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Opened 22 months ago
Closed 22 months ago
#14401 closed defect (not a bug)
Invalid wheel filename: 'Isolde.whl'
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Tool Shed | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.5.0-14-generic-x86_64-with-glibc2.38
ChimeraX Version: 1.7rc202311220128 (2023-11-22 01:28:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7rc202311220128 (2023-11-22)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/azinas/Projects/Petra/RefmacServalcat/J214/refined.pdb
Chain information for refined.pdb #1
---
Chain | Description
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Af | No description available
Ag | No description available
> hide atoms
> show cartoons
> open /home/azinas/J214_resampled.mrc format mrc
No such file/path: /home/azinas/J214_resampled.mrc
> open /home/azinas/Projects/ClpG_Y541A/J214_resampled.mrc
Summary of feedback from opening
/home/azinas/Projects/ClpG_Y541A/J214_resampled.mrc
---
notes | open kw {}
Opened J214_resampled.mrc as #2, grid size 338,338,338, pixel 1, shown at
level 1.17, step 2, values float32
> color zone #2 near #1 distance 6
> volume #2 level 2.733
> volume #2 level 8.548
> open /home/azinas/Projects/ClpG_Y541A/j214_open/J214_emready.pdb
Chain information for J214_emready.pdb #3
---
Chain | Description
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Af | No description available
Ag | No description available
> close #3
> open /home/azinas/Projects/ClpG_Y541A/j214_open/j214_open_raw.cif
Summary of feedback from opening
/home/azinas/Projects/ClpG_Y541A/j214_open/j214_open_raw.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for j214_open_raw.cif #3
---
Chain | Description
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
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 h | No description available
g | 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
> hide atoms
> show cartoons
> select #3/c:1-16
143 atoms, 142 bonds, 16 residues, 1 model selected
> select ~sel & ##selected
30475 atoms, 30862 bonds, 3878 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #3
143 atoms, 142 bonds, 16 residues, 1 model selected
> style sel stick
Changed 143 atom styles
> show sel atoms
> volume #2 level 6.853
> volume #2 level 5.723
> volume #2 level 2.035
> volume #2 step 1
> volume #2 level 5.947
> close
> open /home/azinas/Downloads/cryosparc_P10_J249_007_volume_map.mrc
Summary of feedback from opening
/home/azinas/Downloads/cryosparc_P10_J249_007_volume_map.mrc
---
notes | open kw {}
Opened cryosparc_P10_J249_007_volume_map.mrc as #1, grid size 400,400,400,
pixel 0.846, shown at level 0.0263, step 2, values float32
> volume resample #1 spacing 1.0
Opened cryosparc_P10_J249_007_volume_map.mrc resampled as #2, grid size
338,338,338, pixel 1, shown at step 1, values float32
> open /home/azinas/Projects/ClpG_Y541A/J249_emready.mrc
Summary of feedback from opening
/home/azinas/Projects/ClpG_Y541A/J249_emready.mrc
---
notes | open kw {}
Opened J249_emready.mrc as #3, grid size 400,400,400, pixel 0.846, shown at
level 1.09, step 2, values float32
> lighting soft
> volume #3 level 3.103
> lighting soft
> lighting full
> lighting soft
> volume #3 step 1
> open /home/azinas/Projects/Petra/ModelCraft/J214_Starting/modelcraft.cif
Summary of feedback from opening
/home/azinas/Projects/Petra/ModelCraft/J214_Starting/modelcraft.cif
---
warnings | Unknown polymer entity '1' near line 335
Unknown polymer entity '2' near line 999
Unknown polymer entity '4' near line 1597
Unknown polymer entity '6' near line 2138
Unknown polymer entity '7' near line 2516
67 messages similar to the above omitted
Chain information for modelcraft.cif #4
---
Chain | Description
Ac | No description available
Ad | No description available
Ae | No description available
Af | No description available
H | No description available
> hide atoms
> show cartoons
> show atoms
> select /Ac:1-14
70 atoms, 69 bonds, 14 residues, 1 model selected
> select /Ad:131-173
301 atoms, 263 bonds, 1 pseudobond, 42 residues, 2 models selected
> select /Ae:425-426
9 atoms, 8 bonds, 2 residues, 1 model selected
> select /Af:554-555
12 atoms, 11 bonds, 2 residues, 1 model selected
> select /H:1-61
305 atoms, 304 bonds, 61 residues, 1 model selected
> close #4
> show #!3 models
> open /home/azinas/Projects/ClpG_Y541A/j214_open/j214_open_raw.cif format
> mmcif
Summary of feedback from opening
/home/azinas/Projects/ClpG_Y541A/j214_open/j214_open_raw.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for j214_open_raw.cif #4
---
Chain | Description
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
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 h | No description available
g | 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
> close #4
> open /home/azinas/Projects/ClpG_Y541A/J214_resampled.mrc format mrc
Summary of feedback from opening
/home/azinas/Projects/ClpG_Y541A/J214_resampled.mrc
---
notes | open kw {}
Opened J214_resampled.mrc as #4, grid size 338,338,338, pixel 1, shown at
level 1.17, step 2, values float32
Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 2 maps.
