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#3292 closed defect (fixed)

Circular dependency saving surface ("shape icosahedron"?)

Reported by:	chimerax-bug-report@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Sessions	Version:
Keywords:		Cc:	Greg Couch
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/ad5_2019.pdb format pdb

Chain information for ad5_2019.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F I | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U V | No description available  
W | No description available  
X | No description available  
Y Z | No description available  
  

> split #1

Chain information for ad5_2019.pdb A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for ad5_2019.pdb B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for ad5_2019.pdb C #1.3  
---  
Chain | Description  
C | No description available  
  
Chain information for ad5_2019.pdb D #1.4  
---  
Chain | Description  
D | No description available  
  
Chain information for ad5_2019.pdb E #1.5  
---  
Chain | Description  
E | No description available  
  
Chain information for ad5_2019.pdb F #1.6  
---  
Chain | Description  
F | No description available  
  
Chain information for ad5_2019.pdb G #1.7  
---  
Chain | Description  
G | No description available  
  
Chain information for ad5_2019.pdb H #1.8  
---  
Chain | Description  
H | No description available  
  
Chain information for ad5_2019.pdb I #1.9  
---  
Chain | Description  
I | No description available  
  
Chain information for ad5_2019.pdb J #1.10  
---  
Chain | Description  
J | No description available  
  
Chain information for ad5_2019.pdb K #1.11  
---  
Chain | Description  
K | No description available  
  
Chain information for ad5_2019.pdb L #1.12  
---  
Chain | Description  
L | No description available  
  
Chain information for ad5_2019.pdb M #1.13  
---  
Chain | Description  
M | No description available  
  
Chain information for ad5_2019.pdb N #1.14  
---  
Chain | Description  
N | No description available  
  
Chain information for ad5_2019.pdb O #1.15  
---  
Chain | Description  
O | No description available  
  
Chain information for ad5_2019.pdb P #1.16  
---  
Chain | Description  
P | No description available  
  
Chain information for ad5_2019.pdb Q #1.17  
---  
Chain | Description  
Q | No description available  
  
Chain information for ad5_2019.pdb R #1.18  
---  
Chain | Description  
R | No description available  
  
Chain information for ad5_2019.pdb S #1.19  
---  
Chain | Description  
S | No description available  
  
Chain information for ad5_2019.pdb T #1.20  
---  
Chain | Description  
T | No description available  
  
Chain information for ad5_2019.pdb U #1.21  
---  
Chain | Description  
U | No description available  
  
Chain information for ad5_2019.pdb V #1.22  
---  
Chain | Description  
V | No description available  
  
Chain information for ad5_2019.pdb W #1.23  
---  
Chain | Description  
W | No description available  
  
Chain information for ad5_2019.pdb X #1.24  
---  
Chain | Description  
X | No description available  
  
Chain information for ad5_2019.pdb Y #1.25  
---  
Chain | Description  
Y | No description available  
  
Chain information for ad5_2019.pdb Z #1.26  
---  
Chain | Description  
Z | No description available  
  
Split ad5_2019.pdb (#1) into 26 models  

> lighting simple

> close #1.21-23,25-26#1.1-16,24

> select #1.19

647 atoms, 653 bonds, 2 pseudobonds, 2 models selected  

> color (#!1.19 & sel) cyan

> select #1.17

874 atoms, 884 bonds, 2 pseudobonds, 2 models selected  

> color (#!1.17 & sel) magenta

> select #1.18

698 atoms, 706 bonds, 2 pseudobonds, 2 models selected  

> color (#!1.18 & sel) hot pink

> select #1.20

663 atoms, 669 bonds, 2 pseudobonds, 2 models selected  

> color (#!1.20 & sel) purple

> select clear

> sym #1 I,222r

> show surfaces

> select #1.17.2

874 atoms, 1 model selected  

> color (#!1.17 & sel) magenta

> select #1.18.2

698 atoms, 1 model selected  

> color (#!1.18 & sel) hot pink

> select #1.19.2

647 atoms, 1 model selected  

> color (#!1.19 & sel) cyan

> select #1.20.2

663 atoms, 1 model selected  

> color (#!1.20 & sel) purple

> select clear

> view orient

> shape icosahedron radius 450 orientation 222r mesh true divisions 2

> view orient

> toolshed show "Side View"

