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Opened 5 years ago
Closed 5 years ago
#3511 closed defect (duplicate)
tape-measure mouse mode using dead MarkerSet
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-3.10.0-957.12.2.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/coot_files/NEW/finalView2.cxs
> format session
Log from Tue Jul 14 14:26:04 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/coot_files/NEW/sideview2.cxs
> format session
Log from Mon Jul 13 14:22:23 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/coot_files/session_globalsideView2.cxs
> format session
Log from Mon Jul 13 11:29:47 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/coot_files/new.cxs format
> session
Log from Fri Jul 10 13:59:48 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Some installed bundles are out of date. Please update the following bundles:
* UI to version 1.2.1 (currently 1.0)
* UI to version 1.2 (currently 1.0)
> open /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/test.mrc format mrc
Opened test.mrc, grid size 420,420,420, pixel 3.45, shown at level 0.0102,
step 2, values float32
> set bgColor white
> open /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/coot_files/ring9.pdb
> /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/coot_files/ring8.pdb
> /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/coot_files/ring2.pdb
> /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/coot_files/ring3.pdb
> /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/coot_files/ring4.pdb
> /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/coot_files/ring5.pdb
> /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/coot_files/ring6.pdb
> /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/coot_files/ring7.pdb
> /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/coot_files/newRing.pdb
Chain information for ring9.pdb #2
---
Chain | Description
A B C H I J M N O P U V Y Z a b g h | No description available
D E F G K L Q R S T W X c d e f i j | No description available
Chain information for ring8.pdb #3
---
Chain | Description
A B C H I J M N O P U V Y Z a b g h | No description available
D E F G K L Q R S T W X c d e f i j | No description available
Chain information for ring2.pdb #4
---
Chain | Description
A B C H I J M N O P U V Y Z a b g h | No description available
D E F G K L Q R S T W X c d e f i j | No description available
Chain information for ring3.pdb #5
---
Chain | Description
A B C H I J M N O P U V Y Z a b g h | No description available
D E F G K L Q R S T W X c d e f i j | No description available
Chain information for ring4.pdb #6
---
Chain | Description
A B C H I J M N O P U V Y Z a b g h | No description available
D E F G K L Q R S T W X c d e f i j | No description available
Chain information for ring5.pdb #7
---
Chain | Description
A B C H I J M N O P U V Y Z a b g h | No description available
D E F G K L Q R S T W X c d e f i j | No description available
Chain information for ring6.pdb #8
---
Chain | Description
A B C H I J M N O P U V Y Z a b g h | No description available
D E F G K L Q R S T W X c d e f i j | No description available
Chain information for ring7.pdb #9
---
Chain | Description
A B C H I J M N O P U V Y Z a b g h | No description available
D E F G K L Q R S T W X c d e f i j | No description available
Chain information for newRing.pdb #10
---
Chain | Description
A B C H I J M N O P U V Y Z a b g h | No description available
D E F G K L Q R S T W X c d e f i j | No description available
> volume #1 color #d3d7cf80
> hide atoms
> show cartoons
> lighting soft
> lighting full
> volume #1 color #1e90ff33
> volume #1 color #ffffff33
> volume #1 color #d3d7cf80
> volume #1 color #1e90ff33
> volume #1 color #729fcf
> lighting flat
> volume #1 color #1e90ff33
> volume #1 level 0.009732
> color red #8
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #8 red
> color #7 magenta
> color #7 orange
> color #7 orangered
> color #6 yellow
> hide #10 models
> show #10 models
> color #10 green
> hide #10 models
> show #10 models
> hide #9 models
> show #9 models
> color #9 magenta
> hide #4 models
> show #4 models
> color #4 purple
> color #4 darkred purple
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #4 darkpurple
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> hide #5 models
> show #5 models
> color #5 navy blue
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #5 dark blue
> hide #3 models
> show #3 models
> color #3 blue
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #7 models
> show #7 models
