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Opened 5 years ago
Closed 5 years ago
#4492 closed defect (can't reproduce)
wrapped C/C++ object of type ChainMenuButton has been deleted
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202102240806 (2021-02-24 08:06:34 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.dev202102240806 (2021-02-24)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/rjk/MANUSCRIPTS/NRMCB review/Oxa1_superfamily.cxs"
Log from Tue Apr 6 13:59:28 2021UCSF ChimeraX version: 1.2.dev202102240806
(2021-02-24)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/rjk/MANUSCRIPTS/NRMCB review/Oxa1_superfamily.cxs"
Log from Tue Apr 6 12:13:29 2021UCSF ChimeraX version: 1.2.dev202102240806
(2021-02-24)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/rjk/MANUSCRIPTS/NRMCB review/Oxa1_superfamily.cxs"
Log from Mon Apr 5 19:14:45 2021UCSF ChimeraX version: 1.2.dev202102240806
(2021-02-24)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/rjk/Downloads/6so5.cif
6so5.cif title:
Homo sapiens WRB/CAML heterotetramer in complex with a TRC40 dimer [more
info...]
Chain information for 6so5.cif #1
---
Chain | Description
A B | ATPase ASNA1
C D | Tail-anchored protein insertion receptor WRB
E F | Calcium signal-modulating cyclophilin ligand
Non-standard residues in 6so5.cif #1
---
ZN — zinc ion
> open /Users/rjk/Downloads/6ww7.cif
Summary of feedback from opening /Users/rjk/Downloads/6ww7.cif
---
note | Fetching CCD NAG from http://ligand-expo.rcsb.org/reports/N/NAG/NAG.cif
6ww7.cif title:
Structure of the human ER membrane protein complex in a lipid nanodisc [more
info...]
Chain information for 6ww7.cif #2
---
Chain | Description
A | ER membrane protein complex subunit 1
B | ER membrane protein complex subunit 2
C | ER membrane protein complex subunit 3
D | ER Membrane Protein Complex Subunit 4
E | Membrane magnesium transporter 1
F | ER membrane protein complex subunit 6
G | ER membrane protein complex subunit 7
H | ER membrane protein complex subunit 8
I | ER membrane protein complex subunit 10
Non-standard residues in 6ww7.cif #2
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
> open /Users/rjk/Downloads/6w6l.cif
Summary of feedback from opening /Users/rjk/Downloads/6w6l.cif
---
warning | Atom H1 is not in the residue template for UNK /y:1
6w6l.cif title:
Cryo-EM structure of the human ribosome-TMCO1 translocon [more info...]
Chain information for 6w6l.cif #3
---
Chain | Description
1 | Protein transport protein Sec61 subunit α isoform 1
2 | Protein transport protein Sec61 subunit γ
3 | Protein transport protein Sec61 subunit β
4 | Transmembrane protein 147
5 | Nicalin
6 | Calcium load-activated calcium channel
7 | Coiled-coil domain-containing protein 47
A | 60S ribosomal protein L8
B | 60S ribosomal protein L3
C | 60S ribosomal protein L4
D | 5.8S ribosomal RNA
E | 5S ribosomal RNA
F | 60S ribosomal protein L5
G | 60S ribosomal protein L6
H | 60S ribosomal protein L7
I | 60S ribosomal protein L7a
J | 60S ribosomal protein L9
K | 60S ribosomal protein L10
L | 60S ribosomal protein L11
M | 60S ribosomal protein L13
N | 60S ribosomal protein L14
O | 60S ribosomal protein L15
P | 60S ribosomal protein L13a
Q | 60S ribosomal protein L17
R | 60S ribosomal protein L18
S | 60S ribosomal protein L19
T | 60S ribosomal protein L18a
U | 60S ribosomal protein L21
V | 60S ribosomal protein L22
W | 60S ribosomal protein L23
X | 60S ribosomal protein L24
Y | 60S ribosomal protein L23a
Z | 60S ribosomal protein L26
a | 60S ribosomal protein L27
b | 60S ribosomal protein L27a
c | 60S ribosomal protein L29
d | 60S ribosomal protein L30
e | 60S ribosomal protein L31
f | 60S ribosomal protein L32
g | 60S ribosomal protein L35a
h | 60S ribosomal protein L34
i | 60S ribosomal protein L35
j | 60S ribosomal protein L36
k | 60S ribosomal protein L37
l | 60S ribosomal protein L38
m | 60S ribosomal protein L39
o | 60S ribosomal protein L41
p | 60S ribosomal protein L36a
q | 60S ribosomal protein L37a
r | 60S ribosomal protein L28
t | 28S ribosomal RNA
u | tRNA
v | tRNA
y | Nascent chain mixture
Non-standard residues in 6w6l.cif #3
---
MG — magnesium ion
ZN — zinc ion
> open /Users/rjk/Downloads/6al2.cif
Summary of feedback from opening /Users/rjk/Downloads/6al2.cif
---
note | Fetching CCD OLC from http://ligand-expo.rcsb.org/reports/O/OLC/OLC.cif
6al2.cif title:
Crystal structure of E. coli YidC at 2.8 A resolution [more info...]
Chain information for 6al2.cif #4
---
Chain | Description
A B | Membrane protein insertase YidC
Non-standard residues in 6al2.cif #4
---
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
6al2.cif mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> hide #4 models
> show #4 models
> hide #!3 models
> show #!3 models
> save "/Users/rjk/MANUSCRIPTS/NRMCB review/Oxa1_superfamily_overview.cxs"
> hide #4 models
> show #4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> select #4
7650 atoms, 7851 bonds, 970 residues, 1 model selected
> ~select #4
Nothing selected
> select #4
7650 atoms, 7851 bonds, 970 residues, 1 model selected
> select #4/B:343
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/B:343
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/B:339
7 atoms, 7 bonds, 1 residue, 1 model selected
> ~select #4:b
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4:b
Nothing selected
> select #4:B
Nothing selected
> select #4B
Expected an objects specifier or a keyword
> help select
> select #4/A
3853 atoms, 3953 bonds, 488 residues, 1 model selected
> select #4/B
3797 atoms, 3898 bonds, 482 residues, 1 model selected
> cartoon hide sel
> style sel sphere
Changed 3797 atom styles
> style sel sphere
Changed 3797 atom styles
> select #4/A
3853 atoms, 3953 bonds, 488 residues, 1 model selected
> preset cartoons/nucleotides ribbons/slabs
Changed 288075 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> close #3
> save "/Users/rjk/MANUSCRIPTS/NRMCB review/Oxa1_superfamily_overview.cxs"
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select #4/B
3797 atoms, 3898 bonds, 482 residues, 1 model selected
> delete sel
> save "/Users/rjk/MANUSCRIPTS/NRMCB review/Oxa1_superfamily_overview.cxs"
> preset cartoons/nucleotides licorice/ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> preset "initial styles" "original look"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "space-filling (chain colors)"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> mlp #4
Map values for surface "6al2.cif_A SES surface": minimum -27.28, mean -2.661,
maximum 24.43
> hide #!4 atoms
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> mlp #!4
Map values for surface "6al2.cif_A SES surface": minimum -27.28, mean -2.661,
maximum 24.43
> hide #!4 surfaces
> show #!4 cartoons
> mlp #!4
Map values for surface "6al2.cif_A SES surface": minimum -27.28, mean -2.661,
maximum 24.43
> hide #!4 models
> open /Users/rjk/Downloads/3wo6.cif
Summary of feedback from opening /Users/rjk/Downloads/3wo6.cif
---
note | Fetching CCD CD from http://ligand-expo.rcsb.org/reports/C/CD/CD.cif
3wo6.cif title:
Crystal structure of YidC from Bacillus halodurans (form I) [more info...]
