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Opened 19 months ago
Closed 19 months ago
#14784 closed defect (can't reproduce)
glDrawBuffer: invalid operation
| Reported by: | 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-5.15.0-79-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open EMCV40s-608-zcls1258_88k_1xbin_0_r1_2.5A.mrc
Opened EMCV40s-608-zcls1258_88k_1xbin_0_r1_2.5A.mrc as #1, grid size
608,608,608, pixel 0.83, shown at level 3.97, step 4, values float32
> volume #1 step 2
> volume #1 level 1.783
> open
> /home/chunying/modeling/fromAndrei/2024-01-13-IRES6-tRNA_real_space_refined_000.pdb
Chain information for 2024-01-13-IRES6-tRNA_real_space_refined_000.pdb #2
---
Chain | Description
A | No description available
w | No description available
> hide #!1 models
> show #!1 models
> ui tool show "Fit to Segments"
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule 2024-01-13-IRES6-tRNA_real_space_refined_000.pdb (#2) to map
EMCV40s-608-zcls1258_88k_1xbin_0_r1_2.5A.mrc (#1) using 3368 atoms
average map value = 6.336, steps = 192
shifted from previous position = 19
rotated from previous position = 17.1 degrees
atoms outside contour = 643, contour level = 1.7832
Position of 2024-01-13-IRES6-tRNA_real_space_refined_000.pdb (#2) relative to
EMCV40s-608-zcls1258_88k_1xbin_0_r1_2.5A.mrc (#1) coordinates:
Matrix rotation and translation
0.96069099 -0.24076360 -0.13822342 106.45631149
0.25307460 0.96417510 0.07949607 -73.13169321
0.11413182 -0.11135200 0.98720548 -17.25165224
Axis -0.32540161 -0.43027316 0.84200879
Axis point 369.72705304 357.87359908 0.00000000
Rotation angle (degrees) 17.05263119
Shift along axis -17.70049318
> transparency 50
> hide #!2 target m
> open
> /home/chunying/modeling/fromAndrei/2024-01-13-IRES6-tRNA_real_space_refined_000.pdb
Chain information for 2024-01-13-IRES6-tRNA_real_space_refined_000.pdb #3
---
Chain | Description
A | No description available
w | No description available
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> close #2
> open 6zmw
6zmw title:
Structure of a human 48S translational initiation complex [more info...]
Chain information for 6zmw #2
---
Chain | Description | UniProt
1 | Eukaryotic translation initiation factor 3 subunit B | EIF3B_HUMAN 1-814
2 | Eukaryotic translation initiation factor 3 subunit I | EIF3I_HUMAN 1-325
3 | Eukaryotic translation initiation factor 3 subunit K | EIF3K_HUMAN 1-218
4 | Eukaryotic translation initiation factor 3 subunit F | EIF3F_HUMAN 1-357
5 | Eukaryotic translation initiation factor 3 subunit L | EIF3L_HUMAN 1-564
6 | Eukaryotic translation initiation factor 3 subunit M | EIF3M_HUMAN 1-374
7 | mRNA |
8 | Eukaryotic translation initiation factor 3 subunit H | EIF3H_HUMAN 1-352
9 | 60S ribosomal protein L41 | RL41_HUMAN 1-25
A | 18S rRNA |
B | 40S ribosomal protein S11 | RS11_HUMAN 1-158
C | 40S ribosomal protein S4, X isoform | RS4X_HUMAN 1-263
D | 40S ribosomal protein S9 | RS9_HUMAN 1-194
E | 40S ribosomal protein S23 | RS23_HUMAN 1-143
F | 40S ribosomal protein S30 | RS30_HUMAN 75-133
G | 40S ribosomal protein S7 | RS7_HUMAN 1-194
H | 40S ribosomal protein S27 | RS27_HUMAN 1-84
I | 40S ribosomal protein S13 | RS13_HUMAN 1-151
J | 40S ribosomal protein S15a | RS15A_HUMAN 1-130
K | 40S ribosomal protein S21 | RS21_HUMAN 1-83
L | 40S ribosomal protein S2 | RS2_HUMAN 1-293
M | 40S ribosomal protein S17 | RS17_HUMAN 1-135
N | 40S ribosomal protein SA | RSSA_HUMAN 1-295
O | 40S ribosomal protein S3a | RS3A_HUMAN 1-264
P | 40S ribosomal protein S14 | RS14_HUMAN 1-151
Q | 40S ribosomal protein S26 | RS26_HUMAN 1-115
R | 40S ribosomal protein S8 | RS8_HUMAN 1-208
S | 40S ribosomal protein S6 | RS6_HUMAN 1-249
T | 40S ribosomal protein S24 | RS24_HUMAN 1-133
V | 40S ribosomal protein S5 | RS5_HUMAN 1-204
Y | 40S ribosomal protein S16 | RS16_HUMAN 1-146
Z | 40S ribosomal protein S3 | RS3_HUMAN 1-243
a | 40S ribosomal protein S10 | RS10_HUMAN 1-165