> graphics silhouettes true

> set bgColor white

> lighting shadows true

> lighting shadows false

> lighting full

> lighting full

> lighting simple

> lighting simple

> distance style radius 0.11

> distance style radius 0.12

> distance style radius 0.11

> distance style radius 0.1

Alignment identifier is 1.17.Q  
Alignment identifier is 1.18.R  
Alignment identifier is 1.19.S  
Alignment identifier is 1.20.T  

> cartoon style #1.17.1 with 10

Expected a keyword  

> cartoon style #1.17.1 widh 10

Expected a keyword  

> cartoon style #1.17.1 size 10

Expected a keyword  

> size #1.17.1 pseudobondRadius 10

Changed 2 pseudobond radii  

> size #1.17.1 pseudobondRadius 1

Changed 2 pseudobond radii  

> size #1.18.1 pseudobondRadius 1

Changed 2 pseudobond radii  

> size #1.19.1 pseudobondRadius 1

Changed 2 pseudobond radii  

> size #1.20.1 pseudobondRadius 1

Changed 2 pseudobond radii  

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true

> lighting shadows false

> view name facet

> save /home/mpillana/AD41_MARZO_2020/IX/vijey/ad5.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.  
  

> open /home/mpillana/AD41_MARZO_2020/IX/badv3_ix_fit.pdb

Chain information for badv3_ix_fit.pdb #3  
---  
Chain | Description  
K N O P R U | No description available  
  

> close #3

> open /home/mpillana/AD41_MARZO_2020/IX/all_IX_badv3_facet.pdb

Chain information for all_IX_badv3_facet.pdb #3  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R S T U | No description available  
  

> split #2

> split #3

Chain information for all_IX_badv3_facet.pdb A #3.1  
---  
Chain | Description  
A | No description available  
  
Chain information for all_IX_badv3_facet.pdb B #3.2  
---  
Chain | Description  
B | No description available  
  
Chain information for all_IX_badv3_facet.pdb C #3.3  
---  
Chain | Description  
C | No description available  
  
Chain information for all_IX_badv3_facet.pdb D #3.4  
---  
Chain | Description  
D | No description available  
  
Chain information for all_IX_badv3_facet.pdb E #3.5  
---  
Chain | Description  
E | No description available  
  
Chain information for all_IX_badv3_facet.pdb F #3.6  
---  
Chain | Description  
F | No description available  
  
Chain information for all_IX_badv3_facet.pdb G #3.7  
---  
Chain | Description  
G | No description available  
  
Chain information for all_IX_badv3_facet.pdb H #3.8  
---  
Chain | Description  
H | No description available  
  
Chain information for all_IX_badv3_facet.pdb I #3.9  
---  
Chain | Description  
I | No description available  
  
Chain information for all_IX_badv3_facet.pdb J #3.10  
---  
Chain | Description  
J | No description available  
  
Chain information for all_IX_badv3_facet.pdb K #3.11  
---  
Chain | Description  
K | No description available  
  
Chain information for all_IX_badv3_facet.pdb L #3.12  
---  
Chain | Description  
L | No description available  
  
Chain information for all_IX_badv3_facet.pdb M #3.13  
---  
Chain | Description  
M | No description available  
  
Chain information for all_IX_badv3_facet.pdb N #3.14  
---  
Chain | Description  
N | No description available  
  
Chain information for all_IX_badv3_facet.pdb O #3.15  
---  
Chain | Description  
O | No description available  
  
Chain information for all_IX_badv3_facet.pdb P #3.16  
---  
Chain | Description  
P | No description available  
  
Chain information for all_IX_badv3_facet.pdb Q #3.17  
---  
Chain | Description  
Q | No description available  
  
Chain information for all_IX_badv3_facet.pdb R #3.18  
---  
Chain | Description  
R | No description available  
  
Chain information for all_IX_badv3_facet.pdb S #3.19  
---  
Chain | Description  
S | No description available  
  