Chain information for 3wo6.cif #3
---
Chain | Description
A | Membrane protein insertase YidC 2
Non-standard residues in 3wo6.cif #3
---
CD — cadmium ion
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
> save "/Users/rjk/MANUSCRIPTS/NRMCB review/Oxa1_superfamily_overview.cxs"
> mlp #!3
Map values for surface "3wo6.cif_A SES surface": minimum -25.61, mean -0.1328,
maximum 23.67
> hide #!3 atoms
> hide #!3 atoms
> show #!3 atoms
> show #!3 atoms
> hide #!3 atoms
> lighting simple
> lighting soft
> lighting full
> lighting simple
> ui tool show "Side View"
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> lighting flat
> lighting full
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting full
> lighting soft
> lighting soft
> lighting simple
> lighting full
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> set bgColor gray
> set bgColor white
> ui tool show "Side View"
> lighting full
> save "/Users/rjk/MANUSCRIPTS/NRMCB review/Oxa1_superfamily_overview.cxs"
> save "/Users/rjk/MANUSCRIPTS/NRMCB review/BhYidC_surface_v1.jpg" width 719
> height 739 supersample 3
> save "/Users/rjk/MANUSCRIPTS/NRMCB review/BhYidC_surface_v1..tif" width 719
> height 739 supersample 3 transparentBackground true
> hide #!3 atoms
> hide #!3 cartoons
> lighting full
> lighting simple
> lighting full
> save "/Users/rjk/MANUSCRIPTS/NRMCB review/BhYidC_surface_v1..tif" width 719
> height 739 supersample 3 transparentBackground true
> save "/Users/rjk/MANUSCRIPTS/NRMCB review/Oxa1_superfamily_overview.cxs"
——— End of log from Mon Apr 5 19:14:45 2021 ———
opened ChimeraX session
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!1 models
> show #!1 target m
> view #1 clip false
> hide #!1 atoms
> hide #!1 surfaces
> show #!1 surfaces
> hide #!1 surfaces
> hide #!1 cartoons
> show #!1 cartoons
> show #!1 cartoons
> select #1/F
816 atoms, 838 bonds, 101 residues, 1 model selected
> cartoon hide (#!1 & sel)
> select #1/C:121
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
481 atoms, 491 bonds, 57 residues, 2 models selected
> select up
1160 atoms, 1183 bonds, 144 residues, 2 models selected
> cartoon hide (#!1 & sel)
> cartoon style (#!1 & sel) xsection oval modeHelix default
> kdssp
Unknown command: kdssp
> kdsp
Unknown command: kdsp
> kssp
Unknown command: kssp
> cartoon style
6so5.cif #1
\- helix mode=default xsection=round width=1 height=1 arrow=False arrow
scale=2
\- strand mode=default xsection=round width=1 height=1 arrow=False arrow
scale=2
\- coil xsection=round width=1 height=1
\- nucleic xsection=square width=0.4 height=2
\- divisions=20
\- oval parameters: sides=12
\- barbell parameters: sides=18 scale=0.5
6ww7.cif #2
\- helix mode=default xsection=round width=1 height=1 arrow=False arrow
scale=2
\- strand mode=default xsection=round width=1 height=1 arrow=False arrow
scale=2
\- coil xsection=round width=1 height=1
\- nucleic xsection=square width=0.4 height=2
\- divisions=20
\- oval parameters: sides=12
\- barbell parameters: sides=18 scale=0.5
6al2.cif #4
\- helix mode=default xsection=round width=1 height=1 arrow=False arrow
scale=2
\- strand mode=default xsection=round width=1 height=1 arrow=False arrow
scale=2
\- coil xsection=round width=1 height=1
\- nucleic xsection=square width=0.4 height=2
\- divisions=20
\- oval parameters: sides=12
\- barbell parameters: sides=18 scale=0.5
3wo6.cif #3
\- 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 protein
6so5.cif #1
\- helix mode=default xsection=round width=1 height=1 arrow=False arrow
scale=2
\- strand mode=default xsection=round width=1 height=1 arrow=False arrow
scale=2
\- coil xsection=round width=1 height=1
\- nucleic xsection=square width=0.4 height=2
\- divisions=20
\- oval parameters: sides=12
\- barbell parameters: sides=18 scale=0.5
6ww7.cif #2
\- helix mode=default xsection=round width=1 height=1 arrow=False arrow
scale=2
\- strand mode=default xsection=round width=1 height=1 arrow=False arrow
scale=2
\- coil xsection=round width=1 height=1
\- nucleic xsection=square width=0.4 height=2
\- divisions=20
\- oval parameters: sides=12
\- barbell parameters: sides=18 scale=0.5
3wo6.cif #3
\- 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
6al2.cif #4
\- helix mode=default xsection=round width=1 height=1 arrow=False arrow
scale=2
\- strand mode=default xsection=round width=1 height=1 arrow=False arrow
scale=2
\- coil xsection=round width=1 height=1
\- nucleic xsection=square width=0.4 height=2
\- divisions=20
\- oval parameters: sides=12
\- barbell parameters: sides=18 scale=0.5
> preset ribbon
Changed 29059 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select clear
> select #1/F:263
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/C:109
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
481 atoms, 491 bonds, 57 residues, 2 models selected
> select up
1160 atoms, 1183 bonds, 144 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select #1/F:263
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
340 atoms, 351 bonds, 40 residues, 2 models selected
> select up
816 atoms, 838 bonds, 101 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select #1/A:197
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1/A:197
17 atoms, 15 bonds, 2 residues, 2 models selected
> select up
273 atoms, 275 bonds, 34 residues, 3 models selected
> select up
4766 atoms, 4857 bonds, 606 residues, 3 models selected
> color (#!1 & sel) cornflower blue
> select clear
> select #1/B:182
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/A:220
14 atoms, 12 bonds, 2 residues, 2 models selected
> select up
257 atoms, 259 bonds, 32 residues, 3 models selected
> select up
4766 atoms, 4857 bonds, 606 residues, 3 models selected
> color (#!1 & sel) light gray
> select clear
> select #1/D:19
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
182 atoms, 188 bonds, 22 residues, 2 models selected
> select up
1160 atoms, 1183 bonds, 144 residues, 2 models selected
> color (#!1 & sel) cornflower blue
> select clear
> save "/Users/rjk/MANUSCRIPTS/NRMCB review/Oxa1_superfamily.cxs"
> show #!1 surfaces
> hide
> hide
> hide
> hide #1.F
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1/F
> select /F
1590 atoms, 1633 bonds, 200 residues, 2 models selected
> select /F,G
2474 atoms, 2540 bonds, 311 residues, 2 models selected
> select /F,C
4457 atoms, 4564 bonds, 3 pseudobonds, 553 residues, 4 models selected
> surface hidePatches (#!1 & sel)
> select /F,C
4457 atoms, 4564 bonds, 3 pseudobonds, 553 residues, 4 models selected
> show sel & #!1 surfaces
> select /d,e
2857 atoms, 2923 bonds, 1 pseudobond, 362 residues, 3 models selected
> surface hidePatches (#!1 & sel)
> hide sel & #!1 cartoons
> hide sel & #!1 cartoons
> select #1
8737 atoms, 8919 bonds, 6 pseudobonds, 1098 residues, 3 models selected
> hide sel cartoons
> select clear
> select #1/F:270@CG2
1 atom, 1 residue, 1 model selected
> select add #1/C:110@CG1
2 atoms, 2 residues, 2 models selected
> select subtract #1/C:110@CG1
1 atom, 1 residue, 3 models selected
> select #1/F:263@OG1
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
340 atoms, 351 bonds, 40 residues, 2 models selected
> select up
816 atoms, 838 bonds, 101 residues, 2 models selected
> color (#!1 & sel) orange
> color (#!1 & sel) orange red
> ui tool show "Color Actions"
> color sel coral
> color sel tomato
> color sel coral
> select #1/C:107@CB
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
481 atoms, 491 bonds, 57 residues, 2 models selected
> select up
1160 atoms, 1183 bonds, 144 residues, 2 models selected
> color sel cornflower blue
> select clear
> ui tool show "Side View"
> view clip false
> save "/Users/rjk/MANUSCRIPTS/NRMCB review/Oxa1_superfamily.cxs"
> save "/Users/rjk/MANUSCRIPTS/NRMCB review/WRB_CAML_surface_v1.tif" width
> 1000 height 1028 supersample 3 transparentBackground true
