Opened 4 years ago

Closed 4 years ago

#6539 closed defect (can't reproduce)

Hang during redraw?

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.4.0-210-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 575, resource id:
11349113, major code: 40 (TranslateCoords), minor code: 0  

> open
> /scratch2/jrai/80Sproject/TSV/Realspace/RealSpaceRefine_3/80sfull_jrai_0404a_real_space_refined_003.pdb

Chain information for 80sfull_jrai_0404a_real_space_refined_003.pdb #1  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
A | No description available  
B | No description available  
C | No description available  
E | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
L | No description available  
LB | No description available  
LD | No description available  
LE | No description available  
LG | No description available  
LH | No description available  
LI | No description available  
LJ | No description available  
LM | No description available  
LN | No description available  
LO | No description available  
LP | No description available  
LQ | No description available  
LS | No description available  
LT | No description available  
LU | No description available  
LV | No description available  
LX | No description available  
LZ | No description available  
La | No description available  
Lb | No description available  
Lc | No description available  
Le | No description available  
Lf | No description available  
Lg | No description available  
Li | No description available  
Lj | No description available  
Ll | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 5770, resource id:
11350468, major code: 40 (TranslateCoords), minor code: 0  

> save /scratch2/jrai/80Sproject/TSV/Realspace/RealSpaceRefine_3/test.pdb
> relModel #1

> open /scratch2/jrai/80Sproject/TSV/Realspace/RealSpaceRefine_3/test.pdb

Summary of feedback from opening
/scratch2/jrai/80Sproject/TSV/Realspace/RealSpaceRefine_3/test.pdb  
---  
warnings | Cannot find LINK/SSBOND residue ZN (201 )  
Cannot find LINK/SSBOND residue ZN (201 )  
Cannot find LINK/SSBOND residue ZN (201 )  
Cannot find LINK/SSBOND residue ZN (201 )  
Cannot find LINK/SSBOND residue ZN (202 )  
12 messages similar to the above omitted  
  
Chain information for test.pdb #2  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
A | No description available  
B | No description available  
C | No description available  
E | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
L | No description available  
LB | No description available  
LD | No description available  
LE | No description available  
LG | No description available  
LH | No description available  
LI | No description available  
LJ | No description available  
LM | No description available  
LN | No description available  
LO | No description available  
LP | No description available  
LQ | No description available  
LS | No description available  
LT | No description available  
LU | No description available  
LV | No description available  
LX | No description available  
LZ | No description available  
La | No description available  
Lb | No description available  
Lc | No description available  
Le | No description available  
Lf | No description available  
Lg | No description available  
Li | No description available  
Lj | No description available  
Ll | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 9509, resource id:
11351957, major code: 40 (TranslateCoords), minor code: 0  

> open /disks/li/d5/users/jrai/80Sproject/TSV-
> IRES/Postprocess/ppjob138_80S_eq_job041.mrc

Opened ppjob138_80S_eq_job041.mrc as #3, grid size 400,400,400, pixel 1.06,
shown at level 0.0461, step 2, values float32  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 18841, resource id:
11352642, major code: 40 (TranslateCoords), minor code: 0  

> close #2

> volume #3 level 0.03162

> ui tool show "Fit in Map"

Fit molecule 80sfull_jrai_0404a_real_space_refined_003.pdb (#1) to map
ppjob138_80S_eq_job041.mrc (#3) using 212757 atoms  
average map value = 0.04361, steps = 116  
shifted from previous position = 1.36  
rotated from previous position = 2.59 degrees  
atoms outside contour = 102951, contour level = 0.031622  
  
Position of 80sfull_jrai_0404a_real_space_refined_003.pdb (#1) relative to
ppjob138_80S_eq_job041.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99910777 0.04154839 -0.00757586 -8.41161390  
-0.04166408 0.99900655 -0.01581222 12.06788471  
0.00691136 0.01611375 0.99984628 -4.43653891  
Axis 0.35356805 -0.16044044 -0.92154680  
Axis point 281.67784722 201.50915378 -0.00000000  
Rotation angle (degrees) 2.58768446  
Shift along axis -0.82177644  
  

> hide atoms

> show cartoons

> save /disks/li/d5/users/jrai/80Sproject/TSV-IRES/Postprocess/mapfiton41.pdb
> relModel #1

QXcbConnection: XCB error: 3 (BadWindow), sequence: 25340, resource id:
11355685, major code: 40 (TranslateCoords), minor code: 0  