Chain information for all_IX_badv3_facet.pdb T #3.20  
---  
Chain | Description  
T | No description available  
  
Chain information for all_IX_badv3_facet.pdb U #3.21  
---  
Chain | Description  
U | No description available  
  
Split all_IX_badv3_facet.pdb (#3) into 21 models  

> hide #!1 models

> hide #3.1 models

> show #3.1 models

> hide #3.2 models

> hide #3.3 models

> show #3.3 models

> hide #3.3 models

> hide #3.4 models

> hide #3.5 models

> hide #3.6 models

> hide #3.7 models

> hide #3.8 models

> hide #3.9 models

> hide #3.10 models

> hide #3.11 models

> hide #3.12 models

> hide #3.13 models

> hide #3.14 models

> show #3.14 models

> hide #3.15 models

> show #3.15 models

> hide #3.15 models

> hide #3.16 models

> show #3.16 models

> hide #3.16 models

> hide #3.17 models

> show #3.17 models

> hide #3.18 models

> show #3.18 models

> hide #3.19 models

> hide #3.20 models

> hide #3.21 models

> show #3.21 models

> close #3.2-13,15-16,19-20

> show #!1 models

> hide #3.21 models

> show #3.21 models

> hide #3.17 models

> show #3.17 models

> hide #3.14 models

> show #3.14 models

> hide #3.1 models

> close #3.1

> hide #3.14 models

> show #3.14 models

> hide #3.17 models

> show #3.17 models

> select #3.17

826 atoms, 838 bonds, 1 model selected  

> color sel cyan

> select #3.14

826 atoms, 838 bonds, 1 model selected  

> color sel purple

> select #3.17

826 atoms, 838 bonds, 1 model selected  

> ~select #3.17

Nothing selected  

> select #3.18

826 atoms, 838 bonds, 1 model selected  

> color sel magenta

> select #3.21

826 atoms, 838 bonds, 1 model selected  

> color sel hot pink

> select clear

> sym #3 I,222r

> select #3

3304 atoms, 3352 bonds, 5 models selected  

> show sel surfaces

> hide #!1 models

> show sel atoms

> show sel atoms

> select #3

3304 atoms, 3352 bonds, 9 models selected  

> select #3.14

826 atoms, 838 bonds, 2 models selected  

> select #3.17

826 atoms, 838 bonds, 2 models selected  

> ~select #3.17

1 model selected  

> select #3.14

826 atoms, 838 bonds, 2 models selected  

> color (#!3.14 & sel) purple

> select #3.17.1

826 atoms, 1 model selected  

> color (#!3.17 & sel) cyan

> select #3.18.1

826 atoms, 1 model selected  

> color (#!3.18 & sel) hot pink

> select #3.21.1

826 atoms, 1 model selected  

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> select #3.21.2

1 model selected  

> color #3.21.2 hot pink

> select #3.21.1

826 atoms, 1 model selected  

> color (#!3.21 & sel) hot pink

> select #3.18.1

826 atoms, 1 model selected  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> show #!3 models

> color (#!3.18 & sel) magenta

> select clear

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> view orient

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> open /home/mpillana/AD41_MARZO_2020/D_1292106460_model_P1V44.cif

Summary of feedback from opening
/home/mpillana/AD41_MARZO_2020/D_1292106460_model_P1V44.cif  
---  
warning | Missing or incomplete entity_poly_seq table. Inferred polymer
connectivity.  
  