> fitmap #3 inMap #4
Fit map J249_emready.mrc in map J214_resampled.mrc using 365500 points
correlation = 0.5462, correlation about mean = 0.04647, overlap = 6.163e+06
steps = 128, shift = 6.06, angle = 9.34 degrees
Position of J249_emready.mrc (#3) relative to J214_resampled.mrc (#4)
coordinates:
Matrix rotation and translation
0.98860791 0.11134375 0.10127670 -36.42471993
-0.11731902 0.99156592 0.05507525 16.45371440
-0.09429024 -0.06632951 0.99333265 24.90651785
Axis -0.37417851 0.60275188 -0.70475571
Axis point 86.74500509 315.87007573 0.00000000
Rotation angle (degrees) 9.33626368
Shift along axis 5.99384424
> select add #4
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.29112,-0.926,-0.24036,321.23,-0.95117,-0.30709,0.031035,382.39,-0.10255,0.21959,-0.97019,312.77
> view matrix models
> #4,0.24516,-0.95411,-0.17199,322.32,-0.85158,-0.29672,0.43218,295.82,-0.46337,0.040508,-0.88524,390.58
> view matrix models
> #4,0.30411,-0.9518,-0.040031,289.6,-0.93591,-0.30635,0.17387,355.5,-0.17776,-0.015412,-0.98395,368.55
> view matrix models
> #4,0.50359,0.86394,0.0032748,-66.029,0.86377,-0.50341,-0.022025,117.68,-0.017379,0.01392,-0.99975,338.96
> fitmap #4 inMap #3
Fit map J214_resampled.mrc in map J249_emready.mrc using 48265 points
correlation = 0.9762, correlation about mean = 0.9291, overlap = 1.759e+06
steps = 104, shift = 5.35, angle = 6.71 degrees
Position of J214_resampled.mrc (#4) relative to J249_emready.mrc (#3)
coordinates:
Matrix rotation and translation
0.39817540 0.91730612 -0.00241454 -53.21405204
0.91724235 -0.39817677 -0.01103321 83.11795001
-0.01108224 0.00217844 -0.99993622 338.42498341
Axis 0.83611183 0.54854419 -0.00403561
Axis point 0.00000000 58.21545157 169.28076649
Rotation angle (degrees) 179.54732157
Shift along axis -0.26477999
> volume #4 level 1.853
> volume #4 step 1
> select subtract #4
Nothing selected
> volume #4 level 3.154
> open /home/azinas/Projects/ClpG_Y541A/J249_emready/J249_emready.cif
Summary of feedback from opening
/home/azinas/Projects/ClpG_Y541A/J249_emready/J249_emready.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for J249_emready.cif #5
---
Chain | Description
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Af | No description available
Ag | No description available
Ah | No description available
Ai | No description available
Aj | No description available
Ak | No description available
Al | No description available
Am | No description available
> hide atoms
> show cartoons
> close #3
> open /home/azinas/Projects/ClpG_Y541A/J249_emready.mrc
Summary of feedback from opening
/home/azinas/Projects/ClpG_Y541A/J249_emready.mrc
---
notes | open kw {}
Opened J249_emready.mrc as #3, grid size 400,400,400, pixel 0.846, shown at
level 1.09, step 2, values float32
> volume #3 level 12.27
> show #!4 models
> hide #!3 models
> fitmap #5 inMap #4
Fit molecule J249_emready.cif (#5) to map J214_resampled.mrc (#4) using 21216
atoms
average map value = 9.423, steps = 100
shifted from previous position = 6.02
rotated from previous position = 9.35 degrees
atoms outside contour = 1629, contour level = 3.1542
Position of J249_emready.cif (#5) relative to J214_resampled.mrc (#4)
coordinates:
Matrix rotation and translation
0.39798108 0.91732767 -0.01100078 -51.28929893
0.91739079 -0.39798106 0.00228505 81.10306249
-0.00228196 -0.01100142 -0.99993688 339.14682833
Axis -0.83605371 -0.54863323 0.00397196
