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Opened 5 years ago
Last modified 5 years ago
#3390 assigned defect
Session save: cycle detected
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.3.0-51-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 1.0 (2020-05-09)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.0rc202005091901 (2020-05-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/mpillana/AD41_MARZO_2020/map_general/new_colors_fac4t.cxs format
> session
Log from Mon Jun 1 11:39:50 2020UCSF ChimeraX version: 1.0rc202005091901
(2020-05-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/mpillana/AD41_MARZO_2020/map_general/VI_AD41_FACET.pdb
> /home/mpillana/AD41_MARZO_2020/map_general/H4_AD41_FACET.pdb
> /home/mpillana/AD41_MARZO_2020/map_general/VII_AD41_FACET.pdb
> /home/mpillana/AD41_MARZO_2020/map_general/IX_AD41_FACET.pdb
> /home/mpillana/AD41_MARZO_2020/map_general/VIII_EXTRA_AD41_FACET.pdb
> /home/mpillana/AD41_MARZO_2020/map_general/VIII_AD41_FACET.pdb
> /home/mpillana/AD41_MARZO_2020/map_general/IIIA_AD41_FACET.pdb
> /home/mpillana/AD41_MARZO_2020/map_general/PENTON_AD41_FACET.pdb
> /home/mpillana/AD41_MARZO_2020/map_general/H3_AD41_FACET.pdb
> /home/mpillana/AD41_MARZO_2020/map_general/H2_AD41_FACET.pdb
> /home/mpillana/AD41_MARZO_2020/map_general/H1_AD41_FACET.pdb
Chain information for VI_AD41_FACET.pdb #1
---
Chain | Description
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e u | No
description available
Chain information for H4_AD41_FACET.pdb #2
---
Chain | Description
A B J | No description available
C D K | No description available
E F L | No description available
Chain information for VII_AD41_FACET.pdb #3
---
Chain | Description
A B C D E W | No description available
F G H I J w | No description available
Chain information for IX_AD41_FACET.pdb #4
---
Chain | Description
A B C D E F G H Q R S T | No description available
Chain information for VIII_EXTRA_AD41_FACET.pdb #5
---
Chain | Description
A B C D E O | No description available
Chain information for VIII_AD41_FACET.pdb #6
---
Chain | Description
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e | No description
available
Chain information for IIIA_AD41_FACET.pdb #7
---
Chain | Description
A B C D E F G H N | No description available
Chain information for PENTON_AD41_FACET.pdb #8
---
Chain | Description
A B C D E F G H I J K L M N O | No description available
Chain information for H3_AD41_FACET.pdb #9
---
Chain | Description
A B G | No description available
C D H | No description available
E F I | No description available
Chain information for H2_AD41_FACET.pdb #10
---
Chain | Description
A B C D G H | No description available
E I J K L M | No description available
F N O P Q R | No description available
Chain information for H1_AD41_FACET.pdb #11
---
Chain | Description
A D E F G H | No description available
B I J K L M | No description available
C N O P Q R | No description available
> view orient
> toolshed show "Side View"
> set bgColor white
> lighting full
> lighting soft
> lighting simple
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> select #8
54135 atoms, 55425 bonds, 30 pseudobonds, 2 models selected
> color (#!8 & sel) hot pink
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> select #5
8282 atoms, 8509 bonds, 12 pseudobonds, 2 models selected
> color (#!5 & sel) yellow
> select #6
42749 atoms, 43927 bonds, 62 pseudobonds, 2 models selected
> color (#!6 & sel) yellow
> split #4
Chain information for IX_AD41_FACET.pdb A #4.1
---
Chain | Description
A | No description available
Chain information for IX_AD41_FACET.pdb B #4.2
---
Chain | Description
B | No description available
Chain information for IX_AD41_FACET.pdb C #4.3
---
Chain | Description
C | No description available
Chain information for IX_AD41_FACET.pdb D #4.4
---
Chain | Description
D | No description available
Chain information for IX_AD41_FACET.pdb E #4.5
---
Chain | Description
E | No description available
Chain information for IX_AD41_FACET.pdb F #4.6
---
Chain | Description
F | No description available
Chain information for IX_AD41_FACET.pdb G #4.7
---