> open /disks/li/d5/users/jrai/80Sproject/TSV-IRES/Postprocess/mapfiton41.pdb

Summary of feedback from opening /disks/li/d5/users/jrai/80Sproject/TSV-
IRES/Postprocess/mapfiton41.pdb  
---  
warnings | Cannot find LINK/SSBOND residue ZN (201 )  
Cannot find LINK/SSBOND residue ZN (201 )  
Cannot find LINK/SSBOND residue ZN (201 )  
Cannot find LINK/SSBOND residue ZN (201 )  
Cannot find LINK/SSBOND residue ZN (202 )  
12 messages similar to the above omitted  
  
Chain information for mapfiton41.pdb #2  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
A | No description available  
B | No description available  
C | No description available  
E | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
L | No description available  
LB | No description available  
LD | No description available  
LE | No description available  
LG | No description available  
LH | No description available  
LI | No description available  
LJ | No description available  
LM | No description available  
LN | No description available  
LO | No description available  
LP | No description available  
LQ | No description available  
LS | No description available  
LT | No description available  
LU | No description available  
LV | No description available  
LX | No description available  
LZ | No description available  
La | No description available  
Lb | No description available  
Lc | No description available  
Le | No description available  
Lf | No description available  
Lg | No description available  
Li | No description available  
Lj | No description available  
Ll | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 25924, resource id:
11356297, major code: 40 (TranslateCoords), minor code: 0  

> hide #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!2 models

> show #!2 cartoons

> hide #!2 atoms

> select #2/y:2-207

1603 atoms, 1644 bonds, 206 residues, 1 model selected  

> save /disks/li/d5/users/jrai/80Sproject/TSV-IRES/Postprocess/mapfiton41.pdb
> models #2 relModel #3

QXcbConnection: XCB error: 3 (BadWindow), sequence: 34858, resource id:
11358690, major code: 40 (TranslateCoords), minor code: 0  

> open /disks/li/d5/users/jrai/80Sproject/TSV-IRES/Postprocess/mapfiton41.pdb

Chain information for mapfiton41.pdb #4  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
A | No description available  
B | No description available  
C | No description available  
E | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
L | No description available  
LB | No description available  
LD | No description available  
LE | No description available  
LG | No description available  
LH | No description available  
LI | No description available  
LJ | No description available  
LM | No description available  
LN | No description available  
LO | No description available  
LP | No description available  
LQ | No description available  
LS | No description available  
LT | No description available  
LU | No description available  
LV | No description available  
LX | No description available  
LZ | No description available  
La | No description available  
Lb | No description available  
Lc | No description available  
Le | No description available  
Lf | No description available  
Lg | No description available  
Li | No description available  
Lj | No description available  
Ll | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 36418, resource id:
11359305, major code: 40 (TranslateCoords), minor code: 0  

> hide #!2 models

> show #!2 models

> show sel cartoons

> hide sel atoms

> hide #!4 models

> close #4

> show #!3 models

Fit molecule mapfiton41.pdb (#2) to map ppjob138_80S_eq_job041.mrc (#3) using
212757 atoms  
average map value = 0.04361, steps = 116  
shifted from previous position = 1.36  
rotated from previous position = 2.59 degrees  
atoms outside contour = 102951, contour level = 0.031622  
  
Position of mapfiton41.pdb (#2) relative to ppjob138_80S_eq_job041.mrc (#3)
coordinates:  
Matrix rotation and translation  
0.99910777 0.04154839 -0.00757586 -8.41161390  
-0.04166408 0.99900655 -0.01581222 12.06788471  
0.00691136 0.01611375 0.99984628 -4.43653891  
Axis 0.35356805 -0.16044044 -0.92154680  
Axis point 281.67784722 201.50915378 -0.00000000  
Rotation angle (degrees) 2.58768446  
Shift along axis -0.82177644  
  

> save /disks/li/d5/users/jrai/80Sproject/TSV-IRES/Postprocess/mapfiton41.pdb
> relModel #3

QXcbConnection: XCB error: 3 (BadWindow), sequence: 46363, resource id:
11363923, major code: 40 (TranslateCoords), minor code: 0  

> save /disks/li/d5/users/jrai/80Sproject/TSV-IRES/Postprocess/mapfiton41.pdb
> models #2 relModel #3

QXcbConnection: XCB error: 3 (BadWindow), sequence: 10324, resource id:
11379040, major code: 40 (TranslateCoords), minor code: 0  

> save /disks/li/d5/users/jrai/80Sproject/TSV-IRES/Postprocess/mapfiton41.pdb
> models #2 relModel #3 serialNumbering amber

QXcbConnection: XCB error: 3 (BadWindow), sequence: 54805, resource id:
11399272, major code: 40 (TranslateCoords), minor code: 0  