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting flat
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes width 1 depthJump 0.02
> graphics silhouettes width 1 depthJump 0.05
> graphics silhouettes width 1 depthJump 0.08
> graphics silhouettes width 0.5 depthJump 0.05
> graphics silhouettes width 0.8 depthJump 0.05
> graphics silhouettes width 0.8 depthJump 0.02
> graphics silhouettes width 1 depthJump 0.02
> graphics silhouettes width 2 depthJump 0.02
> graphics silhouettes width 0.5 depthJump 0.02
> graphics silhouettes width 0.9 depthJump 0.02
> graphics silhouettes width 1 depthJump 0.1
> graphics silhouettes width 1 depthJump 0.5
> graphics silhouettes width 1 depthJump 0.1
> graphics silhouettes width 1 depthJump 0.05
> graphics silhouettes width 1 depthJump 0.1
> graphics silhouettes width 0.1 depthJump 0.1
> graphics silhouettes width 0.5 depthJump 0.1
> graphics silhouettes width 0.5
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes width 0.8
> graphics silhouettes width 0.1 depthJump 0.1
> graphics silhouettes width 1 depthJump 0.1
> graphics silhouettes true
> graphics silhouettes width 1 depthJump 0.1
> graphics silhouettes width 1 depthJump 0.5
> volume #1 level 0.009118
> lighting soft
> lighting simple
> lighting soft
> lighting flat
> lighting full
> lighting soft
> lighting flat
> graphics silhouettes width 1 depthJump 0.5
> hidedust
Unknown command: hidedust
> hide dust
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide dust #1
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> surface dust #1
> surface dust #1
> surface dust #1 size 10
> surface dust #1 size 20
> surface dust #1 size 50
> volume #1 level 0.008196
> surface dust #1 size 80
> save FarViewNew1.png supersample 4 transparentBackground true
> save /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/coot_files/new.cxs
opened ChimeraX session
> color magenta #2,3,4,5,6,7,8,9,10
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #2,3,4,5,6,7,8,9,10 magenta
> hide #3 models
> show #3 models
> hide #2 models
> show #2 models
> hide #4 models
> show #4 models
> hide #10 models
> show #10 models
> surface dust #1 size 220
> dssp #10
> ui tool show "Side View"
> surface dust #1 size 220
> volume #1 level 0.008091
> hide #!1 models
> select #10.E
Expected an objects specifier or a keyword
> select #10,E
Expected an objects specifier or a keyword
> select #10:.E
Expected an objects specifier or a keyword
> select #10/E
704 atoms, 703 bonds, 1 model selected
> select #10/E/J/b/G
2824 atoms, 2820 bonds, 1 model selected
> select #10/E/J/B/G
2824 atoms, 2820 bonds, 1 model selected
> select clear
> color dark goldenrod #10/E/J/B/G
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color darkgoldenrod #10/E/J/B/G
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color goldenrod #10/E/J/B/G
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color gold #10/E/J/B/G
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #10/E/J/B/G dark goldenrod
> show #!1 models
> save FarViewNew7.png supersample 4 transparentBackground true
> save
> /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/coot_files/session_globalsideView2.cxs
opened ChimeraX session
> hide #2 models
> show #2 models
> hide #3 models
> hide #9 models
> hide #8 models
> hide #7 models
> hide #6 models
> show #6 models
> hide #5 models
> hide #4 models
> select down
Nothing selected
> color #10,2,6 purple
> color #10/E/J/B/G dark goldenrod
> hide #2 models
> show #2 models
> color #2 yellow
> hide #!1 models
> color #2/B/G navy blue
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #2/B/G navyblue
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #2/B/G dark blue
> color #2/B/G/I/L dark blue
> select down
Nothing selected
> color #2/B/G/I/L/D/P/X/T dark blue
> color #2/B/G/I/L/D/P/X/T/O/C/ dark blue
> color #2/B/G/I/L/D/P/X/T/O/C/V/j/b dark blue
> color #2/B/G/I/L/D/P/X/T/O/C/V/j/b/R dark blue
> color #2/B/G/I/L/D/P/X/T/O/C/V/j/b/R/a/d/h dark blue
> color #2/B/G/I/L/D/P/X/T/O/C/V/j/b/R/a/d/h/f dark blue
> color #2,6,10 orangered
> color #2/B/G/I/L/D/P/X/T/O/C/V/j/b/R/a/d/h/f dark blue
> color #2,6,10/B/G/I/L/D/P/X/T/O/C/V/j/b/R/a/d/h/f dark blue
> show #!1 models
> ui tool show "Side View"
> transparency #1 90
> volume #1 level 0.005569
> surface dust #1 size 220
> save
> /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/coot_files/NEW/sideview1.cxs
> fitmap #6 #1 r 30
Expected keyword "radius", "resolution", or "rotate"
> fitmap #6 #1
Missing required "in_map" argument
> fitmap #6 inMap #1
Fit molecule ring4.pdb (#6) to map test.mrc (#1) using 25416 atoms