> select #1/B:35@CD
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
43 atoms, 42 bonds, 5 residues, 2 models selected
> select up
2301 atoms, 2346 bonds, 292 residues, 2 models selected
> select up
8737 atoms, 8919 bonds, 1098 residues, 2 models selected
> select down
2301 atoms, 2346 bonds, 292 residues, 7 models selected
> cartoon hide (#!1 & sel)
> surface hidePatches (#!1 & sel)
> select #1/A:252@CB
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> select up
152 atoms, 153 bonds, 18 residues, 2 models selected
> select up
2465 atoms, 2511 bonds, 314 residues, 2 models selected
> surface hidePatches (#!1 & sel)
> select #1/F:270@CB
1 atom, 1 residue, 1 model selected
> select #1/C:112@CG
1 atom, 1 residue, 1 model selected
> select add #1/F:267@SD
2 atoms, 2 residues, 2 models selected
> select up
17 atoms, 15 bonds, 2 residues, 3 models selected
> select up
821 atoms, 842 bonds, 97 residues, 3 models selected
> select up
1976 atoms, 2021 bonds, 245 residues, 3 models selected
> hide sel surfaces
> show sel cartoons
> select clear
> select #1/C:171
10 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select clear
> select #1/C:151
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select #1/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/C:171
15 atoms, 14 bonds, 2 residues, 2 models selected
> select up
157 atoms, 159 bonds, 22 residues, 2 models selected
> color (#!1 & sel) magenta
> select clear
> select #1/C:7
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/C:25
19 atoms, 17 bonds, 2 residues, 2 models selected
> select up
174 atoms, 180 bonds, 21 residues, 2 models selected
> color (#!1 & sel) cyan
> select clear
> select #1/C:124
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/C:107
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/C:124
17 atoms, 16 bonds, 2 residues, 2 models selected
> select up
481 atoms, 491 bonds, 57 residues, 2 models selected
> select clear
> select #1/C:123
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #1/C:107
17 atoms, 16 bonds, 2 residues, 2 models selected
> select up
481 atoms, 491 bonds, 57 residues, 2 models selected
> select down
17 atoms, 16 bonds, 2 residues, 2 models selected
> select up
481 atoms, 491 bonds, 57 residues, 2 models selected
> select down
17 atoms, 16 bonds, 2 residues, 2 models selected
> select clear
> select #1/C:106
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/C:121
14 atoms, 15 bonds, 1 residue, 1 model selected
> select add #1/C:106
21 atoms, 21 bonds, 2 residues, 2 models selected
> select down
21 atoms, 21 bonds, 2 residues, 2 models selected
> select up
481 atoms, 491 bonds, 57 residues, 2 models selected
> select down
21 atoms, 21 bonds, 2 residues, 2 models selected
> select up
481 atoms, 491 bonds, 57 residues, 2 models selected
> select down
21 atoms, 21 bonds, 2 residues, 2 models selected
> select down
21 atoms, 21 bonds, 2 residues, 2 models selected
> select down
21 atoms, 21 bonds, 2 residues, 2 models selected
> select up
481 atoms, 491 bonds, 57 residues, 2 models selected
> select down
21 atoms, 21 bonds, 2 residues, 2 models selected
> select down
21 atoms, 21 bonds, 2 residues, 2 models selected
> select up
481 atoms, 491 bonds, 57 residues, 2 models selected
> select down
21 atoms, 21 bonds, 2 residues, 2 models selected
> select down
21 atoms, 21 bonds, 2 residues, 2 models selected
> select up
481 atoms, 491 bonds, 57 residues, 2 models selected
> select clear
> select #1/C:124
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
> select clear
> select #1/C:124
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/c.124
Expected an objects specifier or a keyword
> select #1/C:124-130
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/C:108-124
150 atoms, 155 bonds, 17 residues, 1 model selected
> color (#!1 & sel) lime
> select clear
> save "/Users/rjk/MANUSCRIPTS/NRMCB review/WRB_CAML_cartoon_v1.tif" width
> 1000 height 1028 supersample 3 transparentBackground true
> lighting simple
> select #1/C:171
10 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1 & sel) cornflower blue
> select clear
> save "/Users/rjk/MANUSCRIPTS/NRMCB review/WRB_CAML_cartoon_v1.tif" width 719
> height 739 supersample 3
> save "/Users/rjk/MANUSCRIPTS/NRMCB review/WRB_CAML_cartoon_v1.tif" width 719
> height 739 supersample 3 transparentBackground true
> save "/Users/rjk/MANUSCRIPTS/NRMCB review/WRB_CAML_cartoon_v1.tif" width 973
> height 1000 supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> select #2/F:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #2/C:177
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #2/F:94
22 atoms, 22 bonds, 2 residues, 1 model selected
> select up
318 atoms, 329 bonds, 38 residues, 1 model selected
> select up
2481 atoms, 2543 bonds, 308 residues, 1 model selected
> select ~sel
28354 atoms, 28981 bonds, 12 pseudobonds, 3583 residues, 11 models selected
> cartoon hide (#!2 & sel)
> select #2/F:59
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
176 atoms, 179 bonds, 22 residues, 1 model selected
> select up
774 atoms, 795 bonds, 99 residues, 1 model selected
> ui tool show "Color Actions"
> color sel coral
> select clear
> select #2/C:122
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
129 atoms, 131 bonds, 17 residues, 1 model selected
> select up
1707 atoms, 1748 bonds, 209 residues, 1 model selected
> color sel cornflower blue
> select clear
> select #2/C:186
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:168
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
159 atoms, 164 bonds, 19 residues, 1 model selected
> color sel magenta
> select clear
> select #2/C:131
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:115
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #2/C:131
14 atoms, 12 bonds, 2 residues, 1 model selected
> select up
129 atoms, 131 bonds, 17 residues, 1 model selected
> color sel lime
> select clear
> select #2/C:15
14 atoms, 15 bonds, 1 residue, 1 model selected
> select add #2/C:34
21 atoms, 21 bonds, 2 residues, 1 model selected
> select up
241 atoms, 247 bonds, 29 residues, 1 model selected
> color sel cyan
> select clear
> save "/Users/rjk/MANUSCRIPTS/NRMCB review/EMC3_EMC6_cartoon_v1.tif" width
> 1000 height 1122 supersample 3 transparentBackground true
> select clear
> select #2/C:9
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/C:14
16 atoms, 14 bonds, 2 residues, 1 model selected
> select up
282 atoms, 288 bonds, 34 residues, 1 model selected
> color sel cornflower blue
> select clear
> select #2/C:16
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #2/C:34
14 atoms, 12 bonds, 2 residues, 1 model selected
> select up
241 atoms, 247 bonds, 29 residues, 1 model selected
> select subtract #2/C:38
233 atoms, 240 bonds, 28 residues, 1 model selected
> select subtract #2/C:37
225 atoms, 233 bonds, 27 residues, 1 model selected
> select subtract #2/C:36
217 atoms, 226 bonds, 26 residues, 1 model selected
> select subtract #2/C:35
211 atoms, 221 bonds, 25 residues, 1 model selected
> select subtract #2/C:10
205 atoms, 216 bonds, 24 residues, 1 model selected
> select subtract #2/C:11
197 atoms, 209 bonds, 23 residues, 1 model selected
> select subtract #2/C:12
189 atoms, 202 bonds, 22 residues, 1 model selected
> select subtract #2/C:13
178 atoms, 192 bonds, 21 residues, 1 model selected
> select subtract #2/C:14
170 atoms, 185 bonds, 20 residues, 1 model selected
> color sel cyan
> select clear
> save "/Users/rjk/MANUSCRIPTS/NRMCB review/Oxa1_superfamily.cxs"
——— End of log from Tue Apr 6 12:13:29 2021 ———
opened ChimeraX session
> open "/Users/rjk/TMCO1/Oxa1 superfamily structure
> analysis/3D_modeling/Mj0480compact.pdb"
Mj0480compact.pdb title:
A yidc-like protein In the archaeal plasma membrane [more info...]
