time(s)]
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon-
> ppep-3-wt.v2.png" width 1567 height 1015 supersample 3
> show #!3 models
> 2dlabels #3.4 xpos 0.434 ypos 0.071
> 2dlabels #3.3 xpos 0.079 ypos 0.911
> 2dlabels #3.1 xpos 0.515 ypos 0.598
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon-
> ppep-3-wt.v2.png" width 1567 height 1015 supersample 3
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-pepcomplex-
> wt.v3.cxs"
> hide #!2 models
> show #!4 models
> 2dlabels #3.2 xpos 0.790 ypos 0.625
> 2dlabels #3.4 xpos 0.361 ypos 0.078
> 2dlabels #3.3 xpos 0.300 ypos 0.767
> 2dlabels #3.2 xpos 0.773 ypos 0.617
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/complex.png"
> width 3134 height 2030 supersample 3
> 2dlabels #3.1 xpos 0.515 ypos 0.598
> 2dlabels #3.1 xpos 0.516 ypos 0.590
> ui mousemode right zoom
> ui mousemode right "move label"
> 2dlabels #3.4 xpos 0.338 ypos 0.125
> 2dlabels #3.3 xpos 0.284 ypos 0.849
> hide #!4 models
> show #!2 models
> 2dlabels #3.4 xpos 0.405 ypos 0.122
> 2dlabels #3.4 xpos 0.437 ypos 0.077
> 2dlabels #3.3 xpos 0.074 ypos 0.960
> 2dlabels #3.1 xpos 0.543 ypos 0.612
> 2dlabels #3.1 xpos 0.543 ypos 0.621
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon-
> ppep-3-wt.v3.png" width 3412 height 2334 supersample 4
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-pepcomplex-
> wt.v4.cxs"
> hide #!2 models
> show #!4 models
> 2dlabels #3.3 xpos 0.312 ypos 0.804
> 2dlabels #3.4 xpos 0.366 ypos 0.079
> style #4/E stick
Changed 56 atom styles
> 2dlabels #3.1 xpos 0.541 ypos 0.611
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> label #4:158 text 𝛼4 height 1.3
> hide #!4 models
> show #!4 models
> show #!2 models
> hide #!2 models
> select add #2
1777 atoms, 1822 bonds, 6 pseudobonds, 219 residues, 3 models selected
> select subtract #2
Nothing selected
> show #!2 models
> hide #!2 models
> label #4:81 text 𝛼3 height 1.33
> label #4:68 text 𝛼2 height 1.3
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-pepcomplex-
> wt.v4.cxs"
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon-
> ppep-3-complex.v3.png" width 1706 height 1167 supersample 3
> style #4 sticks
Expected a keyword
> style #4 sticks at
Expected a keyword
> style #4 at stick
Expected a keyword
> style #4 stick
Changed 1747 atom styles
> style #4:ZN ball
Changed 1 atom style
> style #4:ZN sphere
Changed 1 atom style
> hide #!4 models
> show #!2 models
> 2dlabels #3.3 xpos 0.075 ypos 0.968
> 2dlabels #3.4 xpos 0.438 ypos 0.074
> 2dlabels #3.1 xpos 0.543 ypos 0.618
> label #2:217 text 𝛼8 height 1.3
> 2dlabels #3.2 xpos 0.799 ypos 0.652
> show :113 atoms
> style :113 sticks
Expected a keyword
> style :113 ball
Changed 36 atom styles
> label :113 text {0.name}{0.number} height 1.
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon-
> ppep-3-wt.v3.png" width 1706 height 1167 supersample 4
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-pepcomplex-
> wt.v4.cxs"
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> show #!4 models
> style #4:113 stick
Changed 12 atom styles
> 2dlabels #3.4 xpos 0.371 ypos 0.082
> 2dlabels #3.3 xpos 0.314 ypos 0.808
> 2dlabels #3.1 xpos 0.543 ypos 0.607
> 2dlabels #3.2 xpos 0.784 ypos 0.580
> select #4/A:113@OH
1 atom, 1 residue, 1 model selected
> select add #4/E:5@O
2 atoms, 2 residues, 1 model selected
> distance #4/A:113@OH #4/E:5@O
Distance between chain_A_E.pdb #4/A TYR 113 OH and /E PRO 5 O: 2.717Å
> ~distance
> select clear
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-pepcomplex-
> wt.v4.bcxs.cxs"
> open "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/n-pseudobonds.pb"
Line 4 "/a:701@ZN /a:197@oe1
", got 2 atoms for spec "/a:701@ZN", require exactly 1
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-
> pepcomplex.4b.cxs"
——— End of log from Sat Dec 14 12:48:22 2024 ———
opened ChimeraX session
> open "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/n-pseudobonds.pb"
Opened Pseudobonds n-pseudobonds.pb, 5 bonds
> show #4/a:196 atoms
> show /a:196 atoms
> show #!2 models
> hide #!2 models
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-
> pepcomplex.4b.cxs"
> label #4/a:157 text {0.name}{0.number} height 0.8
> 2dlabels #3.4 xpos 0.362 ypos 0.082
> 2dlabels #3.3 xpos 0.313 ypos 0.812
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-
> pepcomplex.4b.cxs"
> open "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/n-pseudobonds.pb"
Opened Pseudobonds n-pseudobonds.pb, 7 bonds
> label #4/a:196 text {0.name}{0.number} height 1.3
> label #4/a:196 text {0.name}{0.number} height 1.
> label #4/a:196 text {0.name}{0.number} height 0.9
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-
> pepcomplex.4b.cxs"
——— End of log from Sat Dec 14 13:01:30 2024 ———
opened ChimeraX session
> transparency #4 0 cartoons
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon-
> ppep-3-complex.v4.notransp.png" width 3412 height 2334 supersample 3
> label #2/a:47 text 𝛼1 height 1.3
> show #!2 models
> hide #!2 models
> label #4/a:47 text 𝛼1 height 1.3
> transparency #4 60 cartoons
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon-
> ppep-3-complex.v4.png" width 3412 height 2334 supersample 3
> 2dlabels "P1"
Expected 'all' or a 2d label name or a label models specifier or a keyword
> 2dlabels text P1
> 2dlabels #3.5 xpos 0.500 ypos 0.500
> ~2dlabels text "P1"
> 2dlabels delete text "P1"
Expected 'all' or a label/arrow models specifier or a keyword
> ~2dlabels "P1"
> 2dlabels delete "P1"
Expected 'all' or a label/arrow models specifier or a keyword
> 2dlabels #3.5 xpos 0.655 ypos 0.525
> ~2dlabels "P11" color cyan
> 2dlabels delete "P11" color cyan
Expected 'all' or a label/arrow models specifier or a keyword
> ~2dlabels text "P1" color cyan
> 2dlabels delete text "P1" color cyan
Expected 'all' or a label/arrow models specifier or a keyword
> 2dlabels text P1 color cyan
> 2dlabels #3.6 xpos 0.675 ypos 0.511
[Repeated 1 time(s)]
> ~2dlabels #3.6
> ~2dlabels #3.5
> 2dlabels text P1 color cyan
> 2dlabels #3.5 xpos 0.656 ypos 0.520
> 2dlabels text P1' color cyan
> 2dlabels #3.6 xpos 0.638 ypos 0.605
> 2dlabels #3.5 xpos 0.651 ypos 0.521
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon-
> ppep-3-complex.v4b.png" width 3412 height 2334 supersample 4
> label #4/a:153 text {0.name}{0.number} height 0.9
> label #4/a:153 text {0.name}{0.number} height 0.8
> 2dlabels #3.2 xpos 0.776 ypos 0.578
> save "/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-
> pepcomplex.4b.cxs"
——— End of log from Sat Dec 14 13:28:52 2024 ———
opened ChimeraX session
> 2dlabels #3.1 xpos 0.553 ypos 0.608
> 2dlabels #3.3 xpos 0.336 ypos 0.825
> 2dlabels #3.4 xpos 0.354 ypos 0.079
> 2dlabels #3.3 xpos 0.319 ypos 0.828
> 2dlabels #3.6 xpos 0.637 ypos 0.614
> 2dlabels #3.5 xpos 0.657 ypos 0.602
> 2dlabels #3.6 xpos 0.632 ypos 0.624
> 2dlabels #3.5 xpos 0.658 ypos 0.603
> 2dlabels #3.6 xpos 0.630 ypos 0.626
> label #4/A:111 text {0.name} size 25 height fixed
> label #4/A:111 text {0.name} {0.number}size 25 height fixed
Expected a keyword
> label #4/A:111 text {0.name} {0.number} size 25 height fixed
