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Opened 3 years ago
Closed 3 years ago
#6993 closed defect (duplicate)
MatchMaker: wrapped C/C++ object of type ChainMenuButton has been deleted
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Comparison | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22000
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> C:\Users\jenni\OneDrive\Documents\B3_structure_figures\20220530_B3SSEA3_background.cxs
> format session
Log from Mon May 30 16:43:59 2022UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> C:\Users\jenni\OneDrive\Documents\B3_structure_figures\20220216_B3SSEA3_background.cxs
> format session
Log from Wed Feb 16 15:18:16 2022UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> C:/Users/jenni/OneDrive/Documents/AMA011_C11/phenix/Refine_17/Gb5SSEA3_11C11_refine_17.pdb
Summary of feedback from opening
C:/Users/jenni/OneDrive/Documents/AMA011_C11/phenix/Refine_17/Gb5SSEA3_11C11_refine_17.pdb
---
warnings | Ignored bad PDB record found on line 4561
TER
Ignored bad PDB record found on line 9230
TER
Ignored bad PDB record found on line 10091
END
Start residue of secondary structure not found: HELIX 1 1 LEU A 42 GLN A 50 1
9
End residue of secondary structure not found: HELIX 2 2 ALA A 75 HIS A 88 1 14
Start residue of secondary structure not found: HELIX 3 3 TYR A 100 PHE A 117
5 18
Start residue of secondary structure not found: HELIX 4 4 VAL A 135 LYS A 145
1 11
Start residue of secondary structure not found: HELIX 5 5 GLY A 195 SER A 207
5 13
Start residue of secondary structure not found: HELIX 6 6 GLU A 214 ARG A 224
1 11
Start residue of secondary structure not found: HELIX 7 7 VAL A 247 ARG A 252
1 6
1 messages similar to the above omitted
End residue of secondary structure not found: HELIX 10 10 ALA B 75 HIS B 88 1
14
Start residue of secondary structure not found: HELIX 11 11 TYR B 100 PHE B
117 5 18
Start residue of secondary structure not found: HELIX 12 12 VAL B 135 LYS B
145 1 11
Start residue of secondary structure not found: HELIX 13 13 GLY B 195 SER B
207 5 13
Start residue of secondary structure not found: HELIX 14 14 GLU B 214 ARG B
224 1 11
Start residue of secondary structure not found: HELIX 15 15 VAL B 247 ARG B
252 1 6
9 messages similar to the above omitted
Chain information for Gb5SSEA3_11C11_refine_17.pdb #1
---
Chain | Description
A | No description available
B | No description available
> set bgColor white
> ui tool show "Basic Actions"
Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.
> hide /B target abp
> hide /B target c
> hide /B target s
Drag select of 18 atoms
> hide sel atoms
> select ::name="M3F"
151 atoms, 159 bonds, 4 residues, 1 model selected
> hide sel atoms
Drag select of 12 atoms, 7 residues, 9 bonds
> hide sel atoms
> select up
73 atoms, 65 bonds, 13 residues, 1 model selected
> hide sel atoms
Drag select of 63 atoms, 28 residues, 56 bonds
> hide sel atoms
> select clear
> select /A:213@CG
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
306 atoms, 321 bonds, 35 residues, 1 model selected
> select down
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> hide sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /A:130@OD1
1 atom, 1 residue, 1 model selected
> select up
16 atoms, 14 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
18 atoms, 17 bonds, 2 residues, 1 model selected
> hide sel atoms
> cartoon style strand
Gb5SSEA3_11C11_refine_17.pdb #1
\- helix mode=default xsection=round width=2 height=0.4 arrow=False arrow
scale=2
\- strand mode=default xsection=square width=2 height=0.4 arrow=True arrow
scale=2
\- coil xsection=round width=0.4 height=0.4
\- nucleic xsection=square width=0.4 height=2
\- divisions=20
\- oval parameters: sides=12