Chain | Description
G | No description available
Chain information for IX_AD41_FACET.pdb H #4.8
---
Chain | Description
H | No description available
Chain information for IX_AD41_FACET.pdb Q #4.9
---
Chain | Description
Q | No description available
Chain information for IX_AD41_FACET.pdb R #4.10
---
Chain | Description
R | No description available
Chain information for IX_AD41_FACET.pdb S #4.11
---
Chain | Description
S | No description available
Chain information for IX_AD41_FACET.pdb T #4.12
---
Chain | Description
T | No description available
Split IX_AD41_FACET.pdb (#4) into 12 models
> hide #1 models
> hide #!2 models
> hide #3 models
> hide #!5 models
> hide #!6 models
> hide #7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #4.1 models
> show #4.1 models
> select #4
4380 atoms, 4488 bonds, 13 models selected
> color sel magenta
> hide #4.1 models
> show #4.1 models
> hide #4.2 models
> show #4.2 models
> hide #4.3 models
> show #4.3 models
> hide #4.4 models
> show #4.4 models
> hide #4.5 models
> show #4.5 models
> hide #4.6 models
> show #4.6 models
> hide #4.7 models
> hide #4.8 models
> hide #4.9 models
> show #4.9 models
> hide #4.10 models
> show #4.10 models
> hide #4.11 models
> show #4.11 models
> hide #4.12 models
> show #4.12 models
> hide #4.12 models
> ~select #4
Nothing selected
> select #4.7
365 atoms, 374 bonds, 1 model selected
> show #4.7 models
> color sel cyan
> show #4.8 models
> select #4.8
365 atoms, 374 bonds, 1 model selected
> color sel cyan
> show #4.12 models
> select #4.12
365 atoms, 374 bonds, 1 model selected
> color sel cyan
> show #!8 models
> show #7 models
> sym #7 I,222r copies true
> select #12
1250640 atoms, 1271160 bonds, 61 models selected
> ~select #12
Nothing selected
> select #12
1250640 atoms, 1271160 bonds, 61 models selected
> select #3
732 atoms, 750 bonds, 1 model selected
> ~select #3
Nothing selected
> select #4
4380 atoms, 4488 bonds, 13 models selected
> ~select #4
Nothing selected
> select #12
1250640 atoms, 1271160 bonds, 61 models selected
> hide #12.1 models
> hide #12.2 models
> hide #12.3 models
> hide #12.4 models
> hide #12.5 models
> hide #12.6 models
> hide #12.7 models
> hide #12.8 models
> hide #12.9 models
> hide #12.10 models
> hide #12.11 models
> hide #12.12 models
> hide #12.13 models
> show #12.13 models
> hide #12.13 models
> hide #12.14 models
> hide #12.15 models
> hide #12.16 models
> hide #12.17 models
> hide #12.18 models
> show #12.18 models
> hide #12.18 models
> show #12.18 models
> hide #12.18 models
> hide #12.19 models
> show #12.19 models
> hide #12.19 models
> hide #12.20 models
> hide #12.21 models
> hide #12.22 models
> hide #12.23 models
> hide #12.24 models
> show #12.24 models
> hide #12.24 models
> hide #12.25 models
> hide #12.26 models
> hide #12.27 models
> hide #12.28 models
> hide #12.29 models
> hide #12.30 models
> hide #12.31 models
> hide #12.32 models
> hide #12.33 models
> hide #12.34 models
> hide #12.35 models
> hide #12.36 models
> hide #12.37 models
> show #12.37 models
> hide #12.37 models
> hide #12.38 models
> hide #12.39 models
> hide #12.40 models
> hide #12.41 models
> hide #12.42 models
> hide #12.43 models
> hide #12.44 models
> hide #12.45 models
> hide #12.46 models
> hide #12.47 models
> hide #12.48 models
> hide #12.49 models
> hide #12.50 models
> hide #12.51 models
> hide #12.52 models
> hide #12.53 models
> hide #12.54 models
> hide #12.55 models
> hide #12.56 models
> show #12.56 models
> hide #12.57 models
> show #12.57 models
> hide #12.58 models
> show #12.58 models
> hide #12.58 models
> hide #12.59 models
> show #12.59 models
> hide #12.60 models
> show #12.60 models
> close #12.1-55
> close #12.58
> color sel orange
> select clear
> view orient
> split #12
Chain information for IIIA_AD41_FACET.pdb A #12.56.1
---
Chain | Description
A | No description available
Chain information for IIIA_AD41_FACET.pdb B #12.56.2
---
Chain | Description
B | No description available
Chain information for IIIA_AD41_FACET.pdb C #12.56.3
---
Chain | Description
C | No description available
Chain information for IIIA_AD41_FACET.pdb D #12.56.4