average map value = 0.01672, steps = 28
shifted from previous position = 0.0678
rotated from previous position = 0.00315 degrees
atoms outside contour = 413, contour level = 0.0055693
Position of ring4.pdb (#6) relative to test.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 0.00005110 -0.00000126 -0.01788670
-0.00005110 1.00000000 -0.00002013 0.00009124
0.00000126 0.00002013 1.00000000 0.06377730
Axis 0.36639345 -0.02295496 -0.93017681
Axis point -27.80608462 -122.33844520 0.00000000
Rotation angle (degrees) 0.00314748
Shift along axis -0.06587983
> fitmap #2 inMap #1
Fit molecule ring9.pdb (#2) to map test.mrc (#1) using 25416 atoms
average map value = 0.01942, steps = 24
shifted from previous position = 0.00997
rotated from previous position = 0.00589 degrees
atoms outside contour = 260, contour level = 0.0055693
Position of ring9.pdb (#2) relative to test.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 0.00005867 0.00000781 0.00627377
-0.00005867 0.99999999 0.00008398 0.00021089
-0.00000781 -0.00008398 1.00000000 0.00774392
Axis -0.81737949 0.07600063 -0.57106451
Axis point 0.00000000 27.37805327 -11.13766513
Rotation angle (degrees) 0.00588684
Shift along axis -0.00953430
> fitmap #10 inMap #1
Fit molecule newRing.pdb (#10) to map test.mrc (#1) using 25416 atoms
average map value = 0.01867, steps = 48
shifted from previous position = 0.648
rotated from previous position = 0.221 degrees
atoms outside contour = 30, contour level = 0.0055693
Position of newRing.pdb (#10) relative to test.mrc (#1) coordinates:
Matrix rotation and translation
0.99999352 -0.00240652 0.00267616 0.16822988
0.00240286 0.99999617 0.00137195 -0.64804922
-0.00267945 -0.00136551 0.99999548 0.09835041
Axis -0.35546459 0.69543781 0.62450875
Axis point 141.37346698 0.00000000 -2.87366559
Rotation angle (degrees) 0.22061985
Shift along axis -0.44905700
> volume #1 step 1
> save
> /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/coot_files/NEW/sideview1.cxs
> vop gaussian #1 sdev 10.4
> volume #11 color #49788633
> volume #11 level 0.005221
> close #11
> save FarViewNew8.png supersample 4 transparentBackground true
> hide #!1 models
> hide #2 models
> hide #6 models
> lighting full
> lighting shadows false
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> save
> /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/coot_files/NEW/sideview2.cxs
> graphics silhouettes width 1 depthJump 0.15
> graphics silhouettes width 1 depthJump 0.5
> save
> /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/coot_files/NEW/sideview2.cxs
opened ChimeraX session
> open /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/4p5.pdb
Summary of feedback from opening
/data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/4p5.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
43880 messages similar to the above omitted
Ignored bad PDB record found on line 105355
END
Chain information for 4p5.pdb #11
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> mmaker #11/E to #10/X
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 newRing.pdb, chain X (#10) with 4p5.pdb, chain E (#11), sequence
alignment score = 890.7
RMSD between 158 pruned atom pairs is 0.437 angstroms; (across all 176 pairs:
19.685)
> select #11
52662 atoms, 53706 bonds, 1 model selected
> show sel cartoons
> hide sel atoms
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> select clear
> color #11 green
> show #!1 models
> ui tool show "Side View"
> open "/run/media/yashar/My Passport/Fitting/4p5.pdb"
Summary of feedback from opening /run/media/yashar/My Passport/Fitting/4p5.pdb
---
warning | Ignored bad PDB record found on line 105427
END
Chain information for 4p5.pdb
---
Chain | Description
12.1/A 12.2/A 12.3/A 12.4/A 12.5/A 12.6/A | No description available
12.1/B 12.2/B 12.3/B 12.4/B 12.5/B 12.6/B | No description available
12.1/C 12.2/C 12.3/C 12.4/C 12.5/C 12.6/C | No description available
12.1/D 12.2/D 12.3/D 12.4/D 12.5/D 12.6/D | No description available
12.1/E 12.2/E 12.3/E 12.4/E 12.5/E 12.6/E | No description available
12.1/F 12.2/F 12.3/F 12.4/F 12.5/F 12.6/F | No description available
> select #12
52662 atoms, 53706 bonds, 7 models selected
> show sel cartoons
> hide sel atoms
> color #12 red
> ui mousemode right "translate selected models"
> select clear
> select #12
52662 atoms, 53706 bonds, 7 models selected
> ui mousemode right "rotate selected models"
> select clear
> volume #1 step 2
> select #12
52662 atoms, 53706 bonds, 7 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> select clear
> select #12.1