Axis point 0.00000000 58.18584097 169.25922401
Rotation angle (degrees) 179.54472605
Shift along axis -0.26814985
> volume #4 level 10.28
> save /home/azinas/Projects/ClpG_Y541A/J249_emready/214_algined.pdb relModel
> #4
> open /home/azinas/Projects/ClpG_Y541A/J249_emready/214_algined.pdb
Chain information for 214_algined.pdb #6
---
Chain | Description
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Af | No description available
Ag | No description available
Ah | No description available
Ai | No description available
Aj | No description available
Ak | No description available
Al | No description available
Am | No description available
> hide #!5 models
> hide #6 atoms
> show #6 cartoons
> select add #6
21216 atoms, 21536 bonds, 2688 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.36241,0.91193,-0.19247,-22.367,0.9317,-0.35986,0.049334,76.348,-0.024273,-0.1972,-0.98006,370.55
> view matrix models
> #6,0.49053,0.76949,-0.40898,17.438,0.86936,-0.4644,0.16896,85.853,-0.059913,-0.43843,-0.89676,406.12
> view matrix models
> #6,0.36608,0.81124,-0.45594,39.142,0.89935,-0.43428,-0.050607,111.99,-0.23906,-0.39152,-0.88857,427.07
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.36608,0.81124,-0.45594,36.634,0.89935,-0.43428,-0.050607,112.57,-0.23906,-0.39152,-0.88857,436.07
> fitmap #6 inMap #4
Fit molecule 214_algined.pdb (#6) to map J214_resampled.mrc (#4) using 21216
atoms
average map value = 9.423, steps = 236
shifted from previous position = 17.7
rotated from previous position = 22.1 degrees
atoms outside contour = 10777, contour level = 10.276
Position of 214_algined.pdb (#6) relative to J214_resampled.mrc (#4)
coordinates:
Matrix rotation and translation
0.95544628 -0.23689777 -0.17607349 83.26626578
0.21222127 0.96594477 -0.14802988 -13.55090272
0.20514521 0.10406806 0.97318307 -41.17667668
Axis 0.39342836 -0.59493641 0.70090284
Axis point 81.09154646 316.37183157 0.00000000
Rotation angle (degrees) 18.68627519
Shift along axis 11.96038627
> save /home/azinas/Projects/ClpG_Y541A/J249_emready/214_algined.pdb models #6
> relModel #4
> close #4
> open /home/azinas/Projects/ClpG_Y541A/J214_resampled.mrc
Summary of feedback from opening
/home/azinas/Projects/ClpG_Y541A/J214_resampled.mrc
---
notes | open kw {}
Opened J214_resampled.mrc as #4, grid size 338,338,338, pixel 1, shown at
level 1.17, step 2, values float32
> fitmap #6 inMap #4
Fit molecule 214_algined.pdb (#6) to map J214_resampled.mrc (#4) using 21216
atoms
average map value = 2.298, steps = 84
shifted from previous position = 0.535
rotated from previous position = 1.02 degrees
atoms outside contour = 9651, contour level = 1.1711
Position of 214_algined.pdb (#6) relative to J214_resampled.mrc (#4)
coordinates:
Matrix rotation and translation
0.62757867 0.70763856 -0.32464240 -9.93909952
0.71160363 -0.69053238 -0.12955818 200.32518620
-0.31585646 -0.14970876 -0.93692156 395.24645648
Axis -0.90209949 -0.39332868 0.17750789
Axis point 0.00000000 103.55261228 196.02489063
Rotation angle (degrees) 179.36006682
Shift along axis 0.33178000
> view matrix models
> #6,0.62758,0.70764,-0.32464,-79.977,0.7116,-0.69053,-0.12956,217.1,-0.31586,-0.14971,-0.93692,387.86
> view matrix models
> #6,0.62758,0.70764,-0.32464,-13.825,0.7116,-0.69053,-0.12956,202.59,-0.31586,-0.14971,-0.93692,397.58
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.86265,-0.11159,0.49334,-43.571,0.20863,0.96702,-0.14608,-6.3663,-0.46077,0.22894,0.85749,54.475