---
Chain | Description
D | No description available
Chain information for IIIA_AD41_FACET.pdb E #12.56.5
---
Chain | Description
E | No description available
Chain information for IIIA_AD41_FACET.pdb F #12.56.6
---
Chain | Description
F | No description available
Chain information for IIIA_AD41_FACET.pdb G #12.56.7
---
Chain | Description
G | No description available
Chain information for IIIA_AD41_FACET.pdb H #12.56.8
---
Chain | Description
H | No description available
Chain information for IIIA_AD41_FACET.pdb N #12.56.9
---
Chain | Description
N | No description available
Split IIIA_AD41_FACET.pdb (#12.56) into 9 models
Chain information for IIIA_AD41_FACET.pdb A #12.57.1
---
Chain | Description
A | No description available
Chain information for IIIA_AD41_FACET.pdb B #12.57.2
---
Chain | Description
B | No description available
Chain information for IIIA_AD41_FACET.pdb C #12.57.3
---
Chain | Description
C | No description available
Chain information for IIIA_AD41_FACET.pdb D #12.57.4
---
Chain | Description
D | No description available
Chain information for IIIA_AD41_FACET.pdb E #12.57.5
---
Chain | Description
E | No description available
Chain information for IIIA_AD41_FACET.pdb F #12.57.6
---
Chain | Description
F | No description available
Chain information for IIIA_AD41_FACET.pdb G #12.57.7
---
Chain | Description
G | No description available
Chain information for IIIA_AD41_FACET.pdb H #12.57.8
---
Chain | Description
H | No description available
Chain information for IIIA_AD41_FACET.pdb N #12.57.9
---
Chain | Description
N | No description available
Split IIIA_AD41_FACET.pdb (#12.57) into 9 models
Chain information for IIIA_AD41_FACET.pdb A #12.59.1
---
Chain | Description
A | No description available
Chain information for IIIA_AD41_FACET.pdb B #12.59.2
---
Chain | Description
B | No description available
Chain information for IIIA_AD41_FACET.pdb C #12.59.3
---
Chain | Description
C | No description available
Chain information for IIIA_AD41_FACET.pdb D #12.59.4
---
Chain | Description
D | No description available
Chain information for IIIA_AD41_FACET.pdb E #12.59.5
---
Chain | Description
E | No description available
Chain information for IIIA_AD41_FACET.pdb F #12.59.6
---
Chain | Description
F | No description available
Chain information for IIIA_AD41_FACET.pdb G #12.59.7
---
Chain | Description
G | No description available
Chain information for IIIA_AD41_FACET.pdb H #12.59.8
---
Chain | Description
H | No description available
Chain information for IIIA_AD41_FACET.pdb N #12.59.9
---
Chain | Description
N | No description available
Split IIIA_AD41_FACET.pdb (#12.59) into 9 models
Chain information for IIIA_AD41_FACET.pdb A #12.60.1
---
Chain | Description
A | No description available
Chain information for IIIA_AD41_FACET.pdb B #12.60.2
---
Chain | Description
B | No description available
Chain information for IIIA_AD41_FACET.pdb C #12.60.3
---
Chain | Description
C | No description available
Chain information for IIIA_AD41_FACET.pdb D #12.60.4
---
Chain | Description
D | No description available
Chain information for IIIA_AD41_FACET.pdb E #12.60.5
---
Chain | Description
E | No description available
Chain information for IIIA_AD41_FACET.pdb F #12.60.6
---
Chain | Description
F | No description available
Chain information for IIIA_AD41_FACET.pdb G #12.60.7
---
Chain | Description
G | No description available
Chain information for IIIA_AD41_FACET.pdb H #12.60.8
---
Chain | Description
H | No description available
Chain information for IIIA_AD41_FACET.pdb N #12.60.9
---
Chain | Description
N | No description available
Split IIIA_AD41_FACET.pdb (#12.60) into 9 models
> hide #12.56.1 models
> hide #12.56.2 models
> hide #12.56.3 models
> hide #12.56.4 models
> hide #12.56.5 models
> show #12.56.5 models
> hide #12.56.6 models
> show #12.56.6 models
> hide #12.56.7 models
> hide #12.56.8 models
> show #12.56.8 models
> hide #12.56.9 models
> show #12.56.9 models
> hide #12.57.1 models
> show #12.57.1 models
> hide #12.57.2 models
> hide #12.57.3 models
> show #12.57.3 models
> hide #12.57.4 models
> hide #12.57.5 models
> show #12.57.5 models