> select #4/LO:2-126

Nothing selected  

> hide #!3 models

> select #4/P:2-176

Nothing selected  

> hide #!2 models

> show #!1 models

> show #!2 models

> hide #!1 models

> select #4/y:2-207

Nothing selected  

> select #4/w:2-82

Nothing selected  

> select #4/n:2-151

Nothing selected  

> open /disks/li/d5/users/jrai/80Sproject/TSV-IRES/Postprocess/mapfiton41.pdb

Summary of feedback from opening /disks/li/d5/users/jrai/80Sproject/TSV-
IRES/Postprocess/mapfiton41.pdb  
---  
warnings | Ignored bad PDB record found on line 103168  
TER ***** PHE P 176  
  
Ignored bad PDB record found on line 104953  
TER ***** ASN Q 244  
  
Ignored bad PDB record found on line 104955  
TER ***** MG R 301  
  
Ignored bad PDB record found on line 106464  
TER ***** LEU T 191  
  
Ignored bad PDB record found on line 108229  
TER ***** ALA U 219  
  
46 messages similar to the above omitted  
CONECT record to nonexistent atom: (113373, 113374)  
CONECT record for nonexistent atom: 113374  
PDB SEQRES record for chain B is incomplete. Ignoring input sequence records
as basis for sequence.  
PDB SEQRES record for chain G is incomplete. Ignoring input sequence records
as basis for sequence.  
PDB SEQRES record for chain H is incomplete. Ignoring input sequence records
as basis for sequence.  
PDB SEQRES record for chain J is incomplete. Ignoring input sequence records
as basis for sequence.  
PDB SEQRES record for chain N is incomplete. Ignoring input sequence records
as basis for sequence.  
17 messages similar to the above omitted  
  
Chain information for mapfiton41.pdb #4  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
E | No description available  
G | No description available  
G | No description available  
H | No description available  
H | No description available  
I | No description available  
I | No description available  
J | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 39955, resource id:
10943468, major code: 40 (TranslateCoords), minor code: 0  

> hide #!2,4 atoms

> show #!2,4 cartoons

> hide #!2 models

> select #4/w:2-82

610 atoms, 620 bonds, 81 residues, 1 model selected  

> select #4/w:2-82

610 atoms, 620 bonds, 81 residues, 1 model selected  

> close #4

> open /disks/li/d5/users/jrai/80Sproject/TSV-
> IRES/Postprocess/mapfiton41_headerdelte.pdb

Chain information for mapfiton41_headerdelte.pdb #4  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
A | No description available  
B | No description available  
C | No description available  
E | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
L | No description available  
LB | No description available  
LD | No description available  
LE | No description available  
LG | No description available  
LH | No description available  
LI | No description available  
LJ | No description available  
LM | No description available  
LN | No description available  
LO | No description available  
LP | No description available  
LQ | No description available  
LS | No description available  
LT | No description available  
LU | No description available  
LV | No description available  
LX | No description available  
LZ | No description available  
La | No description available  
Lb | No description available  
Lc | No description available  
Le | No description available  
Lf | No description available  
Lg | No description available  
Li | No description available  
Lj | No description available  
Ll | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 42987, resource id:
10944300, major code: 40 (TranslateCoords), minor code: 0  

> hide #!4 atoms

> show #!4 cartoons

> select #4/LO:2-126

984 atoms, 995 bonds, 125 residues, 1 model selected  

> close #1

> close #3

> close #4

> open
> /scratch2/jrai/80Sproject/TSV/Realspace/RealSpaceRefine_3/80sfull_jrai_0404a_real_space_refined_003_edited.pdb

Chain information for 80sfull_jrai_0404a_real_space_refined_003_edited.pdb #1  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
A | No description available  
B | No description available  
C | No description available  
E | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
L | No description available  
LB | No description available  
LD | No description available  
LE | No description available  
LG | No description available  
LH | No description available  
LI | No description available  
LJ | No description available  
LM | No description available  
LN | No description available  
LO | No description available  
LP | No description available  
LQ | No description available  
LS | No description available  
LT | No description available  
LU | No description available  
LV | No description available  
LX | No description available  
LZ | No description available  
La | No description available  
Lb | No description available  
Lc | No description available  
Le | No description available  
Lf | No description available  
Lg | No description available  
Li | No description available  
Lj | No description available  
Ll | No description available  
Lo | No description available  
N | No description available  
P | No description available  
Q | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 7120, resource id:
10953961, major code: 40 (TranslateCoords), minor code: 0  

> hide #!1 atoms

> show #!1 cartoons

> show #!2 models

> close #2

> open /disks/li/d5/users/jrai/80Sproject/TSV-
> IRES/Postprocess/ppjob138_80S_eq_job041.mrc