> view matrix models
> #6,0.9379,-0.30452,0.16617,32.882,0.32331,0.94094,-0.10051,-28.977,-0.12575,0.14799,0.98096,-9.114
> fitmap #6 inMap #4
Fit molecule 214_algined.pdb (#6) to map J214_resampled.mrc (#4) using 21216
atoms
average map value = 9.423, steps = 200
shifted from previous position = 19.4
rotated from previous position = 20.3 degrees
atoms outside contour = 540, contour level = 1.1711
Position of 214_algined.pdb (#6) relative to J214_resampled.mrc (#4)
coordinates:
Matrix rotation and translation
0.95538517 -0.23710232 -0.17612977 83.32372033
0.21241116 0.96589517 -0.14808123 -13.57166336
0.20523329 0.10406268 0.97316509 -41.18966398
Axis 0.39326659 -0.59480854 0.70110213
Axis point 81.18077421 316.30765383 0.00000000
Rotation angle (degrees) 18.69778148
Shift along axis 11.96281536
> save /home/azinas/Projects/ClpG_Y541A/J249_emready/214_algined.pdb models #6
> relModel #4
> close #6
> close #4
> close #5
> open /home/azinas/Projects/ClpG_Y541A/J249_emready.mrc
Summary of feedback from opening
/home/azinas/Projects/ClpG_Y541A/J249_emready.mrc
---
notes | open kw {}
Opened J249_emready.mrc as #4, grid size 400,400,400, pixel 0.846, shown at
level 1.09, step 2, values float32
> close #3
> open /home/azinas/Projects/ClpG_Y541A/j214_open/J214_emready-coot-2.pdb
Summary of feedback from opening
/home/azinas/Projects/ClpG_Y541A/j214_open/J214_emready-coot-2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU a 14
GLU a 20 1 7
Start residue of secondary structure not found: HELIX 2 2 ALA a 30 LEU a 40 1
11
Start residue of secondary structure not found: HELIX 3 3 LYS a 58 ALA a 71 1
14
Start residue of secondary structure not found: HELIX 4 4 GLU a 76 LEU a 78 1
3
Start residue of secondary structure not found: HELIX 5 5 ILE a 88 VAL a 92 1
5
334 messages similar to the above omitted
Chain information for J214_emready-coot-2.pdb #3
---
Chain | Description
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Af | No description available
S | No description available
> select add #3
55784 atoms, 56182 bonds, 3656 residues, 1 model selected
> view matrix models
> #3,0.25806,-0.96215,-0.087635,309.99,-0.79365,-0.26284,0.54867,262.6,-0.55093,-0.072037,-0.83144,419.89
> view matrix models
> #3,0.05021,-0.89452,-0.4442,395.01,-0.8418,-0.27724,0.46315,288,-0.53745,0.35067,-0.76693,333.37
> view matrix models
> #3,0.89339,0.096716,-0.43875,76.464,0.034893,-0.98854,-0.14686,363.3,-0.44793,0.11589,-0.88653,378.9
> view matrix models
> #3,0.61974,0.75934,0.1983,-99.43,0.78468,-0.60414,-0.13889,165.57,0.014337,0.24168,-0.97025,291.35
> fitmap #3 inMap #4
Fit molecule J214_emready-coot-2.pdb (#3) to map J249_emready.mrc (#4) using
55784 atoms
average map value = 6.924, steps = 196
shifted from previous position = 4.88
rotated from previous position = 20.4 degrees
atoms outside contour = 1779, contour level = 1.0877
Position of J214_emready-coot-2.pdb (#3) relative to J249_emready.mrc (#4)
coordinates:
Matrix rotation and translation
0.39796046 0.91739891 -0.00258969 -53.16031099
0.91733499 -0.39796383 -0.01101485 83.06638784
-0.01113562 0.00200786 -0.99993599 338.43616799
Axis 0.83604765 0.54864149 -0.00410420
Axis point 0.00000000 58.18776036 169.28138833
Rotation angle (degrees) 179.55376124
Shift along axis -0.25989594
> select subtract #3
Nothing selected
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 40 residues in model #3 to IUPAC-IUB
standards.