Expected a keyword
> label #4/A:111 text "{0.name} {0.number}" size 25 height fixed
> label #4/A:111 text "{0.name} {0.number}" size 20 height fixed
> 2dlabels #3.2 text S-loop color light cyan size 25
> 2dlabels #3.2 text S-loop color lsky size 25
Invalid "color" argument: Expected one of 'auto' or 'default' or a color
> 2dlabels #3.2 text S-loop color skyblue size 25
> 2dlabels #3.2 xpos 0.787 ypos 0.570
> 2dlabels #3.5 text P1 color cyan bold true size 25
> 2dlabels #3.6 text P1' color cyan bold true size 25
> 2dlabels #3.6 text P2' color cyan bold true size 25
> 2dlabels #3.6 text P1' color cyan bold true size 25
> 2dlabels ext "P2'" color cyan bold true size 25
Expected 'all' or a 2d label name or a label models specifier or a keyword
> 2dlabels text P2' color cyan bold true size 25
> 2dlabels #3.7 xpos 0.681 ypos 0.516
> 2dlabels text P2 color cyan bold true size 25
> 2dlabels #3.8 xpos 0.654 ypos 0.445
> 2dlabels text P3 color cyan bold true size 25
> 2dlabels #3.9 xpos 0.594 ypos 0.583
> 2dlabels #3.6 xpos 0.635 ypos 0.623
> 2dlabels #3.5 xpos 0.651 ypos 0.523
> 2dlabels #3.7 xpos 0.683 ypos 0.522
> 2dlabels #3.5 xpos 0.654 ypos 0.598
> 2dlabels #3.4 xpos 0.356 ypos 0.083
> 2dlabels #3.3 xpos 0.323 ypos 0.830
> 2dlabels #3.3 text N true size 30
Expected a keyword
> 2dlabels #3.3 text N size 30
> 2dlabels #3.4 text C size 35
> 2dlabels #3.3 text N size 35
> save /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/peptidecomplex.cxs
> transparency #4 40 ribbons
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/Pepcomplex_1.png
> width 2632 height 1802 supersample 3
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #2 atoms
> ~label #2
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #2/A:111,190,113 atoms
> style #2 stick
Changed 1777 atom styles
> transparence #2 60 at
Unknown command: transparence #2 60 at
> transparency #2 60 atoms
> transparency #2 80 atoms
> transparency #2 60 ribbons
> transparency #2 80 ribbons
> transparency #4 20 ribbons
> save /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/overlay-apo-
> bound.cxs
——— End of log from Tue Dec 17 14:25:57 2024 ———
opened ChimeraX session
> show #2/B:191 atoms
> show #2/A:191 atoms
> show #4/A:191 atoms
> ui mousemode right "move label"
> 2dlabels #3.2 xpos 0.848 ypos 0.655
> label #4/A:190,113,196,197,111,190,191,153,157 text{0.1}{0.number} size 20
> height fix
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label #4/A:190,113,196,197,111,190,191,153,157 text {0.1}{0.number} size 20
> height fixed
> label #4/A:190,113,196,197,111,190,191,153,157 text {0.1-letter}{0.number}
> size 20 height fixed
> label #4/A:190,113,196,197,111,190,191,153,157 text {0.code}{0.number} size
> 20 height fixed
> label #4/A:190,113,196,197,111,190,191,153,157 code,number size 20 height
> fix
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label #4/A:190,113,196,197,111,190,191,153,157 "code,number" size 20 height
> fix
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label #4/A:190,113,196,197,111,190,191,153,157 attribute code,number size 20
> height fixed
> label #4/A:190,113,196,197,111,190,191,153,157 text "{0.1-letter
> code}{0.number}" size 20 height fixed
> label #4/A:154,190,113,196,197,111,190,191,153,157 text "{0.1-letter
> code}{0.number}" size 20 height fixed
> label #4/A:154,190,113,196,197,111,190,191,153,157 text "{0.1-letter
> code}{0.number}" size 25 height fixed
> show#2/A:154 at
Unknown command: show#2/A:154 at
> show #2/A:154 atoms
> label #4/A:154,190,113,196,197,111,190,191,153,157 text "{0.1-letter
> code}{0.number}" size 25 height fixed
> label #4/A:154,190,113,196,197,111,190,191,153,157 text {0.code}{0.number}
> size 25 height fixed
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> label #4/A:154,190,113,196,197,111,190,191,153,157 text {0.number} size 25
> height fixed
> select #4/A:154,190,113,196,197,111,190,191,153,157
88 atoms, 87 bonds, 2 pseudobonds, 9 residues, 2 models selected
> label (#!4 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #4/A::190 text "Y/F 190" size 20 height fix
Expected an objects specifier or a keyword
> label #4/A::190 text "Y/F 190" size 20 height fix
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label #4/A:190 text "Y/F 190" size 20 height fixed
> select clear
> save /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/overlay-apo-
> bound.2.png width 1816 height 1243 supersample 3
> save /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/apo-
> bound_PPEP3_1lettercode.cxs
——— End of log from Tue Dec 17 18:26:58 2024 ———
opened ChimeraX session
> label #4/A:154 text "E/A 154" size 20 height fixed
> ui mousemode right "move label"
> 2dlabels #3.3 xpos 0.003 ypos 0.951
> 2dlabels #3.4 xpos 0.334 ypos 0.072
> 2dlabels #3.5 xpos 0.679 ypos 0.591
> 2dlabels #3.6 xpos 0.644 ypos 0.614
> 2dlabels #3.7 xpos 0.718 ypos 0.515
> 2dlabels #3.9 xpos 0.619 ypos 0.597
> 2dlabels #3.6 xpos 0.657 ypos 0.618
> 2dlabels #3.9 xpos 0.619 ypos 0.571
> 2dlabels #3.8 xpos 0.682 ypos 0.445
[Repeated 1 time(s)]
> 2dlabels #3.9 xpos 0.619 ypos 0.575
> 2dlabels #3.6 xpos 0.654 ypos 0.622
> 2dlabels #3.2 xpos 0.931 ypos 0.661
> select ~sel & ##selected
Nothing selected
> lable #4/A:153,157196,197,113,111,191 text "{0.label_1_letter_code}{0.name}"
> size 25 height fixed
Unknown command: lable #4/A:153,157196,197,113,111,191 text
"{0.label_1_letter_code}{0.name}" size 25 height fixed
> label #4/A:153,157196,197,113,111,191 text {0.label_1_letter_code}{0.name}
> size 25 height fixed
> select #4/A:113@CG
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> label sel attribute label_one_letter_code
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> label #4/A:153,157196,197,113,111,191 text {0.label_one_letter_code}{0.name}
> size 25 height fixed
> label #4/A:153,157196,197,113,111,191 text {0.label_one_letter_code}{0.name}
> size 20 height fixed
> ~label
> label #4/A:153,157196,197,113,111,191 text {0.label_one_letter_code}{0.name}
> size 20 height fixed
> ~label
> select clear
> label #4/A:153,157196,197,113,111,191 text {0.label_one_letter_code}{0.name}
> size 20 height fixed
> label #4/A:153,157196,197,113,111,191 text
> {0.label_one_letter_code}{0.number} size 20 height fixed
> label #4/A:153,157,196,197,113,111,191 text
> {0.label_one_letter_code}{0.number} size 20 height fixed
> label #4/A:154 text "E/A 154" size 20 height fixed
> label #4/A:190 text "Y/F 190" size 20 height fixed
> 2dlabels #3.3 xpos -0.001 ypos 0.958
> 2dlabels #3.4 xpos 0.335 ypos 0.073
> label #4/A:104 text η4 height fixed size 30
> transparency #2 90
> transparency #2 95
> ribbon
> transparency #2 95 ribbons
> transparency #2 90 ribbons
> transparency #2 93 ribbons
> 2dlabels #3.1 xpos 0.552 ypos 0.612
> 2dlabels #3.5 xpos 0.682 ypos 0.517
> 2dlabels #3.6 xpos 0.667 ypos 0.608
> 2dlabels #3.7 xpos 0.719 ypos 0.516
> hide #4/E ribbons
> transparency #2 91 ribbons
> color #4 grey coil
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #4 grey ribbons & coil
Expected ',' or a keyword
> color #4 & coil grey ribbons
> color #4 & coil lightgrey ribbons