8777 atoms, 8951 bonds, 1 model selected
> ui mousemode right "translate selected models"
> mmaker #12.1 to #10
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 newRing.pdb, chain A (#10) with 4p5.pdb, chain B (#12.1), sequence
alignment score = 908.5
RMSD between 177 pruned atom pairs is 0.001 angstroms; (across all 177 pairs:
0.001)
> hide #11 models
> hide #!1 models
> color #12 green
> hide #10 models
> hide #12.6 models
> show #12.6 models
> hide #12.5 models
> show #12.5 models
> show #10 models
> mmaker #12.1 to #10/G
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 newRing.pdb, chain G (#10) with 4p5.pdb, chain A (#12.1), sequence
alignment score = 903.8
RMSD between 176 pruned atom pairs is 0.001 angstroms; (across all 176 pairs:
0.001)
> mmaker #12.1/C to #10/G
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 newRing.pdb, chain G (#10) with 4p5.pdb, chain C (#12.1), sequence
alignment score = 897.2
RMSD between 162 pruned atom pairs is 0.532 angstroms; (across all 176 pairs:
1.182)
> mmaker #12.4/C to #10/J
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 newRing.pdb, chain J (#10) with 4p5.pdb, chain C (#12.4), sequence
alignment score = 905.5
RMSD between 168 pruned atom pairs is 0.527 angstroms; (across all 177 pairs:
0.909)
> close #11
> close #12
> open "/run/media/yashar/My Passport/Fitting/4p5.pdb"
Summary of feedback from opening /run/media/yashar/My Passport/Fitting/4p5.pdb
---
warning | Ignored bad PDB record found on line 105427
END
Chain information for 4p5.pdb
---
Chain | Description
11.1/A 11.2/A 11.3/A 11.4/A 11.5/A 11.6/A | No description available
11.1/B 11.2/B 11.3/B 11.4/B 11.5/B 11.6/B | No description available
11.1/C 11.2/C 11.3/C 11.4/C 11.5/C 11.6/C | No description available
11.1/D 11.2/D 11.3/D 11.4/D 11.5/D 11.6/D | No description available
11.1/E 11.2/E 11.3/E 11.4/E 11.5/E 11.6/E | No description available
11.1/F 11.2/F 11.3/F 11.4/F 11.5/F 11.6/F | No description available
> color #11 green$
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #11 green
> show #10#11.1-6 cartoons
> hide #10#11.1-6 atoms
> select #11
52662 atoms, 53706 bonds, 7 models selected
> ui mousemode right "translate selected models"
> select clear
> select #11
52662 atoms, 53706 bonds, 7 models selected
> select clear
> select #11
52662 atoms, 53706 bonds, 7 models selected
> ui mousemode right "rotate selected models"
> select clear
> show #!1 models
> hide #10 models
> hide #11.4 models
> show #11.4 models
> hide #11.2 models
> show #11.2 models
> hide #11.5 models
> show #11.5 models
> select #11.2.5
Nothing selected
> select #11.2,11.5
Nothing selected
> select #11.2, 11.5
Nothing selected
> select #11.2 #11.5
17554 atoms, 17902 bonds, 2 models selected
> fitmap #11.2 #11.5 inMap #1
Fit molecules 4p5.pdb (#11.2), 4p5.pdb (#11.5) to map test.mrc (#1) using
17554 atoms
average map value = 0.01713, steps = 84
shifted from previous position = 11.8
rotated from previous position = 1.44 degrees
atoms outside contour = 660, contour level = 0.0055693
Position of 4p5.pdb (#11.2) relative to test.mrc (#1) coordinates:
Matrix rotation and translation
0.99973140 -0.02257549 0.00524085 8.87326208
0.02262486 0.99969831 -0.00956047 6.47019928
-0.00502343 0.00967647 0.99994056 -3.85681502
Axis 0.38332409 0.20453085 0.90068295
Axis point -269.66837685 375.01672335 0.00000000
Rotation angle (degrees) 1.43783158
Shift along axis 1.25092297
Position of 4p5.pdb (#11.5) relative to test.mrc (#1) coordinates:
Matrix rotation and translation
0.99973140 -0.02257549 0.00524085 8.87326208
0.02262486 0.99969831 -0.00956047 6.47019928
-0.00502343 0.00967647 0.99994056 -3.85681502
Axis 0.38332409 0.20453085 0.90068295
Axis point -269.66837685 375.01672335 0.00000000
Rotation angle (degrees) 1.43783158
Shift along axis 1.25092297
> fitmap #11.1 #11.4 inMap #1
Fit molecules 4p5.pdb (#11.1), 4p5.pdb (#11.4) to map test.mrc (#1) using
17554 atoms
average map value = 0.01713, steps = 104
shifted from previous position = 16.2
rotated from previous position = 1.12 degrees
atoms outside contour = 661, contour level = 0.0055693
Position of 4p5.pdb (#11.1) relative to test.mrc (#1) coordinates:
Matrix rotation and translation
0.99981064 -0.01878205 0.00509039 0.90416315
0.01878350 0.99982355 -0.00023728 6.48838512
-0.00508503 0.00033285 0.99998702 14.77054154
Axis 0.01464771 0.26142149 0.96511359
Axis point -122.89265955 36.92821613 0.00000000
Rotation angle (degrees) 1.11514492
Shift along axis 15.96469765
Position of 4p5.pdb (#11.4) relative to test.mrc (#1) coordinates:
Matrix rotation and translation