> hide #12.57.5 models
> hide #12.57.6 models
> show #12.57.6 models
> hide #12.57.7 models
> hide #12.57.8 models
> show #12.57.8 models
> hide #12.57.9 models
> show #12.57.9 models
> hide #12.59.1 models
> hide #12.59.2 models
> hide #12.59.3 models
> show #12.59.3 models
> hide #12.59.4 models
> hide #12.59.5 models
> hide #12.59.6 models
> show #12.59.6 models
> hide #12.59.7 models
> hide #12.59.8 models
> hide #12.60.1 models
> show #12.60.1 models
> hide #12.60.2 models
> hide #12.60.3 models
> hide #12.60.4 models
> hide #12.60.5 models
> show #12.60.5 models
> hide #12.60.6 models
> hide #12.60.7 models
> hide #12.60.8 models
> show #12.60.8 models
> hide #12.60.9 models
> show #!5 models
> show #!6 models
> graphics silhouettes true
> lighting full
> hide #!5 models
> hide #!6 models
> hide #!8 models
> hide #12 models
> hide #!4 models
> show #!11 models
> show #!10 models
> show #!9 models
> select #9
65115 atoms, 66918 bonds, 18 pseudobonds, 2 models selected
> ~select #9
Nothing selected
> color #9-11 light sea green
> select #9
65115 atoms, 66918 bonds, 18 pseudobonds, 2 models selected
> show #!4 models
> hide #!4 models
> show #!4 models
> select clear
> show #!2 models
> select #2
65202 atoms, 67008 bonds, 24 pseudobonds, 2 models selected
> select clear
> show #!8 models
> show #12 models
> hide #12.56.1 models
> hide #12.56.2 models
> hide #12.56.3 models
> hide #12.56.4 models
> hide #12.56.5 models
> show #12.56.5 models
> hide #12.56.5 models
> show #12.56.5 models
> show #12.56.4 models
> hide #12.56.4 models
> hide #12.56.5 models
> show #12.56.5 models
> hide #12.56.6 models
> show #12.56.6 models
> hide #12.56.7 models
> hide #12.56.8 models
> show #12.56.8 models
> hide #12.56.9 models
> show #12.56.9 models
> close #12.56.1-4,7
> hide #12.57.1 models
> show #12.57.1 models
> hide #12.57.2 models
> hide #12.57.3 models
> show #12.57.3 models
> hide #12.57.4 models
> hide #12.57.5 models
> show #12.57.5 models
> hide #12.57.5 models
> hide #12.57.6 models
> show #12.57.6 models
> hide #12.57.7 models
> hide #12.57.8 models
> show #12.57.8 models
> hide #12.57.8 models
> show #12.57.8 models
> hide #12.57.9 models
> show #12.57.9 models
> close #12.57.2,4-5,7
> hide #12.59.1 models
> show #12.59.1 models
> hide #12.59.1 models
> hide #12.59.2 models
> hide #12.59.3 models
> show #12.59.3 models
> hide #12.59.4 models
> hide #12.59.5 models
> hide #12.59.6 models
> show #12.59.6 models
> hide #12.59.7 models
> hide #12.59.8 models
> hide #12.59.9 models
> show #12.59.9 models
> close #12.59.1-2,4-5,7-8
> hide #12.60.1 models
> show #12.60.1 models
> hide #12.60.2 models
> hide #12.60.3 models
> hide #12.60.4 models
> hide #12.60.5 models
> show #12.60.5 models
> hide #12.60.6 models
> hide #12.60.7 models
> hide #12.60.8 models
> show #12.60.8 models
> hide #12.60.9 models
> close #12.60.2-4,6-7,9
> view orient
> show #!5 models
> show #!6 models
> view orient
> split #5 #6
Chain information for VIII_EXTRA_AD41_FACET.pdb A #5.1
---
Chain | Description
A | No description available
Chain information for VIII_EXTRA_AD41_FACET.pdb B #5.2
---
Chain | Description
B | No description available
Chain information for VIII_EXTRA_AD41_FACET.pdb C #5.3
---
Chain | Description
C | No description available
Chain information for VIII_EXTRA_AD41_FACET.pdb D #5.4
---
Chain | Description
D | No description available
Chain information for VIII_EXTRA_AD41_FACET.pdb E #5.5
---
Chain | Description
E | No description available
Chain information for VIII_EXTRA_AD41_FACET.pdb O #5.6
---
Chain | Description
O | No description available
Split VIII_EXTRA_AD41_FACET.pdb (#5) into 7 models
Chain information for VIII_AD41_FACET.pdb A #6.1
---
Chain | Description
A | No description available
Chain information for VIII_AD41_FACET.pdb B #6.2
---
Chain | Description
B | No description available
Chain information for VIII_AD41_FACET.pdb C #6.3
---
Chain | Description
C | No description available
Chain information for VIII_AD41_FACET.pdb D #6.4
---
Chain | Description
D | No description available
Chain information for VIII_AD41_FACET.pdb E #6.5
---
Chain | Description