b | 40S ribosomal protein S15 | RS15_HUMAN 1-145
c | Receptor of activated protein C kinase 1 | RACK1_HUMAN 1-317
d | 40S ribosomal protein S19 | RS19_HUMAN 1-145
e | 40S ribosomal protein S25 | RS25_HUMAN 1-125
f | 40S ribosomal protein S18 | RS18_HUMAN 1-152
g | Eukaryotic translation initiation factor 4 gamma 1 | IF4G1_HUMAN 290-1599
h | 40S ribosomal protein S20 | RS20_HUMAN 1-119
i | 40S ribosomal protein S29 | RS29_HUMAN 1-56
j | Eukaryotic initiation factor 4A-I | IF4A1_HUMAN 1-406
k | Ubiquitin-40S ribosomal protein S27a | RS27A_HUMAN 1-156
m | 40S ribosomal protein S12 | RS12_HUMAN 1-132
n | 40S ribosomal protein S28 | RS28_HUMAN 1-69
o | Eukaryotic translation initiation factor 3 subunit G | EIF3G_HUMAN 1-320
p | Eukaryotic translation initiation factor 1 | EIF1_HUMAN 1-113
q | Eukaryotic translation initiation factor 1A, X-chromosomal | IF1AX_HUMAN
1-144
r | Eukaryotic translation initiation factor 2 subunit 1 | IF2A_HUMAN 1-315
s | Eukaryotic translation initiation factor 2 subunit 2 | IF2B_HUMAN 1-333
t | Eukaryotic translation initiation factor 2 subunit 3 | IF2G_HUMAN 1-472
u | Eukaryotic translation initiation factor 3 subunit A | EIF3A_HUMAN 1-1382
v | Eukaryotic translation initiation factor 3 subunit E | EIF3E_HUMAN 1-445
w | Initiator Met-tRNA-i |
x | Eukaryotic translation initiation factor 3 subunit D | EIF3D_HUMAN 1-548
y | Eukaryotic translation initiation factor 3 subunit C | EIF3C_HUMAN 1-913
z | Eukaryotic translation initiation factor 3 subunit J | EIF3J_HUMAN 1-258
Non-standard residues in 6zmw #2
---
MG — magnesium ion
ZN — zinc ion
> hide #!2 models
> hide #!1 models
> hide #!3 models
> show #!2 models
> hide #!2 atoms
> show #!2 cartoons
> show #!1 models
> select add #1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,7.4275,0,1,0,134.77,0,0,1,-7.1047
> undo
> select subtract #1
Nothing selected
> select add #2
118147 atoms, 123656 bonds, 1743 pseudobonds, 13029 residues, 4 models
selected
> view matrix models #2,1,0,0,12.753,0,1,0,159.82,0,0,1,-13.32
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.82634,-0.39254,-0.40383,271.45,0.19996,0.87484,-0.44122,258.65,0.52648,0.28385,0.8014,-174.73
> view matrix models
> #2,0.47871,-0.87771,-0.021378,383.53,0.79349,0.44294,-0.41735,197.76,0.37578,0.18282,0.9085,-137.46
> view matrix models
> #2,0.16833,0.78519,0.59594,-121.73,-0.18128,-0.5696,0.80168,383.62,0.96892,-0.24298,0.046459,45.675
> view matrix models
> #2,-0.015578,0.88793,0.45972,-59.33,-0.44725,-0.41741,0.79104,421.33,0.89427,-0.19329,0.40363,-45.29
> view matrix models
> #2,-0.052134,0.89145,0.4501,-47.5,-0.38843,-0.43333,0.81323,403.02,0.92,-0.13244,0.36886,-58.088
> view matrix models
> #2,-0.29879,0.91364,0.27567,63.075,-0.44678,-0.38917,0.80556,410.05,0.84328,0.11753,0.52447,-143.17
> view matrix models
> #2,-0.14412,0.98895,0.034629,68.311,-0.43918,-0.095283,0.89333,309.48,0.88676,0.11354,0.44806,-132.96
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.14412,0.98895,0.034629,-25.328,-0.43918,-0.095283,0.89333,228.3,0.88676,0.11354,0.44806,-75.732
> view matrix models
> #2,-0.14412,0.98895,0.034629,-15.469,-0.43918,-0.095283,0.89333,145,0.88676,0.11354,0.44806,-122.76
> view matrix models
> #2,-0.14412,0.98895,0.034629,-13.701,-0.43918,-0.095283,0.89333,141.86,0.88676,0.11354,0.44806,-123.43
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.14051,0.98784,0.066555,-23.26,-0.4541,-0.12403,0.88228,156.28,0.8798,0.093742,0.466,-121.49
> select subtract #2
Nothing selected
> select add #2
118147 atoms, 123656 bonds, 1743 pseudobonds, 13029 residues, 4 models
selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.14051,0.98784,0.066555,-2.4222,-0.4541,-0.12403,0.88228,167.58,0.8798,0.093742,0.466,-142.45
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.091535,0.99416,0.057209,-14.897,-0.41658,-0.090411,0.90459,142.6,0.90448,0.058969,0.42242,-128.39