Chain information for D_1292106460_model_P1V44.cif #4  
---  
Chain | Description  
A | B2ZX09_ADE41 Hexon protein OS=Human adenovirus F serotype 41  
B | B2ZX09_ADE41 Hexon protein OS=Human adenovirus F serotype 41  
C J | B2ZX09_ADE41 Hexon protein OS=Human adenovirus F serotype 41  
D I | B2ZX09_ADE41 Hexon protein OS=Human adenovirus F serotype 41  
E | B2ZX09_ADE41 Hexon protein OS=Human adenovirus F serotype 41  
F G | B2ZX09_ADE41 Hexon protein OS=Human adenovirus F serotype 41  
H | B2ZX09_ADE41 Hexon protein OS=Human adenovirus F serotype 41  
K | B2ZX09_ADE41 Hexon protein OS=Human adenovirus F serotype 41  
L | B2ZX09_ADE41 Hexon protein OS=Human adenovirus F serotype 41  
M | Q9QAH8_ADE41 Penton protein OS=Human adenovirus F serotype 41  
N | Q67716_ADE41 Pre-hexon-linking protein IIIa OS=Human adenovirus F serotype
41  
O P | B5SNS9_ADE41 Pre-hexon-linking protein VIII OS=Human adenovirus F
serotype 41  
Q R S T | B5SNR3_ADE41 Hexon-interlacing protein OS=Human adenovirus F
serotype 41  
U V Y u | B5SNS4_ADE41 Pre-protein VI OS=Human adenovirus F serotype 41  
W | B5SNS1_ADE41 Pre-histone-like nucleoprotein OS=Human adenovirus F serotype
41  
w | B5SNS1_ADE41 Pre-histone-like nucleoprotein OS=Human adenovirus F serotype
41  
  

> lighting simple

> graphics silhouettes false

> lighting shadows true

> lighting shadows false

> split #4

Chain information for D_1292106460_model_P1V44.cif A #4.1  
---  
Chain | Description  
A | No description available  
  
Chain information for D_1292106460_model_P1V44.cif B #4.2  
---  
Chain | Description  
B | No description available  
  
Chain information for D_1292106460_model_P1V44.cif C #4.3  
---  
Chain | Description  
C | No description available  
  
Chain information for D_1292106460_model_P1V44.cif D #4.4  
---  
Chain | Description  
D | No description available  
  
Chain information for D_1292106460_model_P1V44.cif E #4.5  
---  
Chain | Description  
E | No description available  
  
Chain information for D_1292106460_model_P1V44.cif F #4.6  
---  
Chain | Description  
F | No description available  
  
Chain information for D_1292106460_model_P1V44.cif G #4.7  
---  
Chain | Description  
G | No description available  
  
Chain information for D_1292106460_model_P1V44.cif H #4.8  
---  
Chain | Description  
H | No description available  
  
Chain information for D_1292106460_model_P1V44.cif I #4.9  
---  
Chain | Description  
I | No description available  
  
Chain information for D_1292106460_model_P1V44.cif J #4.10  
---  
Chain | Description  
J | No description available  
  
Chain information for D_1292106460_model_P1V44.cif K #4.11  
---  
Chain | Description  
K | No description available  
  
Chain information for D_1292106460_model_P1V44.cif L #4.12  
---  
Chain | Description  
L | No description available  
  
Chain information for D_1292106460_model_P1V44.cif M #4.13  
---  
Chain | Description  
M | No description available  
  
Chain information for D_1292106460_model_P1V44.cif N #4.14  
---  
Chain | Description  
N | No description available  
  
Chain information for D_1292106460_model_P1V44.cif O #4.15  
---  
Chain | Description  
O | No description available  
  
Chain information for D_1292106460_model_P1V44.cif P #4.16  
---  
Chain | Description  
P | No description available  
  
Chain information for D_1292106460_model_P1V44.cif Q #4.17  
---  
Chain | Description  
Q | No description available  
  
Chain information for D_1292106460_model_P1V44.cif R #4.18  
---  
Chain | Description  
R | No description available  
  
Chain information for D_1292106460_model_P1V44.cif S #4.19  
---  
Chain | Description  
S | No description available  
  
Chain information for D_1292106460_model_P1V44.cif T #4.20  
---  
Chain | Description  
T | No description available  
  
Chain information for D_1292106460_model_P1V44.cif U #4.21  
---  
Chain | Description  
U | No description available  
  
Chain information for D_1292106460_model_P1V44.cif V #4.22  
---  
Chain | Description  
V | No description available  
  
Chain information for D_1292106460_model_P1V44.cif W #4.23  
---  
Chain | Description  
W | No description available  
  
Chain information for D_1292106460_model_P1V44.cif Y #4.24  
---  
Chain | Description  
Y | No description available  
  