> color #4 & coil silver ribbons
> 2dlabels #3.6 xpos 0.672 ypos 0.601
> label #4/A:192 text 𝛼6 height fixed size 30
> save /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/overlay-apo-
> bound.4.png width 1281 height 1077 supersample 3
> hide #4/A:111 atoms
> show #4/A:111 atoms
> transparency 70 #4/A:111
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 70 #4/A:111 at
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency #4/A:111 70 atoms
> transparency #4/A:111 60 atoms
> transparency #4/A:111 50 atoms
> transparency #4/A:111 40 atoms
> save /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/overlay-apo-
> bound.4.png width 1562 height 1313 supersample 3
> save /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/apo-
> bound_PPEP3_1lettercode.transparencyup.2.cxs
——— End of log from Wed Dec 18 14:27:06 2024 ———
opened ChimeraX session
> transparency #4/A 0 cartoons,atoms
> transparency #42A 95 cart,at
Missing or invalid "percent" argument: Expected a number
> transparency #2A 95 cart,at
Missing or invalid "percent" argument: Expected a number
> transparency #2/A 95 cartoons,atoms
> 2dlabels #3.8 xpos 0.679 ypos 0.449
> transparency #2/A 90 cartoons,atoms
> 2dlabels #3.7 xpos 0.717 ypos 0.517
> label #4/E:7 text P3' height fixed size 25 color cyan
> 2dlabels #3.3 xpos 0.001 ypos 0.947
> 2dlabels #3.4 xpos 0.330 ypos 0.096
> 2dlabels #3.1 xpos 0.563 ypos 0.610
> 2dlabels #3.2 xpos 0.936 ypos 0.655
> 2dlabels #3.4 xpos 0.348 ypos 0.102
> 2dlabels #3.3 xpos 0.010 ypos 0.950
> 2dlabels #3.1 xpos 0.574 ypos 0.613
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PPE3-peptidecomplex-
> apo-overlay.2.cxs
——— End of log from Sun Dec 29 22:24:38 2024 ———
opened ChimeraX session
> show #2,4/A:101 atoms
> distance #2/A:113@CA #4/A:113@CA color hotpink dig 1
Expected a keyword
> distance #2/A:113@CA #4/A:113@CA color hotpink decimalPlaces 1
Distance between PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A TYR
113 CA and chain_A_E.pdb #4/A TYR 113 CA: 3.8Å
> 2dlabels #3.3 xpos 0.285 ypos 0.808
> distance #2/A:101@CA #4/A:101@CA color hotpink decimalPlaces 1
Distance between PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A ILE
101 CA and chain_A_E.pdb #4/A ILE 101 CA: 2.7Å
> distance #2/A:101@CA #4/A:101@CA color cyan decimalPlaces 1
Distance already exists; modify distance properties with 'distance style'
> distance style color cyan decimalPlaces 1
> distance style color cyan
> distance style color hotpink decimalPlaces 1
> distance style color hotpink
> distance #2/A:191@CG #4/A:191@CG color hotpink decimalPlaces 1
Distance between PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A PHE
191 CG and chain_A_E.pdb #4/A PHE 191 CG: 1.8Å
> close #3.5-9
> label #4/E:6 text P2' size 25 color navy
> label #4/E:6 text P2' size 25 height fixed color blue
> label #4/E:6 text P2' size 25 height fixed color cyan
> label #4/E:5 text P1' size 25 height fixed color cyan
> label #4/E:4 text P1 size 25 height fixed color cyan
> label #4/E:3 text P2 size 25 height fixed color cyan
> label #4/E:2 text P3 size 25 height fixed color cyan
> distance #2/A:111@CG #4/A:111@CG color hotpink decimalPlaces 1
Distance between PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A ARG
111 CG and chain_A_E.pdb #4/A ARG 111 CG: 5.2Å
> label #4/A:101 text {0.one_letter_code}{0.number} height fixed size 25
> select #4/E:3
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #fa4743 interModel false intraRes false reveal true
2 hydrogen bonds found
> select clear
> 2dlabels #3.3 xpos 0.292 ypos 0.810
> label #4/A:103 text η3 height fixed size 30
> label #4/A:103 text η3 height fixed size 30 color white
> label #4/A:104 text η4 height fixed size 30 color white
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PPE3-peptidecomplex-
> apo-overlay.2.cxs
> label #4/E:2 text P3 size 25 height fixed color blue
> label #4/E:3 text P2 size 25 height fixed color blue
> label #4/E:4 text P1 size 25 height fixed color blue
> label #4/E:5 text P1' size 25 height fixed color blue
> label #4/E:6 text P2' size 25 height fixed color blue
> label #4/E:7 text P3' size 25 height fixed color blue
> ~distance #4/A:101@CG #2/A:101@CG
> ~distance #4/A:111@CG #2/A:111@CG
> distance #4/A:111@CA #2/A:111@CA color hotpink decimalPlaces 1
Distance between chain_A_E.pdb #4/A ARG 111 CA and
PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A ARG 111 CA: 3.9Å
> 2dlabels #3.4 xpos 0.277 ypos 0.033
> 2dlabels #3.3 xpos 0.209 ypos 0.858
> 2dlabels #3.1 xpos 0.533 ypos 0.627
> 2dlabels #3.2 xpos 0.933 ypos 0.683
> 2dlabels #3.4 xpos 0.296 ypos 0.065
> 2dlabels #3.3 xpos 0.225 ypos 0.825
> 2dlabels #3.1 xpos 0.528 ypos 0.625
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PPE3-peptidecomplex-
> apo-overlay.2.cxs
> save /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/PPEP3-apo-
> peptide_overlay.2.png width 3110 height 2680 supersample 3
> 2dlabels #3.2 xpos 0.897 ypos 0.688
> color #2,4/:108-118 lightcyan ribb
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color lightcyan #2,4/:108-118 ribb
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color lightcyan #2,4/A:108-118 ribb
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color lightcyan #2,4/A:108-118 cartoon
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #2,4/A:108-118 lightcyan cartoons
> 2dlabels #3.2 xpos 0.856 ypos 0.629
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PPE3-peptidecomplex-
> apo-overlay.2.cxs
> save /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/PPEP3-apo-
> peptide_overlay.2.png width 3110 height 2680 supersample 3
[Repeated 1 time(s)]
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PPE3-peptidecomplex-
> apo-overlay.2.cxs
> select #4/A:111@NH2
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
4 hydrogen bonds found
> color #7 #fa2b31ff models
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PPE3-peptidecomplex-
> apo-overlay.2.cxs
——— End of log from Mon Dec 30 17:49:48 2024 ———
opened ChimeraX session
> show :161 atoms
> label #4/A:161 text {0.one_letter_code}{0.number} height 25
> label #4/A:161 text {0.one_letter_code}{0.number} height fixed size 25
> transparency #2 0 atoms
> color #2 #8b8b8b19
> color #2 #cdcdcd19
> color #2 #e2e2e219
> transparency #2 0 atoms
> color sel byhetero
> color #2 byhetat
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #2 byhetero
> 2dlabels #3.2 xpos 0.879 ypos 0.409
> ~distance
> hide #2 atoms, cartoons
> show #2/A:161 atoms
> show #2/A:161 atoms !@C,O
Expected ',' or a keyword
> show #2/A:161 atoms ~@C,O
Expected ',' or a keyword
> hide #2/A:161@C,O
> 2dlabels #3.1 xpos 0.749 ypos 0.680
> hide #3.3 models
> hide #3.4 models
> 2dlabels #3.1 xpos 0.686 ypos 0.739
> show #4/A surfaces
> color lightgrey surfaces
> transparency 50 surfaces
> show #4/A:131,133,104,127 atoms
> 2dlabels #3.1 xpos 0.712 ypos 0.632
> select #4/E:3@CD2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel HIS rotLib Dunbrack
chain_A_E.pdb #4/E LEU 3: phi -113.1, psi 128.2 trans
Changed 288 bond radii
> swapaa interactive sel HIS rotLib Dunbrack