\- barbell parameters: sides=18 scale=0.5
> cartoon style strand xsection width 1
Invalid "xsection" argument: Should be one of 'barbell', 'oval', 'piping',
'rectangle', 'round', or 'square'
> cartoon style strand xsection rectangle width 1
> cartoon style strand xsection rectangle width 1.5
> cartoon style strand xsection rectangle thickness 0.5
> cartoon style strand xsection rectangle thickness 0.2
> cartoon style coil xsection round width 0.2
> cartoon style coil xsection round width 0.4
> cartoon style coil xsection round width 0.2
> cartoon style coil xsection round 0.4
Expected a keyword
> cartoon style coil xsection round thickness 0.2
> cartoon style coil xsection round thickness 0.3
> cartoon style coil xsection round thickness 0.4
> cartoon style coil xsection round thickness 0.25
> cartoon style coil xsection round thickness 0.3
> cartoon style coil xsection round thickness 0.4
> cartoon style helix xsection round width 1.5
> cartoon style helix xsection round thickness 0.25
> cartoon style helix xsection round thickness 0.4
> cartoon style helix xsection round thickness 0.3
> cartoon style helix xsection round thickness 0.25
> cartoon style25
Expected an atoms specifier or a keyword
> cartoon style
Gb5SSEA3_11C11_refine_17.pdb #1
\- helix mode=default xsection=round width=1.5 height=0.25 arrow=False arrow
scale=2
\- strand mode=default xsection=square width=1.5 height=0.2 arrow=True arrow
scale=2
\- coil xsection=round width=0.4 height=0.4
\- nucleic xsection=square width=0.4 height=2
\- divisions=20
\- oval parameters: sides=12
\- barbell parameters: sides=18 scale=0.5
> cartoon style strand xsection square thickness 0.2
> cartoon style strand xsection square thickness 0.25
> cartoon style strand xsection square thickness 0.3
> cartoon style strand xsection square thickness 0.4
> cartoon style strand xsection square thickness 0.25
> cartoon style strand xsection square height 0.5
Expected a keyword
> select clear
> select clear
> select /A:294
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
114 atoms, 117 bonds, 13 residues, 1 model selected
> select up
2346 atoms, 2413 bonds, 274 residues, 1 model selected
> select up
4944 atoms, 4841 bonds, 785 residues, 1 model selected
> select down
2346 atoms, 2413 bonds, 274 residues, 1 model selected
> select down
114 atoms, 117 bonds, 13 residues, 1 model selected
> select clear
> select /A:289
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
114 atoms, 117 bonds, 13 residues, 1 model selected
> select up
2346 atoms, 2413 bonds, 274 residues, 1 model selected
> color sel & C thistle
> color sel & C pale violet red
> color sel & C thistle
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
25 atoms, 26 bonds, 1 residue, 1 model selected
> color sel & C khaki
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
25 atoms, 26 bonds, 1 residue, 1 model selected
> color sel & C goldenrod
> color sel & C light goldenrod yellow
> color sel & C dark goldenrod
> color sel & C yeloow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color sel & C yellow
> color sel & C darkred yellow
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel & C gold
> select clear
> select /A:334@C36
1 atom, 1 residue, 1 model selected
> select up
48 atoms, 51 bonds, 1 residue, 1 model selected
> select up
2346 atoms, 2413 bonds, 274 residues, 1 model selected
> select down
48 atoms, 51 bonds, 1 residue, 1 model selected
> color sel & C orchid
> color sel & C dark orchid
> color sel & C corchid
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color sel & C medium orchid
> color sel & C dark violet
> color sel & C blue violet
> color sel & C firebrick
> color sel & C violet
> color sel & C dark magenta
> color sel & C medium violet red
> color sel & C dark violet