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.091535,0.99416,0.057209,-11.563,-0.41658,-0.090411,0.90459,149.13,0.90448,0.058969,0.42242,-131.95
> select subtract #2
Nothing selected
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule 6zmw (#2) to map EMCV40s-608-zcls1258_88k_1xbin_0_r1_2.5A.mrc
(#1) using 118147 atoms
average map value = 8.138, steps = 340
shifted from previous position = 7.78
rotated from previous position = 16.7 degrees
atoms outside contour = 21187, contour level = 1.7832
Position of 6zmw (#2) relative to EMCV40s-608-zcls1258_88k_1xbin_0_r1_2.5A.mrc
(#1) coordinates:
Matrix rotation and translation
-0.09091071 0.97308140 0.21177306 -53.81990818
-0.16986917 -0.22468958 0.95950980 107.74095910
0.98126434 0.05125600 0.18572322 -88.28658590
Axis -0.55036813 -0.46628319 -0.69258567
Axis point 56.37364629 95.58569169 0.00000000
Rotation angle (degrees) 124.39802298
Shift along axis 40.52898857
> select #3/w
1601 atoms, 1783 bonds, 75 residues, 1 model selected
> show #!3 models
> color #3 #204a87ff
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,1.1549,0,1,0,9.0296,0,0,1,1.2725
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.97173,0.21442,0.098828,-62.743,-0.23351,0.93465,0.26814,-7.0541,-0.034873,-0.28364,0.9583,75.183
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.97173,0.21442,0.098828,-66.499,-0.23351,0.93465,0.26814,-7.9958,-0.034873,-0.28364,0.9583,79.528
> view matrix models
> #3,0.97173,0.21442,0.098828,-54.368,-0.23351,0.93465,0.26814,-14.978,-0.034873,-0.28364,0.9583,91.301
> view matrix models
> #3,0.97173,0.21442,0.098828,-45.605,-0.23351,0.93465,0.26814,-11.64,-0.034873,-0.28364,0.9583,94.557
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.8878,0.010904,-0.4601,181.5,0.031624,0.99591,0.084626,-27.68,0.45914,-0.089681,0.88383,-31.573
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.8878,0.010904,-0.4601,184.32,0.031624,0.99591,0.084626,-17.697,0.45914,-0.089681,0.88383,-32.187
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.8878,0.010904,-0.4601,192.21,0.031624,0.99591,0.084626,-18.451,0.45914,-0.089681,0.88383,-39.322
> ui tool show "Fit to Segments"
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit molecule 2024-01-13-IRES6-tRNA_real_space_refined_000.pdb (#3) to map
EMCV40s-608-zcls1258_88k_1xbin_0_r1_2.5A.mrc (#1) using 3368 atoms
average map value = 8.352, steps = 224
shifted from previous position = 12.7
rotated from previous position = 27.8 degrees
atoms outside contour = 62, contour level = 1.7832
Position of 2024-01-13-IRES6-tRNA_real_space_refined_000.pdb (#3) relative to
EMCV40s-608-zcls1258_88k_1xbin_0_r1_2.5A.mrc (#1) coordinates:
Matrix rotation and translation
0.99999809 0.00062993 -0.00184907 18.59261650
-0.00062795 0.99999923 0.00107273 18.92703566
0.00184974 -0.00107157 0.99999771 19.71749733
Axis -0.48114830 -0.82995908 -0.28224855
Axis point -6045.71309048 0.00000000 2197.86008060
Rotation angle (degrees) 0.12767275
Shift along axis -30.21970583
> select add #3
3368 atoms, 3755 bonds, 158 residues, 1 model selected
> select subtract #3
Nothing selected
> hide #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:519
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/A
1767 atoms, 1972 bonds, 83 residues, 1 model selected
> color sel red
> select add #3
3368 atoms, 3755 bonds, 158 residues, 1 model selected
> select subtract #3
Nothing selected
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> color #3 dodgerblue
> select #3/A:524
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/A:524
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/A:519
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/A
1767 atoms, 1972 bonds, 83 residues, 1 model selected
> color sel red
> select add #3
3368 atoms, 3755 bonds, 158 residues, 1 model selected
> select subtract #3
Nothing selected
> color #1 #d3d7cfff models
> color #1 #babdb6ff models
> color #1 #d3d7cfff models
> color #1 #babdb6ff models