0.99981064 -0.01878205 0.00509039 0.90416315
0.01878350 0.99982355 -0.00023728 6.48838512
-0.00508503 0.00033285 0.99998702 14.77054154
Axis 0.01464771 0.26142149 0.96511359
Axis point -122.89265955 36.92821613 0.00000000
Rotation angle (degrees) 1.11514492
Shift along axis 15.96469765
> ui mousemode right "translate selected models"
> select #11.1 #11.4
17554 atoms, 17902 bonds, 2 models selected
> select clear
> volume #1 level 0.008826
> show #10 models
> hide #10 models
> volume #1 color #204a87
> volume #1 color #1e90ff33
> select #11.1 #11.4
17554 atoms, 17902 bonds, 2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> select #11.2 #11.5
17554 atoms, 17902 bonds, 2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> select #11.1 #11.4
17554 atoms, 17902 bonds, 2 models selected
> select #11.2 #11.6
17554 atoms, 17902 bonds, 2 models selected
> ui mousemode right "rotate selected models"
> select #11.2 #11.5
17554 atoms, 17902 bonds, 2 models selected
> select #11.3 #11.6
17554 atoms, 17902 bonds, 2 models selected
> ui mousemode right "translate selected models"
> select clear
> hide #!11 models
> show #10 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #10 models
> show #10 models
> hide #!11 models
> volume #1 color #49788633
> volume #1 color #49788619
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting full
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> hide #10 models
> show #!11 models
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> open "/run/media/yashar/My Passport/Fitting/4p5.pdb"
Summary of feedback from opening /run/media/yashar/My Passport/Fitting/4p5.pdb
---
warning | Ignored bad PDB record found on line 105427
END
Chain information for 4p5.pdb
---
Chain | Description
12.1/A 12.2/A 12.3/A 12.4/A 12.5/A 12.6/A | No description available
12.1/B 12.2/B 12.3/B 12.4/B 12.5/B 12.6/B | No description available
12.1/C 12.2/C 12.3/C 12.4/C 12.5/C 12.6/C | No description available
12.1/D 12.2/D 12.3/D 12.4/D 12.5/D 12.6/D | No description available
12.1/E 12.2/E 12.3/E 12.4/E 12.5/E 12.6/E | No description available
12.1/F 12.2/F 12.3/F 12.4/F 12.5/F 12.6/F | No description available
> mmaker #12.4/C to #11.4/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 4p5.pdb, chain C (#11.4) with 4p5.pdb, chain C (#12.4), sequence
alignment score = 983.4
RMSD between 189 pruned atom pairs is 0.000 angstroms; (across all 189 pairs:
0.000)
> close #12
> open "/run/media/yashar/My Passport/Fitting/4p5.pdb"
Summary of feedback from opening /run/media/yashar/My Passport/Fitting/4p5.pdb
---
warning | Ignored bad PDB record found on line 105427
END
Chain information for 4p5.pdb
---
Chain | Description
12.1/A 12.2/A 12.3/A 12.4/A 12.5/A 12.6/A | No description available
12.1/B 12.2/B 12.3/B 12.4/B 12.5/B 12.6/B | No description available
12.1/C 12.2/C 12.3/C 12.4/C 12.5/C 12.6/C | No description available
12.1/D 12.2/D 12.3/D 12.4/D 12.5/D 12.6/D | No description available
12.1/E 12.2/E 12.3/E 12.4/E 12.5/E 12.6/E | No description available
12.1/F 12.2/F 12.3/F 12.4/F 12.5/F 12.6/F | No description available
> select #12
52662 atoms, 53706 bonds, 7 models selected
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> select clear
> ui mousemode right translate
> hide #!11 models
> show #10 models
> select #12
52662 atoms, 53706 bonds, 7 models selected
> show sel cartoons
> hide sel atoms
> ui mousemode right "rotate selected models"
> color black #12
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #12 black
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> select clear
> graphics silhouettes false
> volume #1 level 0.008091
> hide #!12 models
> show #!11 models
> hide #10 models
> show #10 models
> hide #!11 models
> show #!11 models
> show #9 models
> hide #9 models
> hide #10 models
> show #10 models
> hide #!11 models
> hide #10 models
> show #!11 models
> show #10 models
> hide #!11 models
> hide #10 models
> show #9 models
> hide #9 models
> show #10 models
> show #!11 models
> hide #10 models
> show #!12 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> hide #!12 models
> show #10 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #10 models
> hide #!12 models
> show #10 models
> hide #10 models
> show #10 models
> graphics silhouettes true
> surface dust 300
Missing or invalid "surfaces" argument: invalid surfaces specifier
> surface dust #1 300
Expected a keyword
> surface dust #1 220
Expected a keyword
> surface dust 220
Missing or invalid "surfaces" argument: invalid surfaces specifier
> surface dust #1 size 250
> surface dust #1 size 450