chain_A_E.pdb #!4/E LEU 3: phi -113.1, psi 128.2 trans
Changed 288 bond radii
> swapaa #!4/E:3 HIS criteria 7 rotLib Dunbrack
Using Dunbrack library
chain_A_E.pdb #!4/E LEU 3: phi -113.1, psi 128.2 trans
Applying HIS rotamer (chi angles: -63.7 94.6) to chain_A_E.pdb #!4/E HIS 3
> hide sel surfaces
[Repeated 1 time(s)]
> select
5591 atoms, 5731 bonds, 17 pseudobonds, 691 residues, 50 models selected
> hide sel & #4.3.16#!2,4 surfaces
> select #!4/E:3@NE2
1 atom, 1 residue, 1 model selected
> select add #!4/A:161@CZ
2 atoms, 2 residues, 1 model selected
> distance #!4/E:3@NE2 #!4/A:161@CZ
Distance between chain_A_E.pdb #!4/E HIS 3 NE2 and /A TYR 161 CZ: 2.7Å
> select #4/E:2@CA
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel LEU rotLib Dunbrack
chain_A_E.pdb #4/E PRO 2: phi -79.3, psi 110.5 trans
Changed 45 bond radii
> show #4/A surfaces
> swapaa #!4/E:2 LEU criteria 2 rotLib Dunbrack
Using Dunbrack library
chain_A_E.pdb #!4/E PRO 2: phi -79.3, psi 110.5 trans
Applying LEU rotamer (chi angles: -61.7 175.9) to chain_A_E.pdb #!4/E LEU 2
> select clear
> lighting full
> lighting shadows false
> lighting simple
> 2dlabels #3.1 xpos 0.668 ypos 0.587
> lighting full
> lighting shadows false
> lighting soft
> lighting gentle
> lighting full
> lighting shadows false
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.png
> width 3110 height 2662 supersample 3
> lighting ambient 0.1
Expected keyword "ambientColor" or "ambientIntensity"
> lighting ambientIntensity 0.1
> lighting ambientIntensity 0.3
> lighting ambientIntensity 0.4
> lighting ambientIntensity 0.5
> lighting full
> lighting shadows false
> lighting ambientColor black
> lighting ambientColor lightgrey
> 2dlabels #3.1 xpos 0.676 ypos 0.538
> lighting ambientColor lightgrey depthCue true
> lighting soft
> lighting soft multiShadow 512
> lighting soft multiShadow 1024
> lighting full
> lighting shadows false
> lighting gentlemultishadow 1024
Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword
> lighting gentle multiShadow 1024
> lighting softmultishadow 1024
Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword
> lighting full
> lighting soft
> lighting full
> lighting soft
> label #4/A
> 104,131,133 text "{0.one_letter_code}{number}" size 25 height fix
Unknown command: 104,131,133 text "{0.one_letter_code}{number}" size 25 height
fix
> ~label #4/A
> 104,131,133 text "{0.one_letter_code}{number}" size 25 height fix
Unknown command: 104,131,133 text "{0.one_letter_code}{number}" size 25 height
fix
> ~label #4/A:104,131,133,161 text "{0.one_letter_code}{number}" size 25
> height fix
> label delete #4/A:104,131,133,161 text "{0.one_letter_code}{number}" size 25
> height fix
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label #4/A:104,131,133,161 text {0.one_letter_code}{number} size 25 height
> fixed
> ~label #4/A:104,131,133,161 text "{0.one_letter_code}{0.number}" size 25
> height fix
> label delete #4/A:104,131,133,161 text "{0.one_letter_code}{0.number}" size
> 25 height fix
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label #4/A:104,131,133,161 text {0.one_letter_code}{0.number} size 25 height
> fixed
> label #4/A:104,101,131,133,161 text {0.one_letter_code}{0.number} size 25
> height fixed
> label #4/A:104,101,104,131,133,161 text {0.one_letter_code}{0.number} size
> 25 height fixed
> lighting full
> lighting shadows false
> hide #!6 models
> select clear
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.png
> width 3110 height 2662 supersample 3
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select
5304 atoms, 5443 bonds, 18 pseudobonds, 655 residues, 16 models selected
> ~select
Nothing selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel interModel false ignoreHiddenModels true select true
> makePseudobonds false log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
7 contacts
atom1 atom2 overlap distance
chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 CD2 0.076 3.564
chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A GLY 127 O 0.027 3.273
chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 CG -0.083 3.573
chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 CE1 -0.167 3.807
chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 NE2 -0.184 3.704
chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 ND1 -0.194 3.714
chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 CB -0.392 4.152
7 contacts
> contacts sel restrict cross interModel false ignoreHiddenModels true select
> true makePseudobonds false log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
21 contacts
atom1 atom2 overlap distance
chain_A_E.pdb #4/A HIS 157 NE2 chain_A_E.pdb #4/A HIS 153 NE2 0.294 2.986
chain_A_E.pdb #4/A HIS 157 CE1 chain_A_E.pdb #4/A ALA 200 CB 0.210 3.430
chain_A_E.pdb #4/A HIS 157 CE1 chain_A_E.pdb #4/A GLU 197 CD 0.048 3.592
chain_A_E.pdb #4/A HIS 157 CB chain_A_E.pdb #4/A GLY 128 N 0.024 3.496
chain_A_E.pdb #4/A HIS 157 NE2 chain_A_E.pdb #4/A ZN 701 ZN 0.016 2.224
chain_A_E.pdb #4/A HIS 157 NE2 chain_A_E.pdb #4/A HIS 153 CD2 -0.020 3.420
chain_A_E.pdb #4/A HIS 157 CB chain_A_E.pdb #4/A ALA 154 O -0.061 3.361
chain_A_E.pdb #4/A HIS 157 CB chain_A_E.pdb #4/A GLY 128 CA -0.125 3.885
chain_A_E.pdb #4/A HIS 157 ND1 chain_A_E.pdb #4/A ALA 200 CB -0.151 3.671
chain_A_E.pdb #4/A HIS 157 CB chain_A_E.pdb #4/A GLY 127 C -0.164 3.654
chain_A_E.pdb #4/A HIS 157 NE2 chain_A_E.pdb #4/A ALA 200 CB -0.168 3.688
chain_A_E.pdb #4/A HIS 157 CD2 chain_A_E.pdb #4/A HIS 153 CD2 -0.185 3.705
chain_A_E.pdb #4/A GLY 127 O chain_A_E.pdb #4/E HIS 3 N -0.191 2.851
chain_A_E.pdb #4/A GLY 127 O chain_A_E.pdb #4/E HIS 3 CA -0.202 3.502
chain_A_E.pdb #4/A HIS 157 NE2 chain_A_E.pdb #4/A GLU 197 CD -0.242 3.762
chain_A_E.pdb #4/A HIS 157 CE1 chain_A_E.pdb #4/A GLU 197 OE2 -0.257 3.437
chain_A_E.pdb #4/A HIS 157 CB chain_A_E.pdb #4/A GLY 127 CA -0.324 4.084
chain_A_E.pdb #4/A HIS 157 CE1 chain_A_E.pdb #4/A GLU 197 OE1 -0.332 3.512
chain_A_E.pdb #4/A GLY 127 O chain_A_E.pdb #4/E GLU 1 O -0.345 3.185
chain_A_E.pdb #4/A HIS 157 CD2 chain_A_E.pdb #4/A HIS 153 O -0.360 3.540
chain_A_E.pdb #4/A HIS 157 CD2 chain_A_E.pdb #4/A HIS 153 NE2 -0.365 3.765
21 contacts
> ~select
Nothing selected
> contacts sel restrict #4/A interModel false ignoreHiddenModels true select
> true makePseudobonds false log true
No atoms match given atom specifier
> contacts sel interModel false ignoreHiddenModels true select true
> makePseudobonds false log true
No atoms match given atom specifier
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> contacts sel restrict #4/A interModel false ignoreHiddenModels true select
> true makePseudobonds false log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
1 contacts
atom1 atom2 overlap distance
chain_A_E.pdb #4/E HIS 3 ND1 chain_A_E.pdb #4/A GLY 128 CA 0.153 3.367
1 contacts
> contacts sel restrict #4/A:161 interModel false ignoreHiddenModels true
> select true makePseudobonds false log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
0 contacts
atom1 atom2 overlap distance
No contacts
> ~select
Nothing selected
> select #4/E:2
