#14784 closed defect (can't reproduce)

glDrawBuffer: invalid operation

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-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 Eric Pettersen, 19 months ago

Component: UnassignedGraphics
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionglDrawBuffer: invalid operation

comment:2 by Tom Goddard, 19 months ago

Resolution: can't reproduce
Status: assignedclosed

Drawing silhouettes, no back buffer. Probable graphics driver bug.

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