> color sel & C blue violet
> select clear
> select /A:330@MN
1 atom, 1 residue, 1 model selected
> cartoon style width 1.7 thickness 0.4
> cartoon style width 1.7 thickness 0.25
> cartoon style width 1.5 thickness 0.25
> select clear
> setattr sel a radius 0.2
Assigning radius attribute to 0 items
> select /A:330@MN
1 atom, 1 residue, 1 model selected
> setattr sel a radius 0.2
Assigning radius attribute to 1 item
> setattr sel a radius 0.3
Assigning radius attribute to 1 item
> setattr sel a radius 0.4
Assigning radius attribute to 1 item
> setattr sel a radius 0.45
Assigning radius attribute to 1 item
> select /A:329@PB
1 atom, 1 residue, 1 model selected
> select clear
> select /A:329@PB
1 atom, 1 residue, 1 model selected
> select clear
> select up
48 atoms, 51 bonds, 1 residue, 1 model selected
> select up
2346 atoms, 2413 bonds, 274 residues, 1 model selected
> setattr sel b radius 0.2
Assigning radius attribute to 2413 items
> setattr sel b radius 0.1
Assigning radius attribute to 2413 items
> setattr sel b radius 0.15
Assigning radius attribute to 2413 items
> setattr sel b radius 0.17
Assigning radius attribute to 2413 items
> select clear
> select up
11 atoms, 4 bonds, 7 residues, 1 model selected
> select up
66 atoms, 62 bonds, 7 residues, 1 model selected
> select down
11 atoms, 4 bonds, 7 residues, 1 model selected
> select up
66 atoms, 62 bonds, 7 residues, 1 model selected
> color sel & C plum
> color sel & C violet
> select clear
> select clear
> select clear
> select /A:131@CG
1 atom, 1 residue, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
Drag select of 1 atoms, 3 residues, 2 bonds
> select clear
> select clear
> select up
12 atoms, 5 bonds, 7 residues, 1 model selected
> select up
60 atoms, 54 bonds, 7 residues, 1 model selected
> color sel & C coral
> color sel & C tomato
> color sel & C light coral
> color sel & C khaki
> hide sel atoms
> show sel atoms
> hide sel atoms
> select clear
> select clear
> select clear
> hide /A target c
> show /A target c
> select clear
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> lighting depthCueStart 0.4
> lighting depthCueStart 0.2
> lighting depthCueStart 0.3
> lighting depthCueStart 0.4
> lighting depthCueEnd 0.8
> lighting depthCueEnd 0.6
> lighting depthCueEnd 0.8
> lighting depthCueStart 0.5
> lighting depthCueStart 0.45
> clip far -1
> clip far -1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip far 1
> clip near -1
> clip near -1
> clip near -1
> clip near -1
> clip near -1
> clip near -1
> clip near -1
> clip near -1
> clip near -1
> clip near -1
> clip near -1
> clip near -1
> clip near -1
> clip near -1
> clip near -1
> clip near -1
> clip near -1
> clip near -1
> clip near 1
> clip near 1
> clip near 1
> clip near 1
> clip near 1
> clip near 1
> clip near 1
> clip near 1
> clip near 1
> clip near 0.2
> clip near 0.2
> clip near 0.2
> clip near 0.2
> clip near 0.2
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> lighting depthCueStart 0.3
> lighting depthCueStart 0.2
> lighting depthCueStart 0.1
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
> select clear
> select /A:188@OE1
1 atom, 1 residue, 1 model selected
> ui tool show Distances
> select clear
> select /A:334@O10
1 atom, 1 residue, 1 model selected
> select clear
> distance /A:188@OE1 /A:334@O10
Distance between /A GLU 188 OE1 and S34 334 O10: 2.839Å
> distance style color #74aa7d
> distance style decimalPlaces 2
> distance style decimalPlaces 2
> distance style dashes 8
> distance style dashes 8
> distance style dashes 7
> distance style dashes 7
> distance style dashes 6
> distance style dashes 6
> distance style dashes 5
> distance style dashes 5
> distance style dashes 4
> distance style dashes 4
> distance style dashes 3