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/E:3
10 atoms, 10 bonds, 1 residue, 1 model selected
> contacts sel interModel false ignoreHiddenModels true select true
> makePseudobonds false log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
35 contacts
atom1 atom2 overlap distance
chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/E GLU 1 CB 0.698 2.942
chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/A TYR 161 CE2 0.623 2.897
chain_A_E.pdb #4/E HIS 3 NE2 chain_A_E.pdb #4/A TYR 161 CZ 0.547 2.703
chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/A TYR 161 CZ 0.405 2.965
chain_A_E.pdb #4/E HIS 3 NE2 chain_A_E.pdb #4/A TYR 161 CE2 0.335 3.065
chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/A TYR 161 CD2 0.166 3.354
chain_A_E.pdb #4/E HIS 3 ND1 chain_A_E.pdb #4/A GLY 128 CA 0.153 3.367
chain_A_E.pdb #4/E HIS 3 NE2 chain_A_E.pdb #4/A TYR 161 OH 0.085 2.615
chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 CD2 0.076 3.564
chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/A TYR 161 CE1 0.074 3.446
chain_A_E.pdb #4/E HIS 3 NE2 chain_A_E.pdb #4/A TYR 161 CE1 0.044 3.356
chain_A_E.pdb #4/E HIS 3 NE2 chain_A_E.pdb #4/E GLU 1 CB 0.031 3.489
chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A GLY 127 O 0.027 3.273
chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/E GLU 1 CG 0.008 3.632
chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 CG -0.083 3.573
chain_A_E.pdb #4/E HIS 3 ND1 chain_A_E.pdb #4/E GLU 1 O -0.118 2.778
chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/E GLU 1 O -0.122 3.302
chain_A_E.pdb #4/E HIS 3 ND1 chain_A_E.pdb #4/E GLU 1 CB -0.141 3.661
chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/E GLU 1 CA -0.152 3.792
chain_A_E.pdb #4/E HIS 3 NE2 chain_A_E.pdb #4/E GLU 1 CG -0.152 3.672
chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 CE1 -0.167 3.807
chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 NE2 -0.184 3.704
chain_A_E.pdb #4/E HIS 3 N chain_A_E.pdb #4/A GLY 127 O -0.191 2.851
chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 ND1 -0.194 3.714
chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/A TYR 161 OH -0.199 3.419
chain_A_E.pdb #4/E HIS 3 CA chain_A_E.pdb #4/A GLY 127 O -0.202 3.502
chain_A_E.pdb #4/E HIS 3 ND1 chain_A_E.pdb #4/E GLU 1 C -0.223 3.473
chain_A_E.pdb #4/E HIS 3 CD2 chain_A_E.pdb #4/A ARG 111 NH2 -0.275 3.675
chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/A TYR 161 CD1 -0.310 3.830
chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/E GLU 1 C -0.317 3.687
chain_A_E.pdb #4/E HIS 3 CD2 chain_A_E.pdb #4/A TYR 161 OH -0.336 3.556
chain_A_E.pdb #4/E HIS 3 O chain_A_E.pdb #4/A ILE 126 CA -0.339 3.639
chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 CB -0.392 4.152
chain_A_E.pdb #4/E HIS 3 O chain_A_E.pdb #4/A ILE 126 CG1 -0.392 3.692
chain_A_E.pdb #4/E HIS 3 C chain_A_E.pdb #4/A TRP 120 CH2 -0.397 3.767
35 contacts
> select #4/E:2
8 atoms, 7 bonds, 1 residue, 1 model selected
> contacts sel interModel false ignoreHiddenModels true select true
> makePseudobonds false log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
13 contacts
atom1 atom2 overlap distance
chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD2 0.881 2.879
chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD1 0.861 2.899
chain_A_E.pdb #4/E LEU 2 CD2 chain_A_E.pdb #4/A ILE 126 CD1 0.825 2.935
chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CG 0.569 3.191
chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A HIS 104 NE2 0.479 3.041
chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A HIS 104 CE1 0.187 3.453
chain_A_E.pdb #4/E LEU 2 CB chain_A_E.pdb #4/A ILE 126 CD1 0.175 3.585
chain_A_E.pdb #4/E LEU 2 CG chain_A_E.pdb #4/A ILE 126 CD1 -0.028 3.788
chain_A_E.pdb #4/E LEU 2 CG chain_A_E.pdb #4/A LEU 105 CD1 -0.039 3.799
chain_A_E.pdb #4/E LEU 2 CD2 chain_A_E.pdb #4/A LEU 105 CD1 -0.134 3.894
chain_A_E.pdb #4/E LEU 2 CA chain_A_E.pdb #4/A ILE 126 CD1 -0.142 3.902
chain_A_E.pdb #4/E LEU 2 CD2 chain_A_E.pdb #4/A ILE 126 CG1 -0.170 3.930
chain_A_E.pdb #4/E LEU 2 CB chain_A_E.pdb #4/A LEU 105 CD1 -0.289 4.049
13 contacts
> show #4/A:105 atoms
> select clear
> 2dlabels #3.1 xpos 0.679 ypos 0.495
> label #4/A:104,101,104,105,131,133,161 text {0.one_letter_code}{0.number}
> size 25 height fixed
> 2dlabels #3.1 xpos 0.637 ypos 0.492
> 2dlabels #3.1 xpos 0.682 ypos 0.492
> ui tool show Clashes
> clashes overlapCutoff 0.4 interModel false intraRes true ignoreHiddenModels
> true log true
Allowed overlap: 0.4
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: True
Detect intra-molecule clashes: True
20 clashes
atom1 atom2 overlap distance
chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD2 0.881 2.879
chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD1 0.861 2.899
chain_A_E.pdb #4/A ILE 126 CD1 chain_A_E.pdb #4/E LEU 2 CD2 0.825 2.935
chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/E GLU 1 CB 0.698 2.942
chain_A_E.pdb #4/A TYR 161 CE2 chain_A_E.pdb #4/E HIS 3 CE1 0.623 2.897
PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A LEU 176 CD2 PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A ARG 222 CB 0.586 3.174
chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CG 0.569 3.191
PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A GLU 154 OE2 PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A PGE 702 C3 0.555 2.745
chain_A_E.pdb #4/A TYR 161 CZ chain_A_E.pdb #4/E HIS 3 NE2 0.547 2.703
chain_A_E.pdb #4/A GLU 63 O chain_A_E.pdb #4/A GLU 66 CG 0.542 2.758
PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A VAL 30 CG1 (alt loc A) PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A VAL 54 CG2 0.499 3.261
chain_A_E.pdb #4/A PHE 190 CE2 chain_A_E.pdb #4/A GLU 197 CD 0.499 3.141
PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A GLU 179 CD PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A ARG 222 NH1 0.493 3.027
chain_A_E.pdb #4/A HIS 104 NE2 chain_A_E.pdb #4/E LEU 2 CD1 0.479 3.041
PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A GLU 154 OE1 PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A BCN 704 O21 0.473 2.367
chain_A_E.pdb #4/A VAL 123 CG1 chain_A_E.pdb #4/E PRO 5 CD 0.457 3.303
PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A THR 93 O PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A PEG 703 C1 0.443 2.857
chain_A_E.pdb #4/A PHE 190 CE2 chain_A_E.pdb #4/A GLU 197 CG 0.427 3.213
PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A THR 93 CB PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A PEG 703 C2 0.422 3.338
chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/A TYR 161 CZ 0.405 2.965
20 clashes
> clashes overlapCutoff 0.4 interModel false intraRes true intraModel false
> ignoreHiddenModels true log true
Allowed overlap: 0.4
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: True
Detect intra-molecule clashes: True
0 clashes
atom1 atom2 overlap distance
No clashes
> select #4/E:2
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Clashes
> clashes overlapCutoff 0.4 interModel false intraRes true intraModel false
> ignoreHiddenModels true log true