Chain information for Mj0480compact.pdb #5
---
Chain | Description
I | No description available
> hide #!2 models
> show #!5 target m
> view #5 clip false
> save "/Users/rjk/MANUSCRIPTS/NRMCB review/Oxa1_superfamily.cxs"
——— End of log from Tue Apr 6 13:59:28 2021 ———
opened ChimeraX session
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!1 models
> show #!1 target m
> view #1 clip false
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!5 models
> help align
> help align
> align #5 toAtoms #2
Unequal number of atoms to pair, 1094 and 16576
> help match
> matchmaker #5 to #2
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 6ww7.cif, chain C (#2) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 92.1
RMSD between 12 pruned atom pairs is 0.763 angstroms; (across all 116 pairs:
39.573)
> matchmaker #5 to #2/C
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 6ww7.cif, chain C (#2) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 92.1
RMSD between 12 pruned atom pairs is 0.763 angstroms; (across all 116 pairs:
39.573)
> matchmaker #5 to #2/C:114-189
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 6ww7.cif, chain C (#2) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 83.3
RMSD between 30 pruned atom pairs is 1.328 angstroms; (across all 67 pairs:
4.972)
> open "/Users/rjk/MANUSCRIPTS/NRMCB review/trRosetta
> models/mj0606_April2021_TR042927_results/model1.pdb"
Chain information for model1.pdb #6
---
Chain | Description
A | No description available
> matchmaker #6 to #2/F
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 6ww7.cif, chain F (#2) with model1.pdb, chain A (#6), sequence
alignment score = 106
RMSD between 30 pruned atom pairs is 1.060 angstroms; (across all 86 pairs:
6.126)
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> matchmaker #6 to #2/F:16-44
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 6ww7.cif, chain F (#2) with model1.pdb, chain A (#6), sequence
alignment score = 41.8
RMSD between 5 pruned atom pairs is 0.863 angstroms; (across all 29 pairs:
15.756)
> matchmaker #6 to #2/F
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 6ww7.cif, chain F (#2) with model1.pdb, chain A (#6), sequence
alignment score = 106
RMSD between 30 pruned atom pairs is 1.060 angstroms; (across all 86 pairs:
6.126)
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> matchmaker #6 to #2/F:16-70
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 6ww7.cif, chain F (#2) with model1.pdb, chain A (#6), sequence
alignment score = 76.9
RMSD between 18 pruned atom pairs is 0.622 angstroms; (across all 54 pairs:
5.902)
> matchmaker #6 to #2/F
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 6ww7.cif, chain F (#2) with model1.pdb, chain A (#6), sequence
alignment score = 106
RMSD between 30 pruned atom pairs is 1.060 angstroms; (across all 86 pairs:
6.126)
> hide #!2 models
> show #!5 models
> hide #6 models
> show #!2 models
> select #5
1094 atoms, 1131 bonds, 2 pseudobonds, 134 residues, 2 models selected
> select clear
> select #5
1094 atoms, 1131 bonds, 2 pseudobonds, 134 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.9321,-0.20641,0.29764,152.18,-0.36052,0.60806,-0.70732,36.8,-0.034985,-0.76659,-0.64118,148
> view matrix models
> #5,-0.92519,-0.28372,0.25206,154.85,-0.37031,0.52953,-0.7632,38.839,0.083065,-0.79944,-0.59498,153.73
> view matrix models
> #5,-0.91869,-0.31797,0.23432,156.2,-0.37267,0.50124,-0.78095,39.73,0.13086,-0.80477,-0.57898,155.3
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.91869,-0.31797,0.23432,156.01,-0.37267,0.50124,-0.78095,39.613,0.13086,-0.80477,-0.57898,155.03
> show #6 models
> ~select #5
Nothing selected
> select #6
1415 atoms, 1433 bonds, 91 residues, 1 model selected
> view matrix models
> #6,-0.48917,0.088548,-0.86768,136.24,0.70862,0.62035,-0.33619,124.39,0.5085,-0.77931,-0.3662,103.23
> view matrix models
> #6,-0.48917,0.088548,-0.86768,136.03,0.70862,0.62035,-0.33619,124.18,0.5085,-0.77931,-0.3662,103.01
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.44339,0.01065,-0.89626,134.59,0.75771,0.53864,-0.36845,122.63,0.47884,-0.84247,-0.2469,104.5
> view matrix models
> #6,-0.43409,-0.019844,-0.90065,134.25,0.77393,0.50349,-0.3841,122.02,0.46109,-0.86377,-0.2032,105.17
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.43409,-0.019844,-0.90065,135.05,0.77393,0.50349,-0.3841,123.13,0.46109,-0.86377,-0.2032,104.94
> view matrix models
> #6,-0.43409,-0.019844,-0.90065,135.02,0.77393,0.50349,-0.3841,123.5,0.46109,-0.86377,-0.2032,104.81
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.41138,-0.0031763,-0.91146,134.59,0.72997,0.59767,-0.33155,125.23,0.54581,-0.80173,-0.24355,103.21
> view matrix models
> #6,-0.21383,-0.042552,-0.97594,130.34,0.80216,0.56252,-0.20028,125.22,0.55751,-0.82569,-0.086153,104.56
> view matrix models
> #6,-0.24828,0.013086,-0.9686,131.26,0.76908,0.6106,-0.18889,126.12,0.58895,-0.79183,-0.16167,103.38
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.24828,0.013086,-0.9686,130.39,0.76908,0.6106,-0.18889,125.66,0.58895,-0.79183,-0.16167,98.208
> matchmaker #6 to #2/F
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 6ww7.cif, chain F (#2) with model1.pdb, chain A (#6), sequence
alignment score = 106
RMSD between 30 pruned atom pairs is 1.060 angstroms; (across all 86 pairs:
6.126)
> view matrix models
> #6,-0.48917,0.088548,-0.86768,136.71,0.70862,0.62035,-0.33619,124.47,0.5085,-0.77931,-0.3662,103.91
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.44357,-0.048958,-0.8949,135.02,0.73036,0.55897,-0.39259,123.23,0.51944,-0.82774,-0.21219,105.13
> ~select #6
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #5
1094 atoms, 1131 bonds, 2 pseudobonds, 134 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.9231,-0.26536,0.27835,155.02,-0.38263,0.56102,-0.73406,38.277,0.038626,-0.78412,-0.61941,150.64
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.9231,-0.26536,0.27835,154.04,-0.38263,0.56102,-0.73406,37.214,0.038626,-0.78412,-0.61941,151.24
> view matrix models
> #5,-0.9231,-0.26536,0.27835,154.03,-0.38263,0.56102,-0.73406,37.173,0.038626,-0.78412,-0.61941,151.24
> view matrix models
> #5,-0.9231,-0.26536,0.27835,154.14,-0.38263,0.56102,-0.73406,37.481,0.038626,-0.78412,-0.61941,151.19
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.97951,-0.15012,0.13422,136.44,-0.1957,0.55252,-0.8102,33.881,0.047467,-0.81987,-0.57058,156.92
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.97951,-0.15012,0.13422,136.62,-0.1957,0.55252,-0.8102,34.409,0.047467,-0.81987,-0.57058,156.83
> ~select #5
Nothing selected
> hide #6 models
> show #6 models
> select #6
1415 atoms, 1433 bonds, 91 residues, 1 model selected
> view matrix models
> #6,-0.44357,-0.048958,-0.8949,134.29,0.73036,0.55897,-0.39259,122.3,0.51944,-0.82774,-0.21219,99.54
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.45237,-0.054716,-0.89015,134.46,0.72584,0.55736,-0.40313,122.26,0.51819,-0.82847,-0.21242,99.556
> view matrix models
> #6,-0.42059,-0.099266,-0.9018,133.59,0.74807,0.52445,-0.40662,121.69,0.51331,-0.84564,-0.14632,100.26
> view matrix models