> transparency 50
> volume #1 step 1
> volume #1 level 1.9
> volume #1 level 2.1
> volume #1 step 2
> volume #1 level 1.633
> surface dust #1 size 8.3
> open /home/chunying/6zmw-FIT.pdb
Summary of feedback from opening /home/chunying/6zmw-FIT.pdb
---
warnings | Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
4921 messages similar to the above omitted
Ignored bad PDB record found on line 104926
TER 104926 GLU u 706
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
600 messages similar to the above omitted
Ignored bad PDB record found on line 105532
TER 105532 PHE v 154
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
2025 messages similar to the above omitted
Ignored bad PDB record found on line 107563
TER 107563 ILE v 422
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
1599 messages similar to the above omitted
Ignored bad PDB record found on line 109168
TER 109168 A w 75
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
324 messages similar to the above omitted
Ignored bad PDB record found on line 109498
TER 109498 TYR x 59
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
180 messages similar to the above omitted
Ignored bad PDB record found on line 109684
TER 109684 THR x 88
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
2312 messages similar to the above omitted
Ignored bad PDB record found on line 112002
TER 112002 PHE x 527
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
897 messages similar to the above omitted
Ignored bad PDB record found on line 112905
TER 112905 LYS y 160
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
1921 messages similar to the above omitted
Ignored bad PDB record found on line 114832
TER 114832 GLN y 522
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
2637 messages similar to the above omitted
Ignored bad PDB record found on line 117475
TER 117475 LEU y 863
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
265 messages similar to the above omitted
Ignored bad PDB record found on line 117746
TER 117746 LYS z 96
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
110 messages similar to the above omitted
Ignored bad PDB record found on line 117862
TER 117862 THR z 135
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
405 messages similar to the above omitted
Chain information for 6zmw-FIT.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
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
S | No description available
T | No description available
V | 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
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | 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
> hide #!4 models
> close #4
> volume style mesh
> volume style surface
> volume style image
> volume style mesh
> volume style surface
> show #!2 models
> color #2 lightgreen
> select #3/A:519
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/A
1767 atoms, 1972 bonds, 83 residues, 1 model selected
> select add #3
3368 atoms, 3755 bonds, 158 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #3
3368 atoms, 3755 bonds, 158 residues, 1 model selected
> show sel surfaces
> select subtract #3
2 models selected
> select #3/A:519
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/A
1767 atoms, 1972 bonds, 83 residues, 1 model selected
> show sel atoms
> show sel cartoons
> hide sel surfaces
> show sel surfaces
> select add #3
3368 atoms, 3755 bonds, 158 residues, 2 models selected
> select subtract #3
2 models selected
> color #2 #e09fc0ff
> color #2 #fce94fff
> color #2 #bfb140ff
> color #2 #c9c07aff
> select #2/7
336 atoms, 363 bonds, 28 residues, 1 model selected
> hide #!2 models
> select add #2
118147 atoms, 123656 bonds, 1743 pseudobonds, 13029 residues, 4 models
selected
> select subtract #2
Nothing selected
> select add #2
118147 atoms, 123656 bonds, 1743 pseudobonds, 13029 residues, 4 models
selected
> show #!2 models