> distance style dashes 3
> distance style dashes 2
> distance style dashes 2
> distance style dashes 1
> distance style dashes 1
> distance style dashes 2
> distance style dashes 2
> distance style dashes 3
> distance style dashes 3
> distance style dashes 4
> distance style dashes 4
> distance style dashes 5
> distance style dashes 5
> distance style dashes 4
> distance style dashes 4
> select clear
> distance style radius 0.09
> distance style radius 0.09
> distance style radius 0.08
> distance style radius 0.08
> distance style radius 0.07
> distance style radius 0.07
> distance style radius 0.06
> distance style radius 0.06
> distance style radius 0.05
> distance style radius 0.05
> distance style radius 0.04
> distance style radius 0.04
> distance style radius 0.05
> distance style radius 0.05
> select clear
> distance style color #529cad
> distance style color #74aa7d
> distance style color #55aa00
> distance style color #55aa7f
> distance style color #55aa00
> distance style color #00aa7f
> distance style color #55aa00
> select clear
> ui mousemode right "move label"
> select /A:185@NZ
1 atom, 1 residue, 1 model selected
> select clear
> select /A:185@NZ
1 atom, 1 residue, 1 model selected
> distance /A:185@NZ /A:334@O07
Distance between /A LYS 185 NZ and S34 334 O07: 3.25Å
> select clear
> distance /A:185@NZ /A:334@O10
Distance between /A LYS 185 NZ and S34 334 O10: 3.04Å
> distance style radius 0.04
> distance style radius 0.04
> distance style radius 0.05
> distance style radius 0.05
> distance style dashes 5
> distance style dashes 5
> distance style dashes 6
> distance style dashes 6
> distance style dashes 5
> distance style dashes 5
> select clear
> distance style color #00aaff
> distance style color #55aa00
> select clear
> select /A:243@OD2
1 atom, 1 residue, 1 model selected
> distance /A:243@OD2 /A:334@O37
Distance between /A ASP 243 OD2 and S34 334 O37: 3.52Å
> select clear
> select clear
> select clear
> select /A:243@OD2
1 atom, 1 residue, 1 model selected
> distance /A:243@OD2 /A:334@O35
Distance between /A ASP 243 OD2 and S34 334 O35: 2.78Å
> select clear
> ~distance /A:243@OD2 /A:334@O37
> distance /A:243@OD1 /A:334@O37
Distance between /A ASP 243 OD1 and S34 334 O37: 4.68Å
> ~distance /A:243@OD1 /A:334@O37
> select clear
> select /A:243@OD2
1 atom, 1 residue, 1 model selected
> distance /A:243@OD2 /A:334@O37
Distance between /A ASP 243 OD2 and S34 334 O37: 3.52Å
> select clear
> select /A:242@OE2
1 atom, 1 residue, 1 model selected
> select clear
> select /A:242@OE2
1 atom, 1 residue, 1 model selected
> select clear
> select /A:242@OE2
1 atom, 1 residue, 1 model selected
> distance /A:242@OE2 /A:334@O44
Distance between /A GLU 242 OE2 and S34 334 O44: 2.55Å
> select clear
> distance /A:242@OE2 /A:334@O46
Distance between /A GLU 242 OE2 and S34 334 O46: 3.91Å
> ~distance /A:242@OE2 /A:334@O46
> select clear
> select /A:154@NZ
1 atom, 1 residue, 1 model selected
> distance /A:154@NZ /A:334@O44
Distance between /A LYS 154 NZ and S34 334 O44: 4.24Å
> ~distance /A:154@NZ /A:334@O44
> select clear
> select /A:154@NZ
1 atom, 1 residue, 1 model selected
> distance /A:154@NZ /A:334@O46
Distance between /A LYS 154 NZ and S34 334 O46: 3.23Å
> select /A:128
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> distance /A:128@OH /A:334@O39
Distance between /A TYR 128 OH and S34 334 O39: 3.88Å
> select clear
> distance /A:128@OH /A:329@O1B
Distance between /A TYR 128 OH and UDP 329 O1B: 2.69Å
> ~distance /A:128@OH /A:334@O39
> select /A:134
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> undo
> select /A:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select clear
> select clear
> select clear
> hide sel atoms
> select clear
> clip near -1
> clip near -1