Allowed overlap: 0.4
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: True
Detect intra-molecule clashes: True
0 clashes
atom1 atom2 overlap distance
No clashes
> select #4/E:3
10 atoms, 10 bonds, 1 residue, 1 model selected
> clashes overlapCutoff 0.4 interModel false intraRes true intraModel false
> ignoreHiddenModels true log true
Allowed overlap: 0.4
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: True
Detect intra-molecule clashes: True
0 clashes
atom1 atom2 overlap distance
No clashes
> select clear
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/P2-P3-modelling.cxs
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.png
> width 3110 height 2662 supersample 3
> show #4/A:126 atoms
> label #4/A:104,101,104,105,131,133,161,126 text
> {0.one_letter_code}{0.number} size 25 height fixed
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.png
> width 3110 height 2662 supersample 3
> 2dlabels #3.2 xpos 0.820 ypos 0.383
> 2dlabels #3.2 xpos 0.848 ypos 0.197
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.png
> width 3110 height 2662 supersample 3
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/P2-P3-modelling.cxs
> select #4/E3
Nothing selected
> select #4/E:3
10 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
chain_A_E.pdb #4/E HIS 3: phi -113.1, psi 128.2 trans
Changed 600 bond radii
> swapaa interactive sel ARG rotLib Dunbrack
chain_A_E.pdb #!4/E HIS 3: phi -113.1, psi 128.2 trans
Changed 600 bond radii
> swapaa #!4/E:3 ARG criteria 10 rotLib Dunbrack
Using Dunbrack library
chain_A_E.pdb #!4/E HIS 3: phi -113.1, psi 128.2 trans
Applying ARG rotamer (chi angles: -176.0 -179.9 -63.3 -84.3) to chain_A_E.pdb
#!4/E ARG 3
> contacts sel interModel false ignoreHiddenModels true select true
> makePseudobonds false log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
5 contacts
atom1 atom2 overlap distance
chain_A_E.pdb #!4/E ARG 3 N chain_A_E.pdb #!4/A GLY 127 O -0.191 2.851
chain_A_E.pdb #!4/E ARG 3 CA chain_A_E.pdb #!4/A GLY 127 O -0.202 3.502
chain_A_E.pdb #!4/E ARG 3 O chain_A_E.pdb #!4/A ILE 126 CA -0.339 3.639
chain_A_E.pdb #!4/E ARG 3 O chain_A_E.pdb #!4/A ILE 126 CG1 -0.392 3.692
chain_A_E.pdb #!4/E ARG 3 C chain_A_E.pdb #!4/A TRP 120 CH2 -0.397 3.767
5 contacts
> contacts sel interModel false ignoreHiddenModels true select true
> makePseudobonds false log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
14 contacts
atom1 atom2 overlap distance
chain_A_E.pdb #!4/A TRP 120 CH2 chain_A_E.pdb #!4/E PRO 4 CB 0.103 3.537
chain_A_E.pdb #!4/A GLY 127 O chain_A_E.pdb #!4/E ARG 3 CB 0.027 3.273
chain_A_E.pdb #!4/A TRP 120 CH2 chain_A_E.pdb #!4/E PRO 4 CA -0.136 3.776
chain_A_E.pdb #!4/A ILE 126 CG1 chain_A_E.pdb #!4/A TRP 120 CZ3 -0.147 3.787
chain_A_E.pdb #!4/A TRP 120 CH2 chain_A_E.pdb #!4/E PRO 4 CD -0.158 3.798
chain_A_E.pdb #!4/A TRP 120 CH2 chain_A_E.pdb #!4/E PRO 4 N -0.168 3.568
chain_A_E.pdb #!4/A ILE 126 CG1 chain_A_E.pdb #!4/E LEU 2 CD2 -0.170 3.930
chain_A_E.pdb #!4/A GLY 127 O chain_A_E.pdb #!4/E ARG 3 N -0.191 2.851
chain_A_E.pdb #!4/A GLY 127 O chain_A_E.pdb #!4/E ARG 3 CA -0.202 3.502
chain_A_E.pdb #!4/A TRP 120 CH2 chain_A_E.pdb #!4/A ILE 126 CD1 -0.246 3.886
chain_A_E.pdb #!4/A ILE 126 CA chain_A_E.pdb #!4/E ARG 3 O -0.339 3.639
chain_A_E.pdb #!4/A GLY 127 O chain_A_E.pdb #!4/E GLU 1 O -0.345 3.185
chain_A_E.pdb #!4/E ARG 3 O chain_A_E.pdb #!4/A ILE 126 CG1 -0.392 3.692
chain_A_E.pdb #!4/A TRP 120 CH2 chain_A_E.pdb #!4/E ARG 3 C -0.397 3.767
14 contacts
> swapaa #!4/E:3 ARG criteria 14 rotLib Dunbrack
Using Dunbrack library
chain_A_E.pdb #!4/E ARG 3: phi -113.1, psi 128.2 trans
Applying ARG rotamer (chi angles: -59.7 -73.4 -178.2 -179.3) to chain_A_E.pdb
#!4/E ARG 3
> select #4/E:3
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show Clashes
> clashes overlapCutoff 0.4 interModel false intraRes true intraModel false
> ignoreHiddenModels true log true
Allowed overlap: 0.4
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: True
Detect intra-molecule clashes: True
0 clashes
atom1 atom2 overlap distance
No clashes
> clashes sel overlapCutoff 0.4 interModel false intraRes true intraModel
> false ignoreHiddenModels true log true
Allowed overlap: 0.4
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: True
Detect intra-molecule clashes: True
0 clashes
atom1 atom2 overlap distance
No clashes
> clashes sel overlapCutoff 0.10000000000000003 interModel false intraRes true
> intraModel false ignoreHiddenModels true log true
Allowed overlap: 0.1
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: True
Detect intra-molecule clashes: True
0 clashes
atom1 atom2 overlap distance
No clashes
> clashes sel restrict cross overlapCutoff 0.10000000000000003 interModel
> false intraRes true intraModel false ignoreHiddenModels true log true
Allowed overlap: 0.1
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: True
Detect intra-molecule clashes: True
0 clashes
atom1 atom2 overlap distance
No clashes
> clashes sel restrict cross overlapCutoff 0.7 interModel false intraRes true
> intraModel false ignoreHiddenModels true log true
Allowed overlap: 0.7
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: True
Detect intra-molecule clashes: True
0 clashes
atom1 atom2 overlap distance
No clashes
> 2dlabels #3.1 xpos 0.672 ypos 0.491
> 2dlabels #3.2 xpos 0.829 ypos 0.444
> select clear
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.Arg.png
> width 1555 height 1331 supersample 3
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/P2-P3-modelling.arg.cxs
> select #4/E:3
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel interModel false ignoreHiddenModels true select true
> makePseudobonds false log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
37 contacts
atom1 atom2 overlap distance
chain_A_E.pdb #4/E ARG 3 NH2 chain_A_E.pdb #4/E GLU 1 OE1 0.891 1.769
chain_A_E.pdb #4/E ARG 3 NH2 chain_A_E.pdb #4/E GLU 1 CD 0.604 2.916
chain_A_E.pdb #4/E ARG 3 NH1 chain_A_E.pdb #4/A ARG 111 NE 0.562 2.718
chain_A_E.pdb #4/E ARG 3 NH1 chain_A_E.pdb #4/A ARG 111 NH2 0.454 2.826
chain_A_E.pdb #4/E ARG 3 NH2 chain_A_E.pdb #4/A TYR 161 OH 0.359 2.341
chain_A_E.pdb #4/E ARG 3 CZ chain_A_E.pdb #4/A TYR 161 OH 0.322 2.748
chain_A_E.pdb #4/E ARG 3 CZ chain_A_E.pdb #4/E GLU 1 OE1 0.321 2.709
chain_A_E.pdb #4/E ARG 3 CD chain_A_E.pdb #4/A ARG 111 NH2 0.171 3.349
chain_A_E.pdb #4/E ARG 3 NH1 chain_A_E.pdb #4/A ARG 111 CZ 0.099 3.151
chain_A_E.pdb #4/E ARG 3 CB chain_A_E.pdb #4/A HIS 157 CD2 0.092 3.548
chain_A_E.pdb #4/E ARG 3 NH1 chain_A_E.pdb #4/A GLU 196 OE2 0.058 2.602
chain_A_E.pdb #4/E ARG 3 NE chain_A_E.pdb #4/E GLU 1 CG 0.048 3.472
chain_A_E.pdb #4/E ARG 3 CB chain_A_E.pdb #4/A GLY 127 O 0.028 3.272
chain_A_E.pdb #4/E ARG 3 NH1 chain_A_E.pdb #4/A GLU 196 CD -0.012 3.532
chain_A_E.pdb #4/E ARG 3 NH2 chain_A_E.pdb #4/E GLU 1 CG -0.022 3.542
chain_A_E.pdb #4/E ARG 3 CB chain_A_E.pdb #4/A HIS 157 CG -0.073 3.563
chain_A_E.pdb #4/E ARG 3 CZ chain_A_E.pdb #4/E GLU 1 CD -0.074 3.564
chain_A_E.pdb #4/E ARG 3 NH2 chain_A_E.pdb #4/A TYR 161 CZ -0.096 3.346
chain_A_E.pdb #4/E ARG 3 NE chain_A_E.pdb #4/A TYR 161 CZ -0.116 3.366