Chain information for J214_emready-coot-2.pdb
---
Chain | Description
3.2/Aa | No description available
3.2/Ab | No description available
3.2/Ac | No description available
3.2/Ad | No description available
3.2/Ae | No description available
3.2/Af | No description available
3.2/S | No description available
> clipper associate #4 toModel #3
Opened J249_emready.mrc as #3.1.1.1, grid size 400,400,400, pixel 0.846, shown
at step 1, values float32
> isolde sim start /Aa-S
Sim termination reason: None
ISOLDE: stopped sim
Failed to add atoms ['HB3', 'HB2'] to atom C because this will lead to having
5 atoms attached, which is more than its assigned geometry can support. This
is probably due to an error in the MD template (SER). If this template is
built into ISOLDE, please report this using Help/Report a bug
Fetching CCD HIC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/HIC/HIC.cif
> delete atoms (#!3.2 & sel)
> delete bonds (#!3.2 & sel)
Traceback (most recent call last):
File "/home/azinas/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 184, in
_fix_button_clicked_cb
indices = [i for i in range(table.rowCount()) if table.item(i,
0).data(USER_ROLE)[0].name == residue.name]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/azinas/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 184, in
<listcomp>
indices = [i for i in range(table.rowCount()) if table.item(i,
0).data(USER_ROLE)[0].name == residue.name]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "atomic_cpp/cymol.pyx", line 1259, in
chimerax.atomic.cymol.CyResidue.name.__get__
RuntimeError: Residue already deleted
RuntimeError: Residue already deleted
File "atomic_cpp/cymol.pyx", line 1259, in
chimerax.atomic.cymol.CyResidue.name.__get__
See log for complete Python traceback.
> delete atoms (#!3.2 & sel)
> delete bonds (#!3.2 & sel)
Traceback (most recent call last):
File "/home/azinas/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 184, in
_fix_button_clicked_cb
indices = [i for i in range(table.rowCount()) if table.item(i,
0).data(USER_ROLE)[0].name == residue.name]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/azinas/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 184, in
<listcomp>
indices = [i for i in range(table.rowCount()) if table.item(i,
0).data(USER_ROLE)[0].name == residue.name]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "atomic_cpp/cymol.pyx", line 1259, in
chimerax.atomic.cymol.CyResidue.name.__get__
RuntimeError: Residue already deleted
RuntimeError: Residue already deleted
File "atomic_cpp/cymol.pyx", line 1259, in
chimerax.atomic.cymol.CyResidue.name.__get__
See log for complete Python traceback.