Chain information for D_1292106460_model_P1V44.cif u #4.25  
---  
Chain | Description  
u | No description available  
  
Chain information for D_1292106460_model_P1V44.cif w #4.26  
---  
Chain | Description  
w | No description available  
  
Split D_1292106460_model_P1V44.cif (#4) into 26 models  

> close #4.14,21-26#4.1-13,15-16

> hide #!1 models

> hide #!4 models

> show #!4 models

> hide #!3 models

> show #!3 models

> select #4.20

365 atoms, 374 bonds, 1 model selected  

> color sel cyan

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> select #4.17

365 atoms, 374 bonds, 1 model selected  

> color sel hot pink

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> color sel magenta

> hide #!4 models

> show #!4 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> select #4.18

365 atoms, 374 bonds, 1 model selected  

> color sel hot pink

> select clear

> sym #4 I,222r

> hide #!3 models

> show #4.17-20 surfaces

> show #!3 models

> hide #!3 models

> select #4.17.1

365 atoms, 1 model selected  

> color (#!4.17 & sel) magenta

> select #4.18.1

365 atoms, 1 model selected  

> color (#!4.18 & sel) hot pink

> select #4.20.1

365 atoms, 1 model selected  

> color (#!4.20 & sel) cyan

> show #!3 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> select clear

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!4 models

> show #!1 models

> hide #!1 models

> show #!1 models

> show #!3 models

> hide #!3 models

> show #!3 models

> save /home/mpillana/AD41_MARZO_2020/IX/vijey/ix_vijey.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        3.2G         10G        146M        1.8G         11G
	Swap:          2.0G        968M        1.1G

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 (7)

comment:1 by pett, 5 years ago

Cc:	Greg Couch added
Component:	Unassigned → Sessions
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Circular dependency saving surface ("shape icosahedron"?)

comment:2 by Tom Goddard, 5 years ago

I tried all the steps the user did up to this session save error and got no error. Open pdb, split, close some models, sym command, surfaces, cartoon, side view, shape icosahedron, show distances, view name, save session. Here is my log.

Startup Messages
warnings QWebEngineUrlScheme::registerScheme: Scheme "cxcmd" already registered
QWebEngineUrlScheme::registerScheme: Scheme "help" already registered
QWebEngineUrlScheme::registerScheme: Scheme "cxcmd" already registered
QWebEngineUrlScheme::registerScheme: Scheme "help" already registered
QWebEngineUrlScheme::registerScheme: Scheme "cxcmd" already registered
8 messages similar to the above omitted
Replacing file-saver for 'DCD coordinates' from MD-crds bundle with that from MDcrds bundle
Replacing opener for 'Gromacs full-precision coordinates' from MD-crds bundle with that from MDcrds bundle
Replacing opener for 'Gromacs compressed coordinates' from MD-crds bundle with that from MDcrds bundle
Replacing opener for 'DCD coordinates' from MD-crds bundle with that from MDcrds bundle
notes Replacing data format 'Gromacs full-precision coordinates' as defined by ChimeraX-MD-crds bundle with definition from ChimeraX-MDcrds bundle
Replacing data format 'Gromacs compressed coordinates' as defined by ChimeraX-MD-crds bundle with definition from ChimeraX-MDcrds bundle
Replacing data format 'DCD coordinates' as defined by ChimeraX-MD-crds bundle with definition from ChimeraX-MDcrds bundle
UCSF ChimeraX version: 1.0rc202005220158 (2020-05-21)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
open 6cgv
Summary of feedback from opening 6cgv fetched from pdb
note Fetching compressed mmCIF 6cgv from http://files.rcsb.org/download/6cgv.cif
6cgv title:
Revised crystal structure of human adenovirus [more info...]