> clip near -1
> clip near 1
> clip near 1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near 0.1
> clip near -0.1
> clip near -0.1
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 3 residues, 1 model selected
> hide sel atoms
> show sel atoms
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> select up
23 atoms, 22 bonds, 4 residues, 1 model selected
> select up
29 atoms, 28 bonds, 4 residues, 1 model selected
> hide sel atoms
> select clear
> select clear
> distance /A:156@OD2 /A:334@O46
Distance between /A ASP 156 OD2 and S34 334 O46: 2.30Å
> select /A:334@O48
1 atom, 1 residue, 1 model selected
> distance /A:156@OD2 /A:334@O48
Distance between /A ASP 156 OD2 and S34 334 O48: 3.40Å
> ~distance /A:156@OD2 /A:334@O48
> select clear
> select clear
> distance style color #55aa7f
> distance style color #55aa00
> distance style radius 0.04
> distance style radius 0.04
> distance style radius 0.05
> distance style radius 0.05
> clip near -0.1
> clip near -0.1
> clip near -0.1
> clip near -0.1
> lighting depthCueEnd 0.7
> lighting depthCueEnd 0.6
> lighting depthCueStart 0.2
> lighting depthCueStart 0.1
> 2dlabels text SSEA3 size [20]
Invalid "size" argument: Expected an integer
> 2dlabels text SSEA3 size 20
> 2dlabels #3.1 xpos 0.579 ypos 0.803
> 2dlabels #3.1 xpos 0.037 ypos 0.763
> 2dlabels text UDP size 20
> 2dlabels #3.2 xpos 0.886 ypos 0.390
> 2dlabels text UDP size 25
> close #3.3
> 2dlabels #3.1 xpos 0.069 ypos 0.759
> 2dlabels #3.2 xpos 0.865 ypos 0.390
> 2dlabels text Trp198 size 12
> 2dlabels #3.3 xpos 0.443 ypos 0.696
> 2dlabels text Glu188 size 12 color #8299d6
> 2dlabels #3.4 xpos 0.048 ypos 0.440
> 2dlabels text Lys185 size 12 color #8299d6
> 2dlabels #3.5 xpos 0.111 ypos 0.118
> 2dlabels text Asp243 size 12 color #8299d6
> 2dlabels #3.6 xpos 0.410 ypos 0.190
> 2dlabels text Glu242 size 12 color #8299d6
> 2dlabels #3.7 xpos 0.529 ypos 0.135
> 2dlabels #3.7 xpos 0.536 ypos 0.135
> 2dlabels text Tyr128 size 12 color #8299d6
> 2dlabels #3.8 xpos 0.740 ypos 0.658
> 2dlabels text Asp158 size 12 color #8299d6
> 2dlabels #3.9 xpos 0.713 ypos 0.056
> ~distance /A:243@OD2 /A:334@O37
> 2dlabels #3.8 xpos 0.743 ypos 0.666
> 2dlabels text Lys154 size 12 color #8299d6
> 2dlabels #3.10 xpos 0.567 ypos 0.005
> 2dlabels text Asp126 size 12 color #8299d6
> 2dlabels #3.11 xpos 0.918 ypos 0.507
> 2dlabels text Thr64 size 12 color #8299d6
> 2dlabels #3.12 xpos 0.839 ypos 0.114
> 2dlabels text Ser157 size 12 color #8299d6
> 2dlabels #3.13 xpos 0.794 ypos 0.054
> 2dlabels #3.12 xpos 0.839 ypos 0.120
> 2dlabels #3.13 xpos 0.793 ypos 0.060
> 2dlabels #3.13 xpos 0.801 ypos 0.052
> 2dlabels #3.13 xpos 0.799 ypos 0.065
> hide #3.12 models
> hide #3.13 models
> hide #3.11 models
> show #3.11 models
> show #3.12 models
> show #3.13 models
> 2dlabels #3.13 xpos 0.759 ypos 0.154
> 2dlabels #3.13 xpos 0.782 ypos 0.154
> 2dlabels #3.12 xpos 0.847 ypos 0.100
> 2dlabels #3.13 xpos 0.777 ypos 0.162
> 2dlabels #3.9 xpos 0.642 ypos 0.222
> hide /A target c
> show /A target c
> save
> C:/Users/jenni/OneDrive/Documents/B3_structure_figures/20220216_B3SSEA3.cxs
> hide /A target c
> select clear
> select clear
Drag select of 2 atoms, 2 bonds
> hide sel atoms
> select up
14 atoms, 10 bonds, 4 residues, 1 model selected
> select up
36 atoms, 34 bonds, 4 residues, 1 model selected
> hide sel atoms
> undo
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide sel atoms
> hide sel atoms
> hide sel atoms
> select clear
> hide atoms
> undo
> select clear
> hide atoms
> undo
> select clear
> select /A:242@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> hide atoms
> undo
> select clear
Drag select of 1 pseudobonds
> select up
4944 atoms, 4841 bonds, 1 pseudobond, 785 residues, 2 models selected
> select down