> surface dust #1 size 600
> volume #1 level 0.007881
> hide #10 models
> select up
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
> save ViewNew11.png supersample 4 transparentBackground true
> show #!11 models
> show #10 models
> hide #!11 models
> hide #10 models
> show #10 models
> hide #10 models
> show #!12 models
> hide #!12 models
> show #10 models
> hide #10 models
> show #!12 models
> hide #!12 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
Empty filename passed to function
> save /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/coot_files/NEW/view1.cxs
> save ViewNew11.png supersample 4
> show #10 models
> color #2/B/G/I/L/D/P/X/T/O/C/V/j/b/R/a/d/h/f dark blue
> color #10 cyan
> color #10/B/G/I/L/D/P/X/T/O/C/V/j/b/R/a/d/h/f dark blue
> volume #1 level 0.0078
> save ViewNew12.png supersample 4
> hide #10 models
> show #!12 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> fitmap #12 inMap #1
Fit molecules 4p5.pdb (#12.1), 4p5.pdb (#12.2), 4p5.pdb (#12.3), 4p5.pdb
(#12.4), 4p5.pdb (#12.5), 4p5.pdb (#12.6) to map test.mrc (#1) using 52662
atoms
average map value = 0.01435, steps = 60
shifted from previous position = 11
rotated from previous position = 3.98 degrees
atoms outside contour = 10245, contour level = 0.0077997
Position of 4p5.pdb (#12.1) relative to test.mrc (#1) coordinates:
Matrix rotation and translation
0.99794227 -0.06007217 -0.02241789 -5.87386645
0.05945611 0.99786016 -0.02720415 1.31643281
0.02400413 0.02581529 0.99937849 0.20011824
Axis 0.38210706 -0.33455996 0.86143127
Axis point -10.93396486 -81.42422401 0.00000000
Rotation angle (degrees) 3.97824633
Shift along axis -2.51248346
Position of 4p5.pdb (#12.2) relative to test.mrc (#1) coordinates:
Matrix rotation and translation
0.99794227 -0.06007217 -0.02241789 -5.87386645
0.05945611 0.99786016 -0.02720415 1.31643281
0.02400413 0.02581529 0.99937849 0.20011824
Axis 0.38210706 -0.33455996 0.86143127
Axis point -10.93396486 -81.42422401 0.00000000
Rotation angle (degrees) 3.97824633
Shift along axis -2.51248346
Position of 4p5.pdb (#12.3) relative to test.mrc (#1) coordinates:
Matrix rotation and translation
0.99794227 -0.06007217 -0.02241789 -5.87386645
0.05945611 0.99786016 -0.02720415 1.31643281
0.02400413 0.02581529 0.99937849 0.20011824
Axis 0.38210706 -0.33455996 0.86143127
Axis point -10.93396486 -81.42422401 0.00000000
Rotation angle (degrees) 3.97824633
Shift along axis -2.51248346
Position of 4p5.pdb (#12.4) relative to test.mrc (#1) coordinates:
Matrix rotation and translation
0.99794227 -0.06007217 -0.02241789 -5.87386645
0.05945611 0.99786016 -0.02720415 1.31643281
0.02400413 0.02581529 0.99937849 0.20011824
Axis 0.38210706 -0.33455996 0.86143127
Axis point -10.93396486 -81.42422401 0.00000000
Rotation angle (degrees) 3.97824633
Shift along axis -2.51248346
Position of 4p5.pdb (#12.5) relative to test.mrc (#1) coordinates:
Matrix rotation and translation
0.99794227 -0.06007217 -0.02241789 -5.87386645
0.05945611 0.99786016 -0.02720415 1.31643281
0.02400413 0.02581529 0.99937849 0.20011824
Axis 0.38210706 -0.33455996 0.86143127
Axis point -10.93396486 -81.42422401 0.00000000
Rotation angle (degrees) 3.97824633
Shift along axis -2.51248346
Position of 4p5.pdb (#12.6) relative to test.mrc (#1) coordinates:
Matrix rotation and translation
0.99794227 -0.06007217 -0.02241789 -5.87386645
0.05945611 0.99786016 -0.02720415 1.31643281
0.02400413 0.02581529 0.99937849 0.20011824
Axis 0.38210706 -0.33455996 0.86143127
Axis point -10.93396486 -81.42422401 0.00000000
Rotation angle (degrees) 3.97824633
Shift along axis -2.51248346
> show #!1 models
> hide #!1 models
> color #102/F/D/B/E blue
> color #12/F/D/B/E blue
> hide #12.1 models
> show #12.1 models
> hide #12.2 models
> show #12.2 models
> hide #12.2 models
> show #12.2 models
> hide #12.3 models
> show #12.3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> save ViewNew13.png supersample 4
> movie record
> turn y 2 180
> wait 180
> movie encode /home/yashar/Desktop/movie1.mp4
Movie saved to /home/yashar/Desktop/movie1.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /home/yashar/Desktop/movie2.mp4
Movie saved to /home/yashar/Desktop/movie2.mp4
> hide #!12 models
> movie record
> turn y 2 180
> wait 180
> movie encode /home/yashar/Desktop/movie3.mp4
Movie saved to /home/yashar/Desktop/movie3.mp4
> hide #!1 models
> show #10 models
> save ViewNew14.png supersample 4
> hide #10 models
> show #!12 models
> show #10 models
> hide #!12 models
> save ViewNew14.png supersample 4
> hide #10 models
> show #!12 models
> save ViewNew15.png supersample 4