> #6,-0.45695,-0.02441,-0.88916,134.69,0.69925,0.60798,-0.37604,123.23,0.54977,-0.79358,-0.26074,98.662
> view matrix models
> #6,-0.47065,-0.14248,-0.87074,134.58,0.59462,0.67788,-0.43232,124.75,0.65185,-0.72123,-0.23432,97.517
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.47065,-0.14248,-0.87074,134.89,0.59462,0.67788,-0.43232,125.29,0.65185,-0.72123,-0.23432,96.301
> view matrix models
> #6,-0.47065,-0.14248,-0.87074,134.55,0.59462,0.67788,-0.43232,125.11,0.65185,-0.72123,-0.23432,96.133
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.42058,-0.19453,-0.88615,133.29,0.61997,0.65148,-0.43727,124.5,0.66238,-0.7333,-0.15339,96.752
> view matrix models
> #6,-0.40844,-0.1722,-0.89639,133.08,0.61131,0.67767,-0.40873,125.07,0.67784,-0.71492,-0.17152,96.378
> view matrix models
> #6,-0.62557,0.10443,-0.77315,139.35,0.66886,0.58193,-0.46258,123.08,0.40162,-0.8065,-0.43389,97.936
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.62557,0.10443,-0.77315,143.33,0.66886,0.58193,-0.46258,121.83,0.40162,-0.8065,-0.43389,98.966
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.55955,0.0010846,-0.8288,141.14,0.65264,0.61696,-0.43981,122.5,0.51086,-0.787,-0.34592,98.107
> view matrix models
> #6,-0.56288,0.01117,-0.82646,141.27,0.65581,0.61462,-0.43835,122.45,0.50306,-0.78874,-0.35328,98.156
> view matrix models
> #6,-0.44346,0.066777,-0.8938,138.76,0.72835,0.60802,-0.31595,122.47,0.52235,-0.79111,-0.31827,98.183
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.44346,0.066777,-0.8938,136.63,0.72835,0.60802,-0.31595,124.29,0.52235,-0.79111,-0.31827,98.714
> view matrix models
> #6,-0.44346,0.066777,-0.8938,136.79,0.72835,0.60802,-0.31595,124.4,0.52235,-0.79111,-0.31827,98.625
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.44212,0.0649,-0.8946,136.75,0.72676,0.61046,-0.31489,124.45,0.52568,-0.78938,-0.31707,98.588
> view matrix models
> #6,-0.39223,0.01291,-0.91977,135.4,0.76373,0.56189,-0.3178,123.56,0.51271,-0.82711,-0.23025,99.556
> ~select #6
Nothing selected
> hide #!2 models
> save "/Users/rjk/MANUSCRIPTS/NRMCB review/Oxa1_superfamily.cxs"
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> hide #6 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #6 models
> show #!5 models
> show #!2 models
> select #5
1094 atoms, 1131 bonds, 2 pseudobonds, 134 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.97942,-0.13515,0.14993,136.55,-0.20044,0.56348,-0.80145,34.164,0.023835,-0.815,-0.57897,155.87
> view matrix models
> #5,-0.96484,-0.24415,0.097316,141.07,-0.2143,0.51642,-0.82908,35.731,0.15217,-0.82079,-0.55059,158.55
> view matrix models
> #5,-0.93622,-0.28377,0.20729,151.05,-0.32387,0.46777,-0.82237,39.273,0.1364,-0.83706,-0.52984,160.99
> view matrix models
> #5,-0.94592,-0.18992,0.26301,147.83,-0.32423,0.52673,-0.78577,37.374,0.010699,-0.82855,-0.55982,158.02
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.94592,-0.18992,0.26301,147.86,-0.32423,0.52673,-0.78577,37.364,0.010699,-0.82855,-0.55982,158.64
> view matrix models
> #5,-0.94592,-0.18992,0.26301,147.93,-0.32423,0.52673,-0.78577,37.417,0.010699,-0.82855,-0.55982,158.53
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.92981,-0.23538,0.28293,152.53,-0.36766,0.55904,-0.74317,37.665,0.016753,-0.79503,-0.60634,153.17
> view matrix models
> #5,-0.92542,-0.27455,0.26118,153.97,-0.37283,0.53646,-0.75711,38.38,0.067749,-0.79802,-0.59881,154.05
> view matrix models
> #5,-0.93823,-0.2846,0.19678,150.53,-0.33451,0.60068,-0.72615,35.876,0.088458,-0.74712,-0.65877,146.63
> view matrix models
> #5,-0.93059,-0.2855,0.22913,152.69,-0.34925,0.5049,-0.78937,38.669,0.10968,-0.8146,-0.56956,157.26
> view matrix models
> #5,-0.93078,-0.27553,0.24028,152.68,-0.35342,0.51009,-0.78415,38.614,0.093495,-0.81479,-0.57216,157.05
> view matrix models
> #5,-0.92335,-0.25162,0.29001,154.17,-0.37288,0.40762,-0.83355,42.755,0.091517,-0.8778,-0.47021,168.09
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.92335,-0.25162,0.29001,155.65,-0.37288,0.40762,-0.83355,41.162,0.091517,-0.8778,-0.47021,170.94
> view matrix models
> #5,-0.92335,-0.25162,0.29001,155.18,-0.37288,0.40762,-0.83355,42.537,0.091517,-0.8778,-0.47021,171.28
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.9373,-0.27582,0.21307,151.95,-0.31177,0.39024,-0.86632,41.907,0.1558,-0.87843,-0.45176,172.73
> view matrix models
> #5,-0.93947,-0.2971,0.17069,150.77,-0.30123,0.47875,-0.82466,38.244,0.16329,-0.82616,-0.53926,163.41
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.93947,-0.2971,0.17069,153.62,-0.30123,0.47875,-0.82466,37.767,0.16329,-0.82616,-0.53926,163.54
> view matrix models
> #5,-0.93947,-0.2971,0.17069,153.41,-0.30123,0.47875,-0.82466,37.798,0.16329,-0.82616,-0.53926,163.4
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.75321,-0.43799,0.49076,184.65,-0.6541,0.41994,-0.62912,53.287,0.06946,-0.79487,-0.6028,156.76
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.75321,-0.43799,0.49076,182.6,-0.6541,0.41994,-0.62912,53.47,0.06946,-0.79487,-0.6028,157.17
> view matrix models
> #5,-0.75321,-0.43799,0.49076,182.37,-0.6541,0.41994,-0.62912,53.434,0.06946,-0.79487,-0.6028,156.59
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.76502,-0.42115,0.48721,180.89,-0.63998,0.41275,-0.64812,52.786,0.07186,-0.80763,-0.58529,158.64
> view matrix models
> #5,-0.75137,-0.46563,0.46758,182.88,-0.6458,0.37329,-0.66603,54.458,0.13558,-0.8024,-0.58119,158.75
> view matrix models
> #5,-0.6454,-0.49723,0.57984,192.7,-0.75132,0.27636,-0.59928,65.323,0.13774,-0.82243,-0.55195,162.06
> view matrix models
> #5,-0.64032,-0.52763,0.55821,193.52,-0.74122,0.23384,-0.62922,66.501,0.20146,-0.81665,-0.54082,162.58
> view matrix models
> #5,-0.6667,-0.43985,0.6017,189.9,-0.74097,0.47837,-0.47131,59.016,-0.080525,-0.76006,-0.64484,150.88
> view matrix models
> #5,-0.94889,-0.17845,0.26031,148.29,-0.31514,0.58035,-0.75092,35.306,-0.017063,-0.79458,-0.60693,156
> view matrix models
> #5,-0.9498,-0.24778,0.19102,148.85,-0.29762,0.5273,-0.79585,36.309,0.096469,-0.81275,-0.57457,159.78
> view matrix models
> #5,-0.9275,-0.29012,0.23573,154.83,-0.36048,0.52723,-0.76947,37.78,0.098958,-0.79866,-0.59359,157.56
> view matrix models
> #5,-0.89858,-0.30202,0.31833,161.06,-0.4181,0.36907,-0.83005,45.075,0.13321,-0.87896,-0.45791,172.12
> view matrix models
> #5,-0.92744,-0.31576,0.20036,154.41,-0.32706,0.42511,-0.84399,40.475,0.18132,-0.84828,-0.49754,167.55
> view matrix models
> #5,-0.93536,-0.34108,0.093566,149.37,-0.25659,0.47235,-0.84324,37.374,0.24342,-0.81274,-0.52934,163.18
> view matrix models
> #5,-0.94316,-0.33178,0.019128,143.92,-0.19811,0.51511,-0.83391,35.101,0.26682,-0.7903,-0.55157,160.23
> view matrix models
> #5,-0.91183,-0.3652,0.18758,157.2,-0.34633,0.43884,-0.82914,40.369,0.22049,-0.821,-0.52663,163.87
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.91183,-0.3652,0.18758,159.32,-0.34633,0.43884,-0.82914,40.863,0.22049,-0.821,-0.52663,164.29
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.91183,-0.3652,0.18758,159.17,-0.34633,0.43884,-0.82914,40.707,0.22049,-0.821,-0.52663,164.81
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.92898,-0.29279,0.22644,156.38,-0.34908,0.48959,-0.79903,38.974,0.12308,-0.82132,-0.55703,162.55