1 pseudobond, 1 model selected
> hide sel
> select /A:128@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
8 atoms, 7 bonds, 2 residues, 1 model selected
> select up
12 atoms, 11 bonds, 2 residues, 1 model selected
> hide sel atoms
> hide sel atoms
> lighting simple
> lighting shadows true
> lighting simple
> lighting full
> lighting simple
> lighting full
> lighting simple
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
> lighting full
> save
> C:/Users/jenni/OneDrive/Documents/B3_structure_figures/20220216_B3SSEA3_atoms.cxs
> save
> C:/Users/jenni/OneDrive/Documents/B3_structure_figures/20220216_B3SSEA3_atoms.tif
> width 3000 height 1993 supersample 4
> show /A target c
> lighting simple
> lighting soft
> lighting simple
> lighting simple
> lighting flat
> lighting simple
> lighting flat
> lighting full
> lighting simple
> graphics silhouettes false
> select up
24 atoms, 21 bonds, 4 residues, 1 model selected
> select up
28 atoms, 25 bonds, 4 residues, 1 model selected
> select up
150 atoms, 149 bonds, 19 residues, 1 model selected
> select up
2346 atoms, 2413 bonds, 274 residues, 1 model selected
> select down
150 atoms, 149 bonds, 19 residues, 1 model selected
> select clear
> select /A
2346 atoms, 2413 bonds, 8 pseudobonds, 274 residues, 2 models selected
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
4390 atoms, 4512 bonds, 534 residues, 1 model selected
> select clear
> select clear
> select clear
> select backbone
2136 atoms, 2134 bonds, 534 residues, 1 model selected
> color sel & C lavender
> color sel & C thistle
> ui tool show "Color Actions"
> color sel #dd8888ff
> color sel #d88ffdff
> color sel #dd8888ff
> color sel #d88fd8ff
> color sel #d889d7ff
> color sel #d88bd7ff
> color sel #d88cd7ff
> color sel #d88dd7ff
> color sel #d88fd7ff
> color sel #d88fd8ff
> color sel #d890d8ff
> color sel #d891d8ff
> color sel #d893d8ff
> color sel #d894d8ff
> color sel #d895d8ff
> color sel #d897d8ff
> color sel #d898d7ff
> color sel #d899d5ff
> color sel #d89cd3ff
> color sel #d89cd2ff
> color sel #d89dd2ff
> color sel #d89fd3ff
> color sel #d8a0d3ff
> color sel #d8a1d3ff
> color sel #d8a3d3ff
> color sel #d8a4d3ff
> color sel #d8a7d3ff
> color sel #d8a8d3ff
> color sel #d8a9d4ff
> color sel #d8aad4ff
> color sel #d8abd4ff
> color sel #d8acd4ff
> color sel #d8aed4ff
> color sel #d8afd4ff
> color sel #d8b0d4ff
> color sel #d8b3d5ff
> color sel #d8b4d3ff
> color sel #d8b5d2ff
> color sel #d8b6d3ff
> color sel #d8b7d3ff
> color sel #d8b8d3ff
> color sel #d8bad3ff
> color sel #d8bbd3ff
> color sel #d8bcd3ff
> color sel #d8bcd2ff
> color sel #d8bfd3ff
> color sel #d8c1d2ff
> color sel #d8c2d2ff
> color sel #d8c3d3ff
> color sel #d8c4d3ff
> color sel #d8c6d4ff
> color sel #d8c7d4ff
> color sel #d8c9d4ff
> color sel #d8c9d5ff
> color sel #d8c9d6ff
> color sel #d8c7d7ff
> color sel #d8c6d8ff
> color sel #d7c6d8ff
> color sel #d6c6d8ff
> color sel #d5c6d8ff
> color sel #d4c4d8ff
> color sel #d3c4d8ff
> color sel #d2c4d8ff
> color sel #d1c3d8ff
> color sel #d0c3d8ff
> color sel #cfc3d8ff
> color sel #cec3d8ff
> color sel #cdc3d8ff
> color sel #ccc3d8ff
> color sel #cbc3d8ff
> color sel #cac3d8ff
> color sel #c9c3d8ff
> color sel #c8c3d8ff
> color sel #c7c3d8ff
> color sel #c6c3d8ff
> color sel #c5c3d8ff
> color sel #c4c3d8ff
> color sel #c4c2d8ff
> color sel #c4c1d8ff
> color sel #c5bfd8ff
> color sel #c5bbd8ff
> color sel #c6bad8ff
> color sel #c6b6d8ff
> color sel #c4b3d8ff
> color sel #c5b2d8ff
> color sel #c4b0d8ff
> color sel #c5b0d8ff
> color sel #c6b0d8ff
> color sel #cbb0d8ff
> color sel #d2b2d8ff
> color sel #d5b3d8ff
> color sel #d5b4d8ff
> color sel #d7b5d8ff
> color sel #d8b5d8ff
> color sel #d8b5d7ff
> color sel #d8b6d7ff
> color sel #d8b6d6ff
> color sel #d8b6d5ff