E | No description available
Chain information for VIII_AD41_FACET.pdb F #6.6
---
Chain | Description
F | No description available
Chain information for VIII_AD41_FACET.pdb G #6.7
---
Chain | Description
G | No description available
Chain information for VIII_AD41_FACET.pdb H #6.8
---
Chain | Description
H | No description available
Chain information for VIII_AD41_FACET.pdb I #6.9
---
Chain | Description
I | No description available
Chain information for VIII_AD41_FACET.pdb J #6.10
---
Chain | Description
J | No description available
Chain information for VIII_AD41_FACET.pdb K #6.11
---
Chain | Description
K | No description available
Chain information for VIII_AD41_FACET.pdb L #6.12
---
Chain | Description
L | No description available
Chain information for VIII_AD41_FACET.pdb M #6.13
---
Chain | Description
M | No description available
Chain information for VIII_AD41_FACET.pdb N #6.14
---
Chain | Description
N | No description available
Chain information for VIII_AD41_FACET.pdb O #6.15
---
Chain | Description
O | No description available
Chain information for VIII_AD41_FACET.pdb P #6.16
---
Chain | Description
P | No description available
Chain information for VIII_AD41_FACET.pdb Q #6.17
---
Chain | Description
Q | No description available
Chain information for VIII_AD41_FACET.pdb R #6.18
---
Chain | Description
R | No description available
Chain information for VIII_AD41_FACET.pdb S #6.19
---
Chain | Description
S | No description available
Chain information for VIII_AD41_FACET.pdb T #6.20
---
Chain | Description
T | No description available
Chain information for VIII_AD41_FACET.pdb U #6.21
---
Chain | Description
U | No description available
Chain information for VIII_AD41_FACET.pdb V #6.22
---
Chain | Description
V | No description available
Chain information for VIII_AD41_FACET.pdb W #6.23
---
Chain | Description
W | No description available
Chain information for VIII_AD41_FACET.pdb X #6.24
---
Chain | Description
X | No description available
Chain information for VIII_AD41_FACET.pdb Y #6.25
---
Chain | Description
Y | No description available
Chain information for VIII_AD41_FACET.pdb Z #6.26
---
Chain | Description
Z | No description available
Chain information for VIII_AD41_FACET.pdb a #6.27
---
Chain | Description
a | No description available
Chain information for VIII_AD41_FACET.pdb b #6.28
---
Chain | Description
b | No description available
Chain information for VIII_AD41_FACET.pdb c #6.29
---
Chain | Description
c | No description available
Chain information for VIII_AD41_FACET.pdb d #6.30
---
Chain | Description
d | No description available
Chain information for VIII_AD41_FACET.pdb e #6.31
---
Chain | Description
e | No description available
Split VIII_AD41_FACET.pdb (#6) into 31 models
> hide #!5.1 models
> show #!5.1 models
> hide #!5.1 models
> show #!5.1 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.3 models
> show #!5.3 models
> hide #!5.4 models
> show #!5.4 models
> hide #!5.5 models
> show #!5.5 models
> hide #!5.5 models
> show #!5.5 models
> hide #!5.6 models
> show #!5.6 models
> hide #5.7 models
> show #5.7 models
> hide #5.7 models
> close #5.7
> hide #!6.31 models
> hide #!6.30 models
> hide #!6.29 models
> hide #!6.28 models
> hide #!6.27 models
> show #!6.27 models
> hide #!6.27 models
> hide #!6.26 models
> show #!6.26 models
> hide #!6.25 models
> hide #!6.24 models
> hide #!6.23 models
> hide #!6.22 models
> show #!6.22 models
> hide #!6.21 models
> show #!6.21 models
> hide #!6.20 models
> show #!6.20 models
> hide #!6.20 models
> show #!6.20 models
> hide #!6.19 models
> show #!6.19 models
> hide #!6.18 models
> show #!6.18 models
> hide #!6.17 models
> show #!6.17 models
> hide #!6.16 models
> show #!6.16 models
> hide #!6.15 models
> show #!6.15 models
> hide #!6.15 models
> hide #!6.14 models
> hide #!6.13 models
> hide #!6.12 models
> hide #!6.11 models
> hide #!6.10 models
> show #!6.10 models
> hide #!6.9 models
> show #!6.9 models
> hide #!6.8 models
> show #!6.8 models
> hide #!6.7 models
> hide #!6.6 models
> hide #!6.5 models
> show #!6.5 models
> hide #!6.4 models
> show #!6.4 models
> hide #!6.3 models