Chain information for 6cgv #1
Chain Description
A B C D E F G H I J K L Hexon protein
M Pre-hexon-linking protein IIIa
N Penton protein
P Q R S Hexon-interlacing protein
U V Pre-hexon-linking protein VIII
W Pre-protein VI
6cgv mmCIF Assemblies
1 complete icosahedral assembly
2 icosahedral asymmetric unit
3 icosahedral pentamer
4 icosahedral 23 hexamer
5 icosahedral asymmetric unit, std point frame
6 crystal asymmetric unit, crystal frame

split #1
Chain information for 6cgv A #1.1
Chain Description
A No description available
Chain information for 6cgv B #1.2
Chain Description
B No description available
Chain information for 6cgv C #1.3
Chain Description
C No description available
Chain information for 6cgv D #1.4
Chain Description
D No description available
Chain information for 6cgv E #1.5
Chain Description
E No description available
Chain information for 6cgv F #1.6
Chain Description
F No description available
Chain information for 6cgv G #1.7
Chain Description
G No description available
Chain information for 6cgv H #1.8
Chain Description
H No description available
Chain information for 6cgv I #1.9
Chain Description
I No description available
Chain information for 6cgv J #1.10
Chain Description
J No description available
Chain information for 6cgv K #1.11
Chain Description
K No description available
Chain information for 6cgv L #1.12
Chain Description
L No description available
Chain information for 6cgv M #1.13
Chain Description
M No description available
Chain information for 6cgv N #1.14
Chain Description
N No description available
Chain information for 6cgv P #1.15
Chain Description
P No description available
Chain information for 6cgv Q #1.16
Chain Description
Q No description available
Chain information for 6cgv R #1.17
Chain Description
R No description available
Chain information for 6cgv S #1.18
Chain Description
S No description available
Chain information for 6cgv U #1.19
Chain Description
U No description available
Chain information for 6cgv V #1.20
Chain Description
V No description available
Chain information for 6cgv W #1.21
Chain Description
W No description available
Split 6cgv (#1) into 21 models
close #1.4-21
sym #1 I,222r
show surfaces
shape icosahedron radius 450 orientation 222r mesh true divisions 2
ui tool show "Side View"
usage distance style
distance style [pbonds] [color a color] [dashes dashes] [radius a number] [decimalPlaces decimalPlaces] [symbol true or false] [setDefaults true or false]

— set distance display properties

pbonds: a pseudobonds specifier or nothing
dashes: an integer ≥ 0
decimalPlaces: an integer ≥ 0

ui mousemode right distance
select #1.1/A:72@OD1
1 atom, 1 model selected
select clear
hide #2 models
distance #1.1/A:73@NE #1.3/C:54@CA
Distance between 6cgv A #1.1/A ARG 73 NE and 6cgv C #1.3/C HIS 54 CA: 61.810Å
show #2 models
distance style radius 0.1
distance #1.2/B:255@OD1 #1.2/B:255@ND2
Distance between 6cgv B #1.2/B ASN 255 OD1 and ND2: 2.252Å
show cartoons
view name facet
save /Users/goddard/Desktop/test.cxs

comment:3 by Tom Goddard, 5 years ago

It is apparent that some actions the user took are not in the bug report log. The used distances and set the distance style but there is no distance command. They showed sequence alignments, I see log lines like "Alignment identifier is 1.17.Q" but there is no command that showed a sequence alignment. The toolbar sequence button is not logging a command.

comment:4 by Tom Goddard, 5 years ago

The error seems to say that two Surface models directly save references to each other. When would a Surface ever save a reference to another Surface? Aha, if a Surface sets "SESSION_SAVE_DRAWING" which the icosahedron shape does (STL the only other case), then it saves all its child drawings. But Model save saves parents. So if the icosahedron drawing had a Surface child model that would cause the circular reference.

It turns out another bug prevents "shape icos ; shape icos model #1.1 ; save test,.cxs" from generating a circular dependency error. The child model claims its parent is root instead of #1.

comment:5 by pett, 5 years ago

It's not 1000% certain that a distance command wasn't logged, though it seems likely. Playing with the Distance preferences can log "distance style" commands with no existing distances.

comment:6 by Tom Goddard, 5 years ago

Found it. "shape icos ; clip ; save test.cxs". The clip cap is the child surface. How did the clip command never appear in the log? I bet side view does not log the clip command.

comment:7 by Tom Goddard, 5 years ago

Resolution:	→ fixed
Status:	assigned → closed

Fixed.

Session save of surface geometry was incorrectly trying to save child drawings.

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