chain_A_E.pdb #4/E ARG 3 CB chain_A_E.pdb #4/A HIS 157 CE1 -0.157 3.797
chain_A_E.pdb #4/E ARG 3 CB chain_A_E.pdb #4/A HIS 157 NE2 -0.167 3.687
chain_A_E.pdb #4/E ARG 3 NE chain_A_E.pdb #4/A TYR 161 OH -0.168 2.868
chain_A_E.pdb #4/E ARG 3 CB chain_A_E.pdb #4/A HIS 157 ND1 -0.187 3.707
chain_A_E.pdb #4/E ARG 3 N chain_A_E.pdb #4/A GLY 127 O -0.191 2.851
chain_A_E.pdb #4/E ARG 3 CZ chain_A_E.pdb #4/E GLU 1 CG -0.192 3.682
chain_A_E.pdb #4/E ARG 3 NE chain_A_E.pdb #4/E GLU 1 CB -0.194 3.714
chain_A_E.pdb #4/E ARG 3 CA chain_A_E.pdb #4/A GLY 127 O -0.202 3.502
chain_A_E.pdb #4/E ARG 3 NH2 chain_A_E.pdb #4/A TYR 161 CE2 -0.212 3.612
chain_A_E.pdb #4/E ARG 3 CZ chain_A_E.pdb #4/A GLU 196 OE2 -0.302 3.332
chain_A_E.pdb #4/E ARG 3 NE chain_A_E.pdb #4/E GLU 1 CD -0.309 3.829
chain_A_E.pdb #4/E ARG 3 CG chain_A_E.pdb #4/E GLU 1 O -0.320 3.620
chain_A_E.pdb #4/E ARG 3 O chain_A_E.pdb #4/A ILE 126 CA -0.339 3.639
chain_A_E.pdb #4/E ARG 3 NH1 chain_A_E.pdb #4/A GLU 196 CG -0.344 3.864
chain_A_E.pdb #4/E ARG 3 NE chain_A_E.pdb #4/A TYR 161 CE2 -0.363 3.763
chain_A_E.pdb #4/E ARG 3 CB chain_A_E.pdb #4/A HIS 157 CB -0.386 4.146
chain_A_E.pdb #4/E ARG 3 O chain_A_E.pdb #4/A ILE 126 CG1 -0.392 3.692
chain_A_E.pdb #4/E ARG 3 C chain_A_E.pdb #4/A TRP 120 CH2 -0.397 3.767
37 contacts
> ui tool show Clashes
> clashes sel restrict cross overlapCutoff 0.7 interModel false intraRes true
> ignoreHiddenModels true log true
Allowed overlap: 0.7
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: True
Detect intra-molecule clashes: True
0 clashes
atom1 atom2 overlap distance
No clashes
> clashes sel restrict cross overlapCutoff 0.5 interModel false intraRes true
> ignoreHiddenModels true log true
Allowed overlap: 0.5
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: True
Detect intra-molecule clashes: True
0 clashes
atom1 atom2 overlap distance
No clashes
> clashes sel overlapCutoff 0.5 interModel false intraRes true
> ignoreHiddenModels true log true
Allowed overlap: 0.5
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: True
Detect intra-molecule clashes: True
3 clashes
atom1 atom2 overlap distance
chain_A_E.pdb #4/E ARG 3 NH2 chain_A_E.pdb #4/E GLU 1 OE1 0.891 1.769
chain_A_E.pdb #4/E GLU 1 CD chain_A_E.pdb #4/E ARG 3 NH2 0.604 2.916
chain_A_E.pdb #4/A ARG 111 NE chain_A_E.pdb #4/E ARG 3 NH1 0.562 2.718
3 clashes
> select clear
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.Arg.clashes.png
> width 3110 height 2662 supersample 3
> ui tool show Rotamers
> select #4/E:3
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel HIS rotLib Dunbrack
chain_A_E.pdb #4/E ARG 3: phi -113.1, psi 128.2 trans
Changed 288 bond radii
> swapaa #!4/E:3 HIS criteria 7 rotLib Dunbrack
Using Dunbrack library
chain_A_E.pdb #!4/E ARG 3: phi -113.1, psi 128.2 trans
Applying HIS rotamer (chi angles: -63.7 94.6) to chain_A_E.pdb #!4/E HIS 3
> clashes sel overlapCutoff 0.5 interModel false intraRes true
> ignoreHiddenModels true log true
Allowed overlap: 0.5
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: True
Detect intra-molecule clashes: True
0 clashes
atom1 atom2 overlap distance
No clashes
> select #4/E:3
10 atoms, 10 bonds, 1 residue, 1 model selected
> clashes sel overlapCutoff 0.5 interModel false intraRes true
> ignoreHiddenModels true log true
Allowed overlap: 0.5
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: True
Detect intra-molecule clashes: True
3 clashes
atom1 atom2 overlap distance
chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/E GLU 1 CB 0.642 2.998
chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/A TYR 161 CE2 0.614 2.906
chain_A_E.pdb #4/E HIS 3 NE2 chain_A_E.pdb #4/A TYR 161 CZ 0.560 2.690
3 clashes
> clashes sel overlapCutoff 0.5 interModel false intraRes true
> ignoreHiddenModels true log true
Allowed overlap: 0.5
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: True
Detect intra-molecule clashes: True
3 clashes
atom1 atom2 overlap distance
chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/E GLU 1 CB 0.642 2.998
chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/A TYR 161 CE2 0.614 2.906
chain_A_E.pdb #4/E HIS 3 NE2 chain_A_E.pdb #4/A TYR 161 CZ 0.560 2.690
3 clashes
> 2dlabels #3.1 xpos 0.650 ypos 0.501
> 2dlabels #3.1 xpos 0.736 ypos 0.575
> select clear
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.His.clashes.png
> width 3110 height 2662 supersample 3
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> clashes sel overlapCutoff 0.5 interModel false intraRes true
> ignoreHiddenModels true log true
Allowed overlap: 0.5
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: True
Detect intra-molecule clashes: True
0 clashes
atom1 atom2 overlap distance
No clashes
> clashes sel overlapCutoff 0.5 interModel false intraRes true
> ignoreHiddenModels true log true
Allowed overlap: 0.5
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: True
Detect intra-molecule clashes: True
0 clashes
atom1 atom2 overlap distance
No clashes
> select #4/E:2
8 atoms, 7 bonds, 1 residue, 1 model selected
> clashes sel overlapCutoff 0.5 interModel false intraRes true
> ignoreHiddenModels true log true
Allowed overlap: 0.5
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: True
Detect intra-molecule clashes: True
4 clashes
atom1 atom2 overlap distance
chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD2 0.881 2.879
chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD1 0.861 2.899
chain_A_E.pdb #4/E LEU 2 CD2 chain_A_E.pdb #4/A ILE 126 CD1 0.825 2.935
chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CG 0.569 3.191
4 clashes
> select clear
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.Leu.clashes.png
> width 1555 height 1331 supersample 3
> select #4/E:3
10 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
chain_A_E.pdb #4/E HIS 3: phi -113.1, psi 128.2 trans
Changed 600 bond radii
> swapaa #!4/E:3 ARG criteria 46 rotLib Dunbrack
Using Dunbrack library
chain_A_E.pdb #!4/E HIS 3: phi -113.1, psi 128.2 trans
Applying ARG rotamer (chi angles: -62.1 -78.1 73.6 81.6) to chain_A_E.pdb
#!4/E ARG 3
> select add #4/E:2
12 atoms, 10 bonds, 2 residues, 1 model selected
> clashes sel overlapCutoff 0.5 interModel false intraRes true
> ignoreHiddenModels true log true
Allowed overlap: 0.5
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: True
Detect intra-molecule clashes: True
4 clashes
atom1 atom2 overlap distance
chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD2 0.881 2.879
chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD1 0.861 2.899
chain_A_E.pdb #4/E LEU 2 CD2 chain_A_E.pdb #4/A ILE 126 CD1 0.825 2.935
chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CG 0.569 3.191
4 clashes
> clashes sel overlapCutoff 0.5 interModel false intraRes true
> ignoreHiddenModels true radius 0.1 log true
Allowed overlap: 0.5
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: True
Detect intra-molecule clashes: True
4 clashes
atom1 atom2 overlap distance
chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD2 0.881 2.879
chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD1 0.861 2.899