> show #!6.3 models
> hide #!6.2 models
> show #!6.2 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.21 models
> close #6.6-7,11-15,21,23-25,27-31
> save /home/mpillana/AD41_MARZO_2020/map_general/new_colors_fac4t.cxs
opened ChimeraX session
> lighting simple
> graphics silhouettes false
> open
> /home/mpillana/AD41_MARZO_2020/MAPS/NEW_MAPS/AD41_PRE_2962_relion_class001.mrc
Opened AD41_PRE_2962_relion_class001.mrc, grid size 780,780,780, pixel 1.38,
shown at step 1, values float32
> toolshed show "Map Coordinates"
> volume #13 region 0,0,0,779,779,779 step 4
> volume #13 region 0,0,0,779,779,779 step 4
> set bgColor black
> toolshed show "Map Eraser"
> volume #13 change image level -0.004528,0 level 0.02895,0.8 level 0.04107,1
> volume copy #13 subregion 149,224,346,633,708,779
> volume erase #15 center 2.4454,104.22,270.25 radius 328.15 outside true
> hide #!4 models
> volume zone #16 nearAtoms #1-3 #5-11 range 3 invert true minimalBounds true
> newMap true
> volume zone #15 nearAtoms #1-3 #5-11 range 3 invert true minimalBounds true
> newMap true
> hide #!2 models
> hide #!5 models
> hide #!6 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #12 models
> volume #16 level 0.01668
> volume #16 level 0.008712
> volume #16 level 0.007654
> volume #16 level 0.005255
> volume #16 level 0.003492
> close #16
> volume zone #15 nearAtoms #1-11 range 3 invert true minimalBounds true
> newMap true
> volume #16 level 0.009346
> vop scale #16 factor 146.97
> volume #16 step 1
> close #17
> vop scale #16 factor 146.97
> volume #17 level 2.103
> volume #17 level 0.796
> volume #17 level 1.077
> volume #17 level 1.25
> volume #17 level 0.7636
> volume zone #17 nearAtoms #4 range 20 invert false minimalBounds true newMap
> true
> volume #18 level 0.102
> show #!4 models
> volume #18 level 0.2085
> volume #18 level 0.4595
> volume #18 level 0.4214
> surface dust #18 size 10
> surface undust #18 size 5
Expected fewer arguments
> surface dust #18 size 5
> surface undust #18
> volume #18 level 0.1857
> surface dust #18 size 5
> volume zone #15 nearAtoms #1-11 range 4 invert true minimalBounds true
> newMap true
> volume #19 level 0.007229
> volume zone #19 nearAtoms #4 range 20 invert false minimalBounds true newMap
> true
> volume #20 level 0.0005589
> vop scale #20 factor 146.97
> surface dust #21 size 5
> surface dust #21 size 8
> surface dust #21 size 10
> volume #21 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.5
> subdivideSurface true subdivisionLevels 1 smoothLines true
> volume #21 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.8
> subdivideSurface true subdivisionLevels 1 smoothLines true
> volume #21 surfaceSmoothing true smoothingIterations 8 smoothingFactor 0.8
> subdivideSurface true subdivisionLevels 1 smoothLines true
> volume #21 surfaceSmoothing true smoothingIterations 8 smoothingFactor 0.8
> subdivideSurface true subdivisionLevels 2 smoothLines true
> volume #21 surfaceSmoothing true smoothingIterations 8 smoothingFactor 0.8
> subdivideSurface true subdivisionLevels 5 smoothLines true
> graphics silhouettes true
> graphics silhouettes false
> volume #21 surfaceSmoothing true smoothingIterations 2 smoothingFactor 0.8
> subdivideSurface true subdivisionLevels 5 smoothLines true
> volume #21 surfaceSmoothing false smoothingIterations 2 smoothingFactor 0.8
> subdivideSurface false subdivisionLevels 5 smoothLines true
> ui mousemode right "pick blobs"
> measure blob #!21.1 triangleNumber 28731 color #8ae234ff outline true
Surface AD41_PRE_2962_relion_class001.mrc copy zone zone scaled #21.1 blob:
volume = 3336.3
area = 2905.6
size = 52.02 47.932 11.863
> transparency #21.1-2 50
> measure blob #!21.1 triangleNumber 21195 color #fce94fff outline true
Surface AD41_PRE_2962_relion_class001.mrc copy zone zone scaled #21.1 blob:
volume = 13997
area = 9485
size = 105.03 79.219 31.845
> measure blob #!21.1 triangleNumber 51766 color #fce94fff outline true
Surface AD41_PRE_2962_relion_class001.mrc copy zone zone scaled #21.1 blob:
volume = 13654
area = 9313.1
size = 95.864 85.401 33.592
> measure blob #!21.1 triangleNumber 28560 color #fce94fff outline true