> delete atoms (#!3.2 & sel)
> delete bonds (#!3.2 & sel)
Traceback (most recent call last):
File "/home/azinas/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 184, in
_fix_button_clicked_cb
indices = [i for i in range(table.rowCount()) if table.item(i,
0).data(USER_ROLE)[0].name == residue.name]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/azinas/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 184, in
<listcomp>
indices = [i for i in range(table.rowCount()) if table.item(i,
0).data(USER_ROLE)[0].name == residue.name]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "atomic_cpp/cymol.pyx", line 1259, in
chimerax.atomic.cymol.CyResidue.name.__get__
RuntimeError: Residue already deleted
RuntimeError: Residue already deleted
File "atomic_cpp/cymol.pyx", line 1259, in
chimerax.atomic.cymol.CyResidue.name.__get__
See log for complete Python traceback.
Failed to add atoms ['HB3'] to atom CB because this will lead to having 5
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (LYS). If this template is built
into ISOLDE, please report this using Help/Report a bug
Failed to add atoms ['HB2', 'HB3'] to atom C because this will lead to having
5 atoms attached, which is more than its assigned geometry can support. This
is probably due to an error in the MD template (SER). If this template is
built into ISOLDE, please report this using Help/Report a bug
[Repeated 1 time(s)]Fetching CCD FME from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/FME/FME.cif
Fetching CCD AME from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/AME/AME.cif
Failed to add atoms ['HA'] to atom CA because this will lead to having 5 atoms
attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (ALA). If this template is built
into ISOLDE, please report this using Help/Report a bug
Failed to add atoms ['HB3'] to atom CB because this will lead to having 5
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (LYS). If this template is built
into ISOLDE, please report this using Help/Report a bug
Failed to add atoms ['HA'] to atom CA because this will lead to having 5 atoms
attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (ALA). If this template is built
into ISOLDE, please report this using Help/Report a bug
> delete atoms (#!3.2 & sel)
> delete bonds (#!3.2 & sel)
> delete atoms (#!3.2 & sel)
> delete bonds (#!3.2 & sel)
> delete atoms (#!3.2 & sel)
> delete bonds (#!3.2 & sel)
> delete atoms (#!3.2 & sel)
> delete bonds (#!3.2 & sel)
> delete atoms (#!3.2 & sel)
> delete bonds (#!3.2 & sel)
> delete atoms (#!3.2 & sel)
> delete bonds (#!3.2 & sel)
> delete atoms (#!3.2 & sel)
> delete bonds (#!3.2 & sel)
> delete atoms (#!3.2 & sel)
> delete bonds (#!3.2 & sel)
> delete atoms (#!3.2 & sel)
> delete bonds (#!3.2 & sel)
> delete atoms (#!3.2 & sel)
> delete bonds (#!3.2 & sel)
> delete atoms (#!3.2 & sel)
> delete bonds (#!3.2 & sel)
> delete atoms (#!3.2 & sel)
> delete bonds (#!3.2 & sel)
> delete atoms (#!3.2 & sel)
> delete bonds (#!3.2 & sel)
> delete atoms (#!3.2 & sel)
> delete bonds (#!3.2 & sel)
> delete atoms (#!3.2 & sel)
> delete bonds (#!3.2 & sel)
> delete atoms (#!3.2 & sel)
> delete bonds (#!3.2 & sel)
> delete atoms (#!3.2 & sel)
> delete bonds (#!3.2 & sel)
> select add #3.2
57419 atoms, 57794 bonds, 18 pseudobonds, 3636 residues, 15 models selected
> isolde sim start /Aa-S
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 98 residues in model #3.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /Aa-S
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 87 residues in model #3.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save /home/azinas/Projects/ClpG_Y541A/j214_open/J214_emready-coot-3.pdb
> close #3.2
Deleting atomic symmetry model...
Deleting atomic symmetry model...
> close
Deleting atomic symmetry model...