> select #2/7
336 atoms, 363 bonds, 28 residues, 1 model selected
> color #2 #5c3566ff
> color #2 #e9b96eff
> select #2/7
336 atoms, 363 bonds, 28 residues, 1 model selected
> select #2/7
336 atoms, 363 bonds, 28 residues, 1 model selected
> select add #2
118147 atoms, 123656 bonds, 1743 pseudobonds, 13029 residues, 4 models
selected
> select subtract #2
Nothing selected
> volume #1 change image level -0.6227,0 level 3.962,0.8 level 35.98,1
> volume #1 level 1.312
> volume #1 level 1.7
> set bgColor white
> color #1 #555753ff models
> color #1 #888a85ff models
> transparency 50
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #1 level 1.8
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> save
> /home/chunying/Figure_40S_IRES/40STM_IRES6-tRNA_real_apce_refined_000.jpg
> width 1124 height 803 supersample 3
> volume #1 level 2.056
> lighting simple
> hide #!3 models
> lighting soft
> lighting simple
> lighting full
> lighting simple
> show #!3 models
> lighting shadows true
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> lighting flat
> lighting simple
> lighting soft
> lighting simple
> set bgColor black
> set bgColor white
> set bgColor black
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> set bgColor white
> lighting simple
> lighting soft
> lighting simple
> lighting full
[Repeated 1 time(s)]
> lighting simple
> show #!2 models
> select #2/7
336 atoms, 363 bonds, 28 residues, 1 model selected
> hide sel atoms
> show sel surfaces
> select add #2
118147 atoms, 123656 bonds, 1743 pseudobonds, 13029 residues, 5 models
selected
> select subtract #2
1 model selected
> hide #!1 models
> hide #!3 models
> show #!1 models
> show #!3 models
> select #3/A:564
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #3/A:529-564
764 atoms, 849 bonds, 36 residues, 1 model selected
> ui tool show "Map Eraser"
> select add #3
3368 atoms, 3755 bonds, 158 residues, 2 models selected
> select subtract #3
2 models selected
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.
GLError(
err = 1282,
description = b'invalid operation',
baseOperation = glDrawBuffer,
cArguments = (GL_BACK,)
)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 84, in draw_new_frame
view.draw(check_for_changes = False)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 188, in draw
self._draw_scene(camera, drawings)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 270, in _draw_scene
silhouette.finish_silhouette_drawing(r)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1825, in finish_silhouette_drawing
fb = r.pop_framebuffer()
^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 764, in pop_framebuffer
fb.activate()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 2313, in activate
GL.glDrawBuffer(self._draw_buffer)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1282,
description = b'invalid operation',
baseOperation = glDrawBuffer,
cArguments = (GL_BACK,)
)
OpenGL version: 3.3.0 NVIDIA 510.108.03
OpenGL renderer: NVIDIA RTX A6000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:2
Manufacturer: Supermicro
Model: X11DAi-N
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 112 Intel(R) Xeon(R) Gold 6258R CPU @ 2.70GHz
Cache Size: 39424 KB
Memory:
total used free shared buff/cache available
Mem: 187Gi 50Gi 113Gi 146Mi 23Gi 135Gi
Swap: 31Gi 15Gi 16Gi
Graphics:
04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)
DeviceName: Aspeed Video 2500
Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000]
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.3
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.7
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 19 months ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → glDrawBuffer: invalid operation |
comment:2 by , 19 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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Drawing silhouettes, no back buffer. Probable graphics driver bug.