Surface AD41_PRE_2962_relion_class001.mrc copy zone zone scaled #21.1 blob:
volume = 13948
area = 9326.2
size = 91.272 87.753 33.15
> transparency #21.1-5 0
> transparency #21.1-5 50
> set bgColor white
> graphics silhouettes true
> view orient
> show #!2 models
> select #2
65202 atoms, 67008 bonds, 24 pseudobonds, 2 models selected
> ~select #2
Nothing selected
> hide #4.1-12#!2 atoms
> show #4.1-12#!2 cartoons
> graphics silhouettes false
> view orient
> show #!9 models
> hide #4.1-12#!2,9 atoms
> show #4.1-12#!2,9 cartoons
> show #4.1-12#!2,9 cartoons
> show #!10 models
> show #4.1-12#!2,9-10 cartoons
> hide #4.1-12#!2,9-10 atoms
> show #!11 models
> hide #4.1-12#!2,9-11 atoms
> show #4.1-12#!2,9-11 cartoons
> show #!8 models
> select #8
54135 atoms, 55425 bonds, 30 pseudobonds, 2 models selected
> hide sel atoms
> show sel cartoons
> select clear
> view orient
> select #4
4380 atoms, 4488 bonds, 13 models selected
> show sel atoms
> select clear
> transparency #21.1 0
> turn x 20
> view orient
> toolshed show "Side View"
> turn x 20
> shape icosahedron radius 450 orientation 222r mesh true d2
Expected a keyword
> shape icosahedron radius 450 orientation 222r mesh true divisions 2
> view orient
> lighting simple
> lighting soft
> lighting full
> lighting full
> view orient
> turn x 20
> hide #!22 models
> turn x -45
> volume #21 level 0.1043
> volume #21 level 0.4519
> volume #21 level 0.3477
> volume #21 level 0.299
> volume #21 level 0.2225
> volume #21 level 0.2
> view orient
> hide #!2 models
> hide #!8 models
> hide #!10 models
> hide #!11 models
> hide #!9 models
> surface undust #21
> surface dust #21 size 5
> measure blob #!21.1 triangleNumber 29464 color #fce94fff outline true
Surface AD41_PRE_2962_relion_class001.mrc copy zone zone scaled #21.1 blob:
volume = 8501.5
area = 6750
size = 90.853 80.865 28.448
> measure blob #!21.1 triangleNumber 16020 color #fce94fff outline true
Surface AD41_PRE_2962_relion_class001.mrc copy zone zone scaled #21.1 blob:
volume = 8487.1
area = 6702.1
size = 97.149 78.124 28.658
> measure blob #!21.1 triangleNumber 35523 color #fce94fff outline true
Surface AD41_PRE_2962_relion_class001.mrc copy zone zone scaled #21.1 blob:
volume = 7998.3
area = 6181.2
size = 84.562 73.231 30.14
> measure blob #!21.1 triangleNumber 26168 color #8ae234ff outline true
Surface AD41_PRE_2962_relion_class001.mrc copy zone zone scaled #21.1 blob:
volume = 2299.7
area = 2137.4
size = 46.17 40.355 10.996
> view orient
> turn x 20
> show #!2 models
> show #!9 models
> show #!10 models
> show #!11 models
> show #!8 models
> measure blob #!21.1 triangleNumber 10912 color #8ae234ff outline true
Surface AD41_PRE_2962_relion_class001.mrc copy zone zone scaled #21.1 blob:
volume = 8501.5
area = 6750
size = 90.853 80.865 28.448
> measure blob #!21.1 triangleNumber 32774 color #fce94fff outline true
Surface AD41_PRE_2962_relion_class001.mrc copy zone zone scaled #21.1 blob:
volume = 8501.5
area = 6750
size = 90.853 80.865 28.448
> save /home/mpillana/AD41_MARZO_2020/IX/2020.06.12/IX_facet.cxs
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 817, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 571, in save
for name, data in mgr.walk():
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 300, in walk
key = next(odg)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/order_dag.py", line 69, in order_dag
yield from _postorder_traversal(path, d, node)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/order_dag.py", line 82, in _postorder_traversal
yield from _postorder_traversal(path, d, dnode)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/order_dag.py", line 82, in _postorder_traversal
yield from _postorder_traversal(path, d, dnode)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/order_dag.py", line 82, in _postorder_traversal
yield from _postorder_traversal(path, d, dnode)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/order_dag.py", line 80, in _postorder_traversal
raise OrderDAGError("cycle detected, reached %s from %s" % (repr(dnode),
repr(path)), path)