> color sel #d8b6d4ff
> color sel #d8b6d2ff
> color sel #d8b7d2ff
> color sel #d8b8d1ff
> color sel #d8b8cfff
> color sel #d8b8ceff
> color sel #d8b8cdff
> color sel #d8baceff
> color sel #d8bbcdff
> color sel #d8bbccff
> color sel #d8bbcaff
> color sel #d8bccaff
> color sel #d9bdcbff
> color sel #dabeccff
> color sel #dcc0ceff
> color sel #ddc1cfff
> color sel #dec2cfff
> color sel #dfc2d0ff
> color sel #e1c4d2ff
> color sel #e2c5d3ff
> color sel #e3c6d4ff
> color sel #e6c9d7ff
> color sel #e7c9d8ff
> color sel #e8cad9ff
> color sel #eaccdbff
> color sel #ebcddcff
> color sel #ecceddff
> color sel #efd0dfff
> color sel #f0d1e0ff
> color sel #f1d2e1ff
> color sel #f4d5e4ff
> color sel #f5d6e5ff
> color sel #f7d7e7ff
> color sel #f9d9e9ff
> color sel #fadaeaff
> color sel #fdddedff
> color sel #feddedff
> color sel #ffdeeeff
> color sel #ffffffff
> color sel #ffddeeff
> color sel #fdeeeeff
> select clear
> lighting depthCueStart 0.1
> lighting depthCueEnd 0.5
> lighting depthCueEnd 0.6
> select up
181 atoms, 186 bonds, 22 residues, 1 model selected
> hide sel cartoons
> lighting soft
> lighting depthCueEnd 0.8
> lighting depthCueStart 0.2
> save
> C:/Users/jenni/OneDrive/Documents/B3_structure_figures/20220216_B3SSEA3_background.tif
> width 3000 height 1993 supersample 4
> save
> C:/Users/jenni/OneDrive/Documents/B3_structure_figures/20220216_B3SSEA3_background.cxs
opened ChimeraX session
> save
> C:/Users/jenni/OneDrive/Documents/B3_structure_figures/20220530_B3SSEA3_background.cxs
opened ChimeraX session
> open
> C:/Users/jenni/OneDrive/Documents/187_Gb4/Refine_16/187_Gb4_refine_16.pdb
Summary of feedback from opening
C:/Users/jenni/OneDrive/Documents/187_Gb4/Refine_16/187_Gb4_refine_16.pdb
---
warnings | Ignored bad PDB record found on line 4857
TER
Ignored bad PDB record found on line 9724
TER
Ignored bad PDB record found on line 10257
END
End residue of secondary structure not found: HELIX 2 2 ALA A 75 HIS A 88 1 14
Start residue of secondary structure not found: HELIX 3 3 TYR A 100 PHE A 117
5 18
Start residue of secondary structure not found: HELIX 4 4 VAL A 135 LYS A 145
1 11
Start residue of secondary structure not found: HELIX 5 5 GLY A 195 SER A 207
5 13
Start residue of secondary structure not found: HELIX 6 6 GLU A 214 ARG A 224
1 11
Start residue of secondary structure not found: HELIX 7 7 VAL A 247 ARG A 252
1 6
1 messages similar to the above omitted
End residue of secondary structure not found: HELIX 10 10 ALA B 75 HIS B 88 1
14
Start residue of secondary structure not found: HELIX 11 11 TYR B 100 PHE B
117 5 18
Start residue of secondary structure not found: HELIX 12 12 VAL B 135 LYS B
145 1 11
Start residue of secondary structure not found: HELIX 13 13 GLY B 195 SER B
207 5 13
Start residue of secondary structure not found: HELIX 14 14 GLU B 214 ARG B
224 1 11
Start residue of secondary structure not found: HELIX 15 15 VAL B 247 ARG B
252 1 6
9 messages similar to the above omitted
Chain information for 187_Gb4_refine_16.pdb #4
---
Chain | Description
A | No description available
B | No description available
> select #4/A:401@MN
1 atom, 1 residue, 1 model selected
> select #4/A:401@MN
1 atom, 1 residue, 1 model selected
> setattr sel b radius 0.2
Assigning radius attribute to 0 items
> setattr sel b radius 0.15
Assigning radius attribute to 0 items
> select #1/A:330@MN
1 atom, 1 residue, 1 model selected
> cartoon style
Gb5SSEA3_11C11_refine_17.pdb #1
\- helix mode=default xsection=round width=1.5 height=0.25 arrow=False arrow
scale=2
\- strand mode=default xsection=square width=1.5 height=0.25 arrow=True arrow
scale=2
\- coil xsection=round width=0.25 height=0.25
\- nucleic xsection=square width=0.4 height=2
\- divisions=20
\- oval parameters: sides=12