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.92898,-0.29279,0.22644,155.54,-0.34908,0.48959,-0.79903,38.109,0.12308,-0.82132,-0.55703,157.37
> view matrix models
> #5,-0.92898,-0.29279,0.22644,154.31,-0.34908,0.48959,-0.79903,37.249,0.12308,-0.82132,-0.55703,158.8
> view matrix models
> #5,-0.92898,-0.29279,0.22644,155.23,-0.34908,0.48959,-0.79903,38.945,0.12308,-0.82132,-0.55703,162.46
> view matrix models
> #5,-0.92898,-0.29279,0.22644,155.04,-0.34908,0.48959,-0.79903,38.854,0.12308,-0.82132,-0.55703,162.61
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.91026,-0.31072,0.27365,159.41,-0.39718,0.46862,-0.78908,40.829,0.11694,-0.82695,-0.54998,163.44
> view matrix models
> #5,-0.89017,-0.39404,0.22877,162.6,-0.40334,0.44791,-0.79793,41.73,0.21194,-0.80256,-0.55765,161.53
> view matrix models
> #5,-0.89792,-0.3535,0.26226,161.8,-0.41598,0.48674,-0.76815,40.799,0.14389,-0.79883,-0.5841,159.33
> view matrix models
> #5,-0.83175,-0.41731,0.36612,173.26,-0.53401,0.4212,-0.73309,47.337,0.15171,-0.80526,-0.57318,160.52
> view matrix models
> #5,-0.81669,-0.47018,0.33459,175.1,-0.53079,0.38449,-0.75527,48.57,0.22646,-0.79442,-0.56357,160.62
> ~select #5
Nothing selected
> hide #!2 models
> show #!2 models
> select #6
1415 atoms, 1433 bonds, 91 residues, 1 model selected
> view matrix models
> #6,-0.37456,-0.019103,-0.92701,134.87,0.77935,0.53515,-0.32592,123.09,0.50231,-0.84454,-0.18555,100.13
> ~select #6
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!5 models
> hide #6 models
> hide #!2 models
> show #!5 models
> show #6 models
> show #!2 models
> hide #!2 models
> select #5
1094 atoms, 1131 bonds, 2 pseudobonds, 134 residues, 2 models selected
> ui tool show "Color Actions"
> color sel cornflower blue
> select clear
> matchmaker #6 to #6/I:26-45
No 'to' model specified
> select #5/I:26-45
143 atoms, 143 bonds, 20 residues, 1 model selected
> color sel cyan
> select #5/I:102-121
181 atoms, 189 bonds, 20 residues, 1 model selected
> color sel lime
> select clear
> select #5/I:176-194
159 atoms, 164 bonds, 19 residues, 1 model selected
> color sel magenta
> select clear
> save "/Users/rjk/MANUSCRIPTS/NRMCB review/Oxa1_superfamily.cxs"
> show #!2 models
> hide #!5 models
> hide #6 models
> hide #!2 models
> show #!1 models
> show #!2 models
> matchmaker #1 to #2/F
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 6ww7.cif, chain F (#2) with 6so5.cif, chain C (#1), sequence
alignment score = 88
RMSD between 30 pruned atom pairs is 0.604 angstroms; (across all 82 pairs:
32.805)
> hide #!2 models
> show #!2 models
> matchmaker #1 to #2/C
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 6ww7.cif, chain C (#2) with 6so5.cif, chain A (#1), sequence
alignment score = 81.1
RMSD between 14 pruned atom pairs is 1.171 angstroms; (across all 126 pairs:
56.892)
> matchmaker #1/C to #2/C
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 6ww7.cif, chain C (#2) with 6so5.cif, chain C (#1), sequence
alignment score = 72.6
RMSD between 13 pruned atom pairs is 1.152 angstroms; (across all 121 pairs:
11.169)
> hide #!2 models
> show #!5 models
> show #6 models
> show #!2 models
> save "/Users/rjk/MANUSCRIPTS/NRMCB review/Oxa1_superfamily.cxs"
> hide #!1 models
> show #!1 models
> hide #6 models
> show #6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #6 models
> show #!5 models
> hide #!2 models
> matchmaker #5 to #1/C
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 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 91.1
RMSD between 21 pruned atom pairs is 0.583 angstroms; (across all 81 pairs:
29.127)
> hide #!5 models
> show #!5 models
> matchmaker #5 to #1/C
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 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 91.1
RMSD between 21 pruned atom pairs is 0.583 angstroms; (across all 81 pairs:
29.127)
> hide #!5 models
> show #!5 models
> matchmaker #5 to #1/C:107-171
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 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 45.8
RMSD between 6 pruned atom pairs is 1.133 angstroms; (across all 35 pairs:
11.902)
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> hide #!5 models
> show #!1 models
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> show #!1 models
> matchmaker #5:121-194 to #1/C:107-171
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 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 37.2
RMSD between 15 pruned atom pairs is 1.004 angstroms; (across all 36 pairs:
5.310)
> hide #!1 models
> show #!1 models
> hide #!5 models
> hide #!1 models
> show #!5 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> hide #!1 models
> show #!5 models
> show #!1 models
> hide #!1 models
> show #!1 models
> matchmaker #5/I:121-194 to #1/C:107-171
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 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 37.2
RMSD between 15 pruned atom pairs is 1.004 angstroms; (across all 36 pairs:
5.310)
> matchmaker #5/I:121-194 to #1/C:107-171
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 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 37.2
RMSD between 15 pruned atom pairs is 1.004 angstroms; (across all 36 pairs:
5.310)
> hide #!5 models
> hide #!1 models
> show #!5 models
> hide #!5 models
> show #!1 models
> matchmaker #5/I to #1/C
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 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 91.1
RMSD between 21 pruned atom pairs is 0.583 angstroms; (across all 81 pairs:
29.127)
> show #!5 models
> matchmaker #5/I:121-194 to #1/C:107-171
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 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 37.2
RMSD between 15 pruned atom pairs is 1.004 angstroms; (across all 36 pairs:
5.310)
> matchmaker #5/I:121-194 to #1/C:107-171 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 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 37.2
RMSD between 15 pruned atom pairs is 1.004 angstroms; (across all 36 pairs:
5.310)
> matchmaker #5/I:121-194 to #1/C:107-171
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 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 37.2
RMSD between 15 pruned atom pairs is 1.004 angstroms; (across all 36 pairs:
5.310)
> matchmaker #5/I:121-194 to #1/C:107-171 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 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 37.2
RMSD between 15 pruned atom pairs is 1.004 angstroms; (across all 36 pairs:
5.310)
> matchmaker #5/I:121-194 to #1/C:107-171 pairing ss matHH 6
Expected a keyword
> matchmaker #5/I:121-194 to #1/C:107-171 pairing ss matHH helix-helix-score 6
Expected a keyword
> matchmaker #5/I:121-194 to #1/C:107-171 matHH helix-helix-score 6
Expected a keyword
> matchmaker #5/I:121-194 to #1/C:107-171 matHH 6
Expected a keyword
> matchmaker #5/I:121-194 to #1/C:107-171 matHH 10
Expected a keyword
> matchmaker #5/I:121-194 to #1/C:107-171 scoring matHH 10
Expected a keyword
> matchmaker #5/I:121-194 to #1/C:107-171 scoring-options matHH 10
Expected a keyword
> matchmaker #5/I:121-194 to #1/C:107-171 scoring-options 10