chain_A_E.pdb #4/E LEU 2 CD2 chain_A_E.pdb #4/A ILE 126 CD1 0.825 2.935
chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CG 0.569 3.191
4 clashes
> select add #4/E:3
19 atoms, 17 bonds, 2 residues, 1 model selected
> clashes sel overlapCutoff 0.5 interModel false intraRes true
> ignoreHiddenModels true radius 0.1 log true
Allowed overlap: 0.5
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: True
Detect intra-molecule clashes: True
7 clashes
atom1 atom2 overlap distance
chain_A_E.pdb #4/E ARG 3 NH1 chain_A_E.pdb #4/E GLU 1 CG 1.608 1.912
chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD2 0.881 2.879
chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD1 0.861 2.899
chain_A_E.pdb #4/E LEU 2 CD2 chain_A_E.pdb #4/A ILE 126 CD1 0.825 2.935
chain_A_E.pdb #4/E ARG 3 NH1 chain_A_E.pdb #4/E GLU 1 CD 0.774 2.746
chain_A_E.pdb #4/E ARG 3 NH1 chain_A_E.pdb #4/E GLU 1 CB 0.752 2.768
chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CG 0.569 3.191
7 clashes
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/P2-P3-modelling.arg_leu.cxs
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.Arg_Leu.clashes.png
> width 3110 height 2662 supersample 3
> select clear
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.Arg_Leu.clashes.png
> width 3110 height 2662 supersample 3
> 2dlabels #3.1 xpos 0.733 ypos 0.599
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.Arg_Leu.clashes.png
> width 3110 height 2662 supersample 3
> lighting soft
> lighting full
> lighting shadows false
> lighting direction -1 -1 1
Invalid "direction" argument: Need exactly 3 ','-separated 3-tuple of numbers
> lighting direction -1, -1, 1,
Invalid "direction" argument: Expected a number
> lighting direction -1, -1, 1
> lighting direction -1, -1, -1
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting full
> lighting shadows false
> lighting direction 0.577,-0.577,-0.5771
> lighting full
> lighting shadows false
> lighting ambie 1.55771
Expected keyword "ambientColor" or "ambientIntensity"
> lighting ambientIntensity 1.55771
> lighting ambientIntensity 0.3
> lighting ambientIntensity 0.5
> lighting ambientIntensity 0.6
> lighting ambientIntensity 0.75
> lighting ambientIntensity 0.75 multiShadow 124
> lighting ambientIntensity 0.75 multiShadow 1024
> lighting ambientIntensity 0.75 multiShadow 256
> 2dlabels #3.2 xpos 0.810 ypos 0.315
> 2dlabels #3.2 xpos 0.805 ypos 0.232
> label #4/A:104,101,104,105,131,133,161,126,157 text
> {0.one_letter_code}{0.number} size 25 height fixed
> label #4/A:104,101,104,105,131,133,161,126,157,111 text
> {0.one_letter_code}{0.number} size 25 height fixed
> 2dlabels #3.2 xpos 0.766 ypos 0.187
> 2dlabels #3.2 xpos 0.803 ypos 0.157
> label #4/A:104,101,104,105,131,133,161,126,157,111,113 text
> {0.one_letter_code}{0.number} size 25 height fixed
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.Arg_Leu.clashes.png
> width 3110 height 2662 supersample 3
> 2dlabels #3.1 xpos 0.665 ypos 0.596
> 2dlabels #3.1 xpos 0.687 ypos 0.572
> 2dlabels #3.2 xpos 0.783 ypos 0.170
> 2dlabels #3.2 xpos 0.837 ypos 0.173
> 2dlabels #3.1 xpos 0.631 ypos 0.584
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.Arg_Leu.clashes.png
> width 3110 height 2662 supersample 3
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/P2-P3-modelling.arg_leu.cxs
> 2dlabels #3.2 xpos 0.797 ypos 0.172
> 2dlabels #3.1 xpos 0.598 ypos 0.585
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/P2-P3-modelling.arg_leu.cxs
> save
> /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.Arg_Leu.clashes.png
> width 3110 height 2662 supersample 3
> save /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/P2-P3.ar_leu.x3d
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 120, in save
return save_x3d(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 1205, in save_x3d
m.x3d_needs(x3d_scene)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1393, in x3d_needs
d.x3d_needs(x3d_scene)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/label/label2d.py", line 724, in x3d_needs
from .. import x3d
ImportError: cannot import name 'x3d' from 'chimerax' (unknown location)
ImportError: cannot import name 'x3d' from 'chimerax' (unknown location)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/label/label2d.py", line 724, in x3d_needs
from .. import x3d
See log for complete Python traceback.
> save /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/test-p3p2.x3d
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 120, in save
return save_x3d(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 1205, in save_x3d
m.x3d_needs(x3d_scene)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1393, in x3d_needs
d.x3d_needs(x3d_scene)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/label/label2d.py", line 724, in x3d_needs
from .. import x3d
ImportError: cannot import name 'x3d' from 'chimerax' (unknown location)
ImportError: cannot import name 'x3d' from 'chimerax' (unknown location)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/label/label2d.py", line 724, in x3d_needs
from .. import x3d
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 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: MacBookPro18,3
Model Number: MKGQ3D/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 11881.61.3
OS Loader Version: 10151.140.19.700.2
Software:
System Software Overview:
System Version: macOS 14.7.2 (23H311)
Kernel Version: Darwin 23.6.0
Time since boot: 21 days, 7 hours, 15 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
ASUS CG32U:
Resolution: 6720 x 3780
UI Looks like: 3360 x 1890 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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
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-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-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-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-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
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
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
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
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
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
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: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (3)
comment:1 by , 10 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Input/Output |
| Milestone: | → 1.10 |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Save X3D failure |
comment:2 by , 10 months ago
| Summary: | Save X3D failure → Save X3D failure saving 2D labels |
|---|
You can probably save X3D if you hide your labels made with the 2dlabel command.
Greg who implemented x3d output away from work until the end of next week.
comment:3 by , 6 months ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed was easier that I expected. It will be in the next daily build.
Note:
See TracTickets
for help on using tickets.
Reported by Ulrich Baumann
The x3d_needs() implementation that Greg added to 2D labels doesn't work.