\- barbell parameters: sides=18 scale=0.5
187_Gb4_refine_16.pdb #4
\- helix mode=default xsection=round width=2 height=0.4 arrow=False arrow
scale=2
\- strand mode=default xsection=square width=2 height=0.4 arrow=True arrow
scale=2
\- coil xsection=round width=0.4 height=0.4
\- nucleic xsection=square width=0.4 height=2
\- divisions=20
\- oval parameters: sides=12
\- barbell parameters: sides=18 scale=0.5
> select #4/A:401@MN
1 atom, 1 residue, 1 model selected
> cartoon style coil xsection width 0.25 height 0.25
Invalid "xsection" argument: Should be one of 'barbell', 'oval', 'piping',
'rectangle', 'round', or 'square'
> cartoon style coil xsection round width 0.25 height 0.25
Expected a keyword
> cartoon style coil xsection round width 0.25
> cartoon style coil xsection round scale 0.5
Expected a keyword
> setattr sel a radius 0.15
Assigning radius attribute to 1 item
> setattr sel a radius 0.25
Assigning radius attribute to 1 item
> setattr sel a radius 0.4
Assigning radius attribute to 1 item
> setattr sel a radius 0.5
Assigning radius attribute to 1 item
> open
> C:/Users/jenni/OneDrive/Documents/20210827_13B_2F/Phenix/Refine_63/B3_2F_827_refine_63.pdb
Summary of feedback from opening
C:/Users/jenni/OneDrive/Documents/20210827_13B_2F/Phenix/Refine_63/B3_2F_827_refine_63.pdb
---
warnings | Ignored bad PDB record found on line 4799
TER
Ignored bad PDB record found on line 9512
TER
Ignored bad PDB record found on line 10255
END
Chain information for B3_2F_827_refine_63.pdb #5
---
Chain | Description
A | No description available
B | No description available
> ui tool show Matchmaker
> matchmaker #1/A#1/A to #4/A#5/A pairing ss
Different number of reference/match chains (2 ref, 1 match)
> matchmaker #1/A to #4/A pairing ss
Parameters
---
Chain pairing | ss
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 187_Gb4_refine_16.pdb, chain A (#4) with
Gb5SSEA3_11C11_refine_17.pdb, chain A (#1), sequence alignment score = 1371.1
RMSD between 268 pruned atom pairs is 0.221 angstroms; (across all 268 pairs:
0.221)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> matchmaker #1/A to #5/A pairing ss
Parameters
---
Chain pairing | ss
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 B3_2F_827_refine_63.pdb, chain A (#5) with
Gb5SSEA3_11C11_refine_17.pdb, chain A (#1), sequence alignment score = 1352.5
RMSD between 268 pruned atom pairs is 0.252 angstroms; (across all 268 pairs:
0.252)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> hide #!2 models
> hide #2.1 models
> hide #!3 models
> hide #1 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select #5/A:301@MN
1 atom, 1 residue, 1 model selected
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> select clear
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 457.63
OpenGL renderer: GeForce GTX 1650/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUSTeK COMPUTER INC.
Model: ROG Strix G531GT_G531GT
OS: Microsoft Windows 11 Home (Build 22000)
Memory: 8,434,601,984
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-Clipper: 0.15.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-ISOLDE: 1.1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
gdcm: 2.8.8
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5+mkl
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pywin32: 228
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
Send2Trash: 1.5.0
SEQCROW: 0.25.2
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
WMI: 1.5.1
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Structure Comparison |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → MatchMaker: wrapped C/C++ object of type ChainMenuButton has been deleted |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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