Expected a keyword
> ui tool show Matchmaker
> hide #!5 models
> show #!5 models
> matchmaker #!5 to #1/C pairing bs ssFraction 0.754 matHh 10.0
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.754
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 10 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 571.006
RMSD between 4 pruned atom pairs is 1.241 angstroms; (across all 108 pairs:
24.171)
> matchmaker #!5 to #1/C pairing bs ssFraction 0.754 matHh 10.0 matHs 0.0
> matSs 0.0 matHo 0.0 matSo 0.0 matOo 0.0
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.754
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 10 | 0 | 0
S | | 0 | 0
O | | | 0
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 632.952
RMSD between 11 pruned atom pairs is 1.012 angstroms; (across all 121 pairs:
32.283)
> matchmaker #!5 to #1/C pairing bs ssFraction 1.0 matHh 10.0 matHs 0.0 matSs
> 0.0 matHo 0.0 matSo 0.0 matOo 0.0
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 1
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 10 | 0 | 0
S | | 0 | 0
O | | | 0
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 878
RMSD between 16 pruned atom pairs is 0.638 angstroms; (across all 121 pairs:
28.618)
> matchmaker #!5 to #1/C pairing bs ssFraction 0.0 matHh 10.0 matHs 0.0 matSs
> 0.0 matHo 0.0 matSo 0.0 matOo 0.0
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 10 | 0 | 0
S | | 0 | 0
O | | | 0
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 25
RMSD between 17 pruned atom pairs is 1.158 angstroms; (across all 22 pairs:
3.324)
> matchmaker #!5 to #1/C pairing bs ssFraction 0.1764 matHh 10.0 matHs 0.0
> matSs 0.0 matHo 0.0 matSo 0.0 matOo 0.0
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.1764
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 10 | 0 | 0
S | | 0 | 0
O | | | 0
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 110.78
RMSD between 21 pruned atom pairs is 0.583 angstroms; (across all 81 pairs:
29.044)
> matchmaker #!5 to #1/C pairing bs ssFraction 0.0588 matHh 10.0 matHs 0.0
> matSs 0.0 matHo 0.0 matSo 0.0 matOo 0.0
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.0588
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 10 | 0 | 0
S | | 0 | 0
O | | | 0
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 39.1624
RMSD between 21 pruned atom pairs is 0.583 angstroms; (across all 81 pairs:
29.044)
> matchmaker #!5 to #1/C pairing bs ssFraction 0.0 matHh 10.0 matHs 0.0 matSs
> 0.0 matHo 0.0 matSo 0.0 matOo 0.0
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 10 | 0 | 0
S | | 0 | 0
O | | | 0
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 25
RMSD between 17 pruned atom pairs is 1.158 angstroms; (across all 22 pairs:
3.324)
> matchmaker #!5 to #1/C pairing bs ssFraction 0.0374 matHh 10.0 matHs 0.0
> matSs 0.0 matHo 0.0 matSo 0.0 matOo 0.0
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.0374
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 10 | 0 | 0
S | | 0 | 0
O | | | 0
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 30.423
RMSD between 17 pruned atom pairs is 1.158 angstroms; (across all 22 pairs:
3.324)
> matchmaker #!5 to #1/C pairing bs ssFraction 0.0374 matHh 2.0 matHs 0.0
> matSs 0.0 matHo 0.0 matSo 0.0 matOo 0.0
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.0374
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 2 | 0 | 0
S | | 0 | 0
O | | | 0
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 25.3366
RMSD between 17 pruned atom pairs is 1.158 angstroms; (across all 22 pairs:
3.324)
> matchmaker #!5 to #1/C pairing bs ssFraction 0.1336 matHh 2.0 matHs 0.0
> matSs 0.0 matHo 0.0 matSo 0.0 matOo 0.0
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.1336
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 2 | 0 | 0
S | | 0 | 0
O | | | 0
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 26.2024
RMSD between 17 pruned atom pairs is 1.158 angstroms; (across all 22 pairs:
3.324)
> matchmaker #!5 to #1/C pairing bs ssFraction 0.353 matHh 2.0 matHs 0.0 matSs
> 0.0 matHo 0.0 matSo 0.0 matOo 0.0
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.353
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 2 | 0 | 0
S | | 0 | 0
O | | | 0
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 32.476
RMSD between 21 pruned atom pairs is 0.583 angstroms; (across all 81 pairs:
28.921)
> matchmaker #!5 to #1/C pairing bs ssFraction 0.2032 matHh 2.0 matHs 0.0
> matSs 0.0 matHo 0.0 matSo 0.0 matOo 0.0
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.2032
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 2 | 0 | 0
S | | 0 | 0
O | | | 0
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 26.8288
RMSD between 17 pruned atom pairs is 1.158 angstroms; (across all 22 pairs:
3.324)
> matchmaker #!5 to #1/C pairing bs ssFraction 0.2032 keepComputedSs true
> matHh 2.0 matHs 0.0 matSs 0.0 matHo 0.0 matSo 0.0 matOo 0.0
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.2032
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 2 | 0 | 0
S | | 0 | 0
O | | | 0
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 26.8288
RMSD between 17 pruned atom pairs is 1.158 angstroms; (across all 22 pairs:
3.324)
> matchmaker #!5 to #1/C pairing bs ssFraction 0.2032 keepComputedSs true
> matHh 2.0 matHs 0.0 matSs 0.0 matHo 0.0 matSo 0.0 matOo 0.0
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.2032
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 2 | 0 | 0
S | | 0 | 0
O | | | 0
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 26.8288
RMSD between 17 pruned atom pairs is 1.158 angstroms; (across all 22 pairs:
3.324)
> matchmaker #!5 to #1/C pairing bs ssFraction 0.2032 keepComputedSs true
> matHh 2.0 matHs 0.0 matSs 0.0 matHo 0.0 matSo 0.0 matOo 0.0
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.2032
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 2 | 0 | 0
S | | 0 | 0
O | | | 0
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 26.8288
RMSD between 17 pruned atom pairs is 1.158 angstroms; (across all 22 pairs:
3.324)
> matchmaker #!5 to #1/C pairing bs ssFraction 0.2032 keepComputedSs true
> matHh 2.0 matHs 0.0 matSs 0.0 matHo 0.0 matSo 0.0 matOo 0.0
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.2032
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 2 | 0 | 0
S | | 0 | 0
O | | | 0
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 26.8288
RMSD between 17 pruned atom pairs is 1.158 angstroms; (across all 22 pairs:
3.324)
> matchmaker #!5 to #1/C pairing bs ssFraction 0.2032 keepComputedSs true
> matHh 2.0 matHs 0.0 matSs 0.0 matHo 0.0 matSo 0.0 matOo 0.0
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.2032
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 2 | 0 | 0
S | | 0 | 0
O | | | 0
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 26.8288
RMSD between 17 pruned atom pairs is 1.158 angstroms; (across all 22 pairs:
3.324)
> matchmaker #!5 to #1/C pairing bs ssFraction 0.2032 matHh 2.0 matHs 0.0
> matSs 0.0 matHo 0.0 matSo 0.0 matOo 0.0
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.2032
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 2 | 0 | 0
S | | 0 | 0