> show #10 models
> save ViewNew16.png supersample 4
> graphics silhouettes false
> graphics silhouettes true
> hide #!12 models
> save ViewNew17.png supersample 4
> hide #10 models
> show #!12 models
> save ViewNew18.png supersample 4
> show #10 models
> hide #10 models
> hide #!12 models
> show #10 models
> hide #10 models
> show #!12 models
> show #10 models
> hide #!12 models
> hide #10 models
> show #!12 models
> hide #!12 models
> show #10 models
> hide #10 models
> show #!12 models
> open /home/yashar/Downloads/ring_edit.pdb
Summary of feedback from opening /home/yashar/Downloads/ring_edit.pdb
---
warning | Ignored bad PDB record found on line 27514
END
Chain information for ring_edit.pdb #13
---
Chain | Description
A C E G I K M O Q | No description available
B D F H J L N P R | No description available
> select #13
27495 atoms, 27990 bonds, 1 model selected
> show sel cartoons
> hide sel atoms
> ui mousemode right "translate selected models"
> color #13 green
> select clear
> show #!1 models
> hide #!12 models
> hide #!1 models
> hide #13 models
> show #10 models
> show #10 surfaces
> hide #!10 surfaces
> show #!1 models
> hide #!1 models
> open /home/yashar/Downloads/new_ChlmayCW_n134_bin2.spi
Opened new_ChlmayCW_n134_bin2.spi, grid size 210,210,210, pixel 1, shown at
level 0.00862, step 1, values float32
> close #14
> open /home/yashar/Downloads/test2.mrc
Opened test2.mrc, grid size 420,420,420, pixel 3.5, shown at level 0.005, step
2, values float32
> volume #14 level 0.01175
> volume #14 level 0.007581
> close #14
> show #!1 models
> hide #!10 models
> close #13
> show #!12 models
> volume #1 level 0.009704
> hide #!12 models
> show #!12 models
> select #12
52662 atoms, 53706 bonds, 7 models selected
> volume #1 level 0.01097
> volume #1 level 0.01074
> volume #1 level 0.01034
> graphics silhouettes false
> graphics silhouettes true
> select clear
> surface dust #1 size 250
> volume #1 level 0.01534
> volume #1 level 0.01986
> volume #1 level 0.007324
Empty filename passed to function
> save
> /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/coot_files/NEW/finalView1.cxs
> volume #1 level 0.008831
> volume #1 level 0.02049
> save
> /data/GUICHARD_LAB/GUICHARD_LAB/Nik/Fitting/coot_files/NEW/finalView2.cxs
opened ChimeraX session
> hide #!12 models
> ui mousemode right "tape measure"
> marker segment #13 position -118.2,112.7,-9.282 toPosition 114.8,104.1,6.526
> color yellow radius 0.8625 label 233.7 labelHeight 23.37 labelColor yellow
> show #!12 models
> hide #!13 models
> marker segment #13 position -115,6.802,-12.03 toPosition 105.4,48.45,7.236
> color yellow radius 0.8625 label 225.2 labelHeight 22.52 labelColor yellow
> ui mousemode right "tape measure"
> marker segment #13 position -114,6.802,-16.38 toPosition 107.3,45.29,6.391
> color yellow radius 0.8625 label 225.8 labelHeight 22.58 labelColor yellow
> show #!13 models
> marker segment #13 position -100.3,106.6,-9.146 toPosition 110.6,49.79,6.593
> color yellow radius 0.8625 label 218.9 labelHeight 21.89 labelColor yellow
> hide #!13 models
> marker segment #13 position 107.3,45.29,6.391 toPosition -110,1.688,-13.27
> color yellow radius 0.8625 label 222.6 labelHeight 22.26 labelColor yellow
> show #!13 models
> marker segment #13 position 14.93,-0.04859,-115.3 toPosition
> -2.827,6.802,113.1 color yellow radius 0.8625 label 229.2 labelHeight 22.92
> labelColor yellow
> ui tool show "Side View"
> ui mousemode right "tape measure"
> marker segment #13 position 10.77,64.58,-112 toPosition -3.444,80.53,73.97
> color yellow radius 0.8625 label 187.2 labelHeight 18.72 labelColor yellow
> marker segment #13 position 11.14,64.58,-112.3 toPosition -2.271,50.35,99.87
> color yellow radius 0.8625 label 213.1 labelHeight 21.31 labelColor yellow
> close #13
> ui mousemode right "tape measure"
> marker segment #13 position -63.16,63.79,-91.02 toPosition 14.07,49.32,97.87
> color yellow radius 0.8625 label 204.6 labelHeight 20.46 labelColor yellow
> hide #13.1 models
> show #13.1 models
> marker segment #13 position 41.15,-172.7,106.3 toPosition 65.28,-161.8,100.2
> color yellow radius 0.8625 label 27.18 labelHeight 2.718 labelColor yellow
> ui mousemode right "tape measure"
> marker segment #13 position -65.63,99.96,-86.25 toPosition 33.85,69.09,98.48
> color yellow radius 0.8625 label 212.1 labelHeight 21.21 labelColor yellow
> close #13
> ui mousemode right "tape measure"
> ui mousemode right "tape measure"
> ui mousemode right "tape measure"
> marker segment #13 position 105.6,73.06,-2.12 toPosition -72.71,76.06,-95.02