chimerax.core.order_dag.OrderDAGError: cycle detected, reached <'Surface', 1>
from ['models', <'Models', 1>, <'Surface', 1>, <'Surface', 2>]
chimerax.core.order_dag.OrderDAGError: cycle detected, reached from ['models',
, , ]
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/order_dag.py", line 80, in _postorder_traversal
raise OrderDAGError("cycle detected, reached %s from %s" % (repr(dnode),
repr(path)), path)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 1543, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 106, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 117, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 48, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2849, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2849, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save
mgr).save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 817, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 571, in save
for name, data in mgr.walk():
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 300, in walk
key = next(odg)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/order_dag.py", line 69, in order_dag
yield from _postorder_traversal(path, d, node)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/order_dag.py", line 82, in _postorder_traversal
yield from _postorder_traversal(path, d, dnode)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/order_dag.py", line 82, in _postorder_traversal
yield from _postorder_traversal(path, d, dnode)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/order_dag.py", line 82, in _postorder_traversal
yield from _postorder_traversal(path, d, dnode)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/order_dag.py", line 80, in _postorder_traversal
raise OrderDAGError("cycle detected, reached %s from %s" % (repr(dnode),
repr(path)), path)
chimerax.core.order_dag.OrderDAGError: cycle detected, reached <'Surface', 1>
from ['models', <'Models', 1>, <'Surface', 1>, <'Surface', 2>]
chimerax.core.order_dag.OrderDAGError: cycle detected, reached from ['models',
, , ]
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/order_dag.py", line 80, in _postorder_traversal
raise OrderDAGError("cycle detected, reached %s from %s" % (repr(dnode),
repr(path)), path)
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 440.82
OpenGL renderer: GeForce MX130/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: HP
Model: HP Pavilion Laptop 14-ce0xxx
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz
Cache Size: 6144 KB
Memory:
total used free shared buff/cache available
Mem: 15G 9.6G 5.3G 112M 618M 5.5G
Swap: 2.0G 135M 1.9G
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 620 [8086:5917] (rev 07)
Subsystem: Hewlett-Packard Company UHD Graphics 620 [103c:84ba]
Kernel driver in use: i915
Change History (2)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Session save: cycle detected |
comment:2 by , 5 years ago
Duplicate of #3292 reported by same user and fixed in ChimeraX 1.0.
Leaving this open for Greg to improve the error message.
This was very difficult to debug a few weeks ago due to the limited error info:
chimerax.core.order_dag.OrderDAGError: cycle detected, reached <'Surface', 1>
from ['models', <'Models', 1>, <'Surface', 1>, <'Surface', 2>]
By a thorough study of the Log I was able to figure out that the final two 'Surface' in the error were a shape icosahedron and a clip cap (even though the log never mentions a clip cap!).
The error reporting should definitely be improved. I suggest the following. Often models are in the chain of saved objects and knowing which model is involved when 10 are opened is crucial to debugging. So include the Model name in the error. The code could check isinstance(x, Model), but maybe to cover a bit more ground might report the name of any object with a name attribute hasattr(x, 'name') and isinstance(x.name, str). Could also include str(x) which helps for Model but often gives no additional info for other objects.
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Seems like the information provided with the error is still inadequate to actually determine the true cause.