O | | | 0
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 26.8288
RMSD between 17 pruned atom pairs is 1.158 angstroms; (across all 22 pairs:
3.324)
> matchmaker #!5 to #1/C pairing bs
Parameters
---
Chain pairing | bs
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 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 91.1
RMSD between 21 pruned atom pairs is 0.583 angstroms; (across all 81 pairs:
29.127)
> matchmaker #!5 to #1/C pairing bs matHh 25.0
Parameters
---
Chain pairing | bs
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 | 25 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 574.1
RMSD between 11 pruned atom pairs is 0.685 angstroms; (across all 109 pairs:
31.919)
> matchmaker #!5 to #1/C pairing bs matHh 100.0
Parameters
---
Chain pairing | bs
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 | 100 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 2635.8
RMSD between 7 pruned atom pairs is 1.451 angstroms; (across all 109 pairs:
31.796)
> matchmaker #!5 to #1/C pairing bs matHh 10.0
Parameters
---
Chain pairing | bs
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 | 10 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 170.3
RMSD between 21 pruned atom pairs is 0.583 angstroms; (across all 81 pairs:
29.127)
> matchmaker #!5 to #1/C pairing bs matHh 1.0
Parameters
---
Chain pairing | bs
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 | 1 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 16.6
RMSD between 17 pruned atom pairs is 1.158 angstroms; (across all 22 pairs:
3.324)
> matchmaker #!5 to #1/C pairing bs matHh 2.0
Parameters
---
Chain pairing | bs
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 | 2 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 21.7
RMSD between 17 pruned atom pairs is 1.158 angstroms; (across all 22 pairs:
3.324)
> matchmaker #!5 to #1/C pairing bs cutoffDistance 3.0 matHh 2.0
Parameters
---
Chain pairing | bs
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 | 2 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 3
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 21.7
RMSD between 19 pruned atom pairs is 1.369 angstroms; (across all 22 pairs:
3.235)
> matchmaker #!5 to #1/C pairing bs cutoffDistance 5.0 matHh 2.0
Parameters
---
Chain pairing | bs
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 | 2 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 5
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 21.7
RMSD between 20 pruned atom pairs is 1.388 angstroms; (across all 22 pairs:
3.319)
> matchmaker #!5 to #1/C pairing bs cutoffDistance 5.0
Parameters
---
Chain pairing | bs
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 | 5
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 91.1
RMSD between 23 pruned atom pairs is 1.474 angstroms; (across all 81 pairs:
28.901)
> matchmaker #5/I to #1/C pairing ss cutoffDistance 5.0
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 | 5
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 91.1
RMSD between 23 pruned atom pairs is 1.474 angstroms; (across all 81 pairs:
28.901)
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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 #!5 to #1 cutoffDistance 5.0
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 | 5
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 91.1
RMSD between 23 pruned atom pairs is 1.474 angstroms; (across all 81 pairs:
28.901)
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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 #!5 to #1/C pairing bs cutoffDistance 5.0
Parameters
---
Chain pairing | bs
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 | 5
Matchmaker 6so5.cif, chain C (#1) with Mj0480compact.pdb, chain I (#5),
sequence alignment score = 91.1
RMSD between 23 pruned atom pairs is 1.474 angstroms; (across all 81 pairs:
28.901)
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> ui tool show Matchmaker
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and setattr(pself, "value", pself.get_attribute()))
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 277, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 277, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and setattr(pself, "value", pself.get_attribute()))
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 277, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 277, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
OpenGL version: 4.1 ATI-4.2.15
OpenGL renderer: AMD Radeon Pro 460 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro13,3
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.9 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 429.80.1.0.0
SMC Version (system): 2.38f12
Software:
System Software Overview:
System Version: macOS 11.2.3 (20D91)
Kernel Version: Darwin 20.3.0
Time since boot: 10 days 9:41
Graphics/Displays:
Radeon Pro 460:
Chipset Model: AMD Radeon Pro 460
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00c0
ROM Revision: 113-C980AF-908
VBIOS Version: 113-C9801AU-029
EFI Driver Version: 01.A0.908
Automatic Graphics Switching: Supported
gMux Version: 4.0.29 [3.2.8]
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Intel HD Graphics 530:
Chipset Model: Intel HD Graphics 530
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x191b
Revision ID: 0x0006
Automatic Graphics Switching: Supported
gMux Version: 4.0.29 [3.2.8]
Metal Family: Supported, Metal GPUFamily macOS 2
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.4.1
chardet: 3.0.4
ChimeraX-AddCharge: 1.0
ChimeraX-AddH: 2.1.4
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.11.1
ChimeraX-AtomicLibrary: 2.0
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.dev202102240806
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.1
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: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
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: 2.2
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: 1.0.1
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: 1.5
ChimeraX-PDB: 2.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
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: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.6.1
ChimeraX-uniprot: 2.1
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: 0.29.21
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 1.1.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.2
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.16
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
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: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.2.0
Change History (2)
comment:1 by , 5 years ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → wrapped C/C++ object of type ChainMenuButton has been deleted |
comment:2 by , 5 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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It looks like somehow the MatchMaker UI stayed up after the Qt side was dead. Not only was ChainMenuButton getting callbacks, but the ChainPairingButton radio button was clickable.