> color yellow radius 0.8625 label 201.1 labelHeight 20.11 labelColor yellow
> close #13
> ui mousemode right "tape measure"
> marker segment #13 position 119.4,74.59,-14.52 toPosition -101.5,70.49,-65.8
> color yellow radius 0.8625 label 226.8 labelHeight 22.68 labelColor yellow
> ui mousemode right "tape measure"
> marker segment #13 position 104.7,69.94,-51.52 toPosition
> -70.99,67.11,-95.02 color yellow radius 0.8625 label 181.1 labelHeight 18.11
> labelColor yellow
> ui mousemode right "tape measure"
> marker segment #13 position 103.1,24.15,43.44 toPosition -110.9,23.13,-7.655
> color yellow radius 0.8625 label 220 labelHeight 22 labelColor yellow
> ui mousemode right "tape measure"
> marker segment #13 position 114.6,98.64,36.95 toPosition -117.9,94.79,-17.23
> color yellow radius 0.8625 label 238.7 labelHeight 23.87 labelColor yellow
> marker segment #13 position 37.86,13.12,114.5 toPosition 37.6,18.71,111.1
> color yellow radius 0.8625 label 6.537 labelHeight 1.725 labelColor yellow
> hide #!12 models
> hide #!1 models
> show #!12 models
> close #13
> ui mousemode right "tape measure"
> marker segment #13 position -99.38,56.93,6.984 toPosition 103.5,64.09,-32.3
> color yellow radius 0.8625 label 206.8 labelHeight 20.68 labelColor yellow
> ui mousemode right "tape measure"
> marker delete #13
> ui mousemode right "tape measure"
> marker segment #13 position -88.52,92.41,32.96 toPosition 98.28,120.6,-26.49
> color yellow radius 0.8625 label 198 labelHeight 19.8 labelColor yellow
> close #13
> hide #!12 models
> show #!1 models
> ui mousemode right "tape measure"
> marker segment #13 position -109.6,104.1,39.2 toPosition 117.8,112.1,-35.45
> color yellow radius 0.8625 label 239.5 labelHeight 23.95 labelColor yellow
> show #!12 models
> hide #!1 models
> ui mousemode right "tape measure"
> marker segment #13 position -8.934,48.77,-107.8 toPosition 20.61,77.4,104.1
> color yellow radius 0.8625 label 215.8 labelHeight 21.58 labelColor yellow
> close #13
> ui mousemode right "tape measure"
> marker segment #13 position -27.64,111.2,-94.47 toPosition 23.23,94.22,97.74
> color yellow radius 0.8625 label 199.5 labelHeight 19.95 labelColor yellow
> close #13
> marker segment #13 position -23.51,56.68,-99.09 toPosition 31.18,111.6,95.68
> color yellow radius 0.8625 label 209.6 labelHeight 20.96 labelColor yellow
> close #13
> ui mousemode right "tape measure"
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up
self._clear()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear
self._log_clear_command()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command
log_equivalent_command(mset.session, cmd)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Structure' object has no attribute 'session'
AttributeError: 'Structure' object has no attribute 'session'
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> ui mousemode right "tape measure"
> ui mousemode right "tape measure"
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event
lm.mouse_up(MouseEvent(event, modifiers=modifiers))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up
self._clear()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear
self._log_clear_command()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command
log_equivalent_command(mset.session, cmd)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Structure' object has no attribute 'session'
AttributeError: 'Structure' object has no attribute 'session'
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up
self._clear()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear
self._log_clear_command()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command
log_equivalent_command(mset.session, cmd)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Structure' object has no attribute 'session'
AttributeError: 'Structure' object has no attribute 'session'
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 410.79
OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 24 Intel(R) Core(TM) i9-9920X CPU @ 3.50GHz
Cache Size: 19712 KB
Memory:
total used free shared buff/cache available
Mem: 125G 14G 1.4G 344M 109G 110G
Swap: 14G 373M 14G
Graphics:
17:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU102 [GeForce RTX 2080 Ti] [10de:1e04] (rev a1)
Subsystem: PNY Device [196e:12af]
Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
Change History (2)
comment:1 by , 5 years ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → tape-measure mouse mode using dead MarkerSet |
comment:2 by , 5 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate of #3457