Opened ppjob138_80S_eq_job041.mrc as #2, grid size 400,400,400, pixel 1.06,
shown at level 0.0461, step 2, values float32  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 13352, resource id:
10955025, major code: 40 (TranslateCoords), minor code: 0  

> volume #2 step 1

Fit molecule 80sfull_jrai_0404a_real_space_refined_003_edited.pdb (#1) to map
ppjob138_80S_eq_job041.mrc (#2) using 212757 atoms  
average map value = 0.04361, steps = 116  
shifted from previous position = 1.36  
rotated from previous position = 2.59 degrees  
atoms outside contour = 120295, contour level = 0.046067  
  
Position of 80sfull_jrai_0404a_real_space_refined_003_edited.pdb (#1) relative
to ppjob138_80S_eq_job041.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99910777 0.04154839 -0.00757586 -8.41161390  
-0.04166408 0.99900655 -0.01581222 12.06788471  
0.00691136 0.01611375 0.99984628 -4.43653891  
Axis 0.35356805 -0.16044044 -0.92154680  
Axis point 281.67784722 201.50915378 -0.00000000  
Rotation angle (degrees) 2.58768446  
Shift along axis -0.82177644  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 22323, resource id:
10956304, major code: 40 (TranslateCoords), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 23880, resource id:
10958142, major code: 40 (TranslateCoords), minor code: 0  

Fit molecule 80sfull_jrai_0404a_real_space_refined_003_edited.pdb (#1) to map
ppjob138_80S_eq_job041.mrc (#2) using 212757 atoms  
average map value = 0.04361, steps = 80  
shifted from previous position = 0.00875  
rotated from previous position = 0.00637 degrees  
atoms outside contour = 120318, contour level = 0.046067  
  
Position of 80sfull_jrai_0404a_real_space_refined_003_edited.pdb (#1) relative
to ppjob138_80S_eq_job041.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99910773 0.04153789 -0.00763864 -8.39788180  
-0.04165396 0.99900840 -0.01572118 12.05371961  
0.00697804 0.01602534 0.99984724 -4.43525663  
Axis 0.35182009 -0.16198435 -0.92194560  
Axis point 281.40466775 201.29053497 0.00000000  
Rotation angle (degrees) 2.58592304  
Shift along axis -0.81799203  
  

> save /disks/li/d5/users/jrai/80Sproject/TSV-IRES/Postprocess/mapfiton41.pdb
> relModel #1

QXcbConnection: XCB error: 3 (BadWindow), sequence: 25684, resource id:
10958980, major code: 40 (TranslateCoords), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 29622, resource id:
10959578, major code: 40 (TranslateCoords), minor code: 0  

Fit molecule 80sfull_jrai_0404a_real_space_refined_003_edited.pdb (#1) to map
ppjob138_80S_eq_job041.mrc (#2) using 212757 atoms  
average map value = 0.04361, steps = 116  
shifted from previous position = 0.0187  
rotated from previous position = 0.0122 degrees  
atoms outside contour = 120317, contour level = 0.046067  
  
Position of 80sfull_jrai_0404a_real_space_refined_003_edited.pdb (#1) relative
to ppjob138_80S_eq_job041.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99910664 0.04158827 -0.00750614 -8.42731956  
-0.04170329 0.99900384 -0.01587938 12.08379761  
0.00683827 0.01617822 0.99984574 -4.44417050  
Axis 0.35464604 -0.15868902 -0.92143582  
Axis point 281.84971680 201.77327787 0.00000000  
Rotation angle (degrees) 2.59045790  
Shift along axis -0.81126361  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 33281, resource id:
10962332, major code: 40 (TranslateCoords), minor code: 0  

Traceback (most recent call last):  
File "/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 460.32.03
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUS
Model: All Series
OS: Ubuntu 16.04 xenial
Architecture: 64bit ELF
Virutal Machine: none
CPU: 16 Intel(R) Core(TM) i7-6900K CPU @ 3.20GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G         32G         14G        314M         15G         28G
	Swap:           15G          0B         15G

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:1b80] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. Device [1043:859b]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Hang during redraw?

comment:2 by Tom Goddard, 4 years ago

Resolution: → can't reproduce
Status: assigned → closed

The user typed ctrl-C at the shell (Linux) to interrupt ChimeraX. No info about why. They log is littered with X windows errors though, so perhaps rendering failed.

QXcbConnection: XCB error: 3 (BadWindow), sequence: 25684, resource id: 10958980, major code: 40 (TranslateCoords), minor code: 0

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