> toolshed show
Downloading bundle ChimeraX_ISOLDE-1.7-cp311-cp311-manylinux_2_28_x86_64.whl
> open /home/azinas/Downloads/cryosparc_P10_J246_011_volume_map_sharp.mrc
Summary of feedback from opening
/home/azinas/Downloads/cryosparc_P10_J246_011_volume_map_sharp.mrc
---
notes | open kw {}
Opened cryosparc_P10_J246_011_volume_map_sharp.mrc as #1, grid size
400,400,400, pixel 0.846, shown at level 0.0403, step 2, values float32
Downloading bundle ChimeraX_ISOLDE-1.7-cp311-cp311-manylinux_2_28_x86_64.whl
> toolshed show
Downloading bundle ChimeraX_NIHPresets-1.1.17-py3-none-any.whl
Installed ChimeraX-NIHPresets (1.1.17)
Downloading bundle ChimeraX_QScore-1.1-cp311-cp311-linux_x86_64.whl
Installed ChimeraX-QScore (1.1)
Downloading bundle ChimeraX_ISOLDE-1.7-cp311-cp311-manylinux_2_28_x86_64.whl
[Repeated 15 time(s)]
> toolshed show
Downloading bundle ChimeraX_ISOLDE-1.7-cp311-cp311-manylinux_2_28_x86_64.whl
[Repeated 2 time(s)]
> open /home/azinas/Projects/ClpG_Y541A/J249_emready.mrc format mrc
Summary of feedback from opening
/home/azinas/Projects/ClpG_Y541A/J249_emready.mrc
---
notes | open kw {}
Opened J249_emready.mrc as #2, grid size 400,400,400, pixel 0.846, shown at
level 1.09, step 2, values float32
> ui mousemode right "rotate selected models"
> select add #2
2 models selected
> view matrix models
> #2,0.87607,-0.46905,0.11176,79.867,0.45045,0.87883,0.15735,-83.159,-0.17202,-0.087512,0.9812,46.934
> view matrix models
> #2,0.9089,-0.39963,-0.11913,101.72,0.40651,0.91279,0.039494,-61.426,0.092962,-0.084326,0.99209,-0.5368
> view matrix models
> #2,0.6817,-0.68671,-0.2524,210.38,0.70663,0.52858,0.4704,-121.6,-0.18962,-0.49903,0.84559,140.89
> view matrix models
> #2,-0.81277,0.53616,-0.22791,258.28,-0.52774,-0.84328,-0.10182,412.02,-0.24678,0.037516,0.96834,41.138
> fitmap #2 inMap #1
Fit map J249_emready.mrc in map cryosparc_P10_J246_011_volume_map_sharp.mrc
using 79986 points
correlation = 0.7824, correlation about mean = 0.5728, overlap = 3.306e+04
steps = 144, shift = 4.78, angle = 10.7 degrees
Position of J249_emready.mrc (#2) relative to
cryosparc_P10_J246_011_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.87821073 0.47357886 -0.06685043 252.13075572
-0.46906347 -0.88014219 -0.07300131 407.45702660
-0.09340977 -0.03275344 0.99508886 19.87193399
Axis 0.04264111 0.02813861 -0.99869412
Axis point 177.64577642 172.36099715 0.00000000
Rotation angle (degrees) 151.83986540
Shift along axis 2.37042722
> view matrix models
> #2,0.9094,0.40301,-0.10282,-34.417,-0.39223,0.91323,0.11028,66.711,0.13834,-0.059961,0.98857,-13.975
> fitmap #2 inMap #1
Fit map J249_emready.mrc in map cryosparc_P10_J246_011_volume_map_sharp.mrc
using 79986 points
correlation = 0.3687, correlation about mean = 0.02283, overlap = 1.08e+04
steps = 84, shift = 3.22, angle = 2.07 degrees
Position of J249_emready.mrc (#2) relative to
cryosparc_P10_J246_011_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.91903802 0.38670106 -0.07636366 -37.06015222
-0.37601137 0.91821522 0.12448403 61.37515325
0.11825639 -0.08569195 0.98927869 -9.36337541
Axis -0.25797085 -0.23887743 -0.93615630
Axis point 138.91583551 122.47605517 0.00000000
Rotation angle (degrees) 24.03934185
Shift along axis 3.66488292
> view matrix models
> #2,0.87048,-0.49126,0.03054,98.461,0.49198,0.86655,-0.083931,-42.683,0.014767,0.088085,0.996,-21.637
> fitmap #2 inMap #1
Fit map J249_emready.mrc in map cryosparc_P10_J246_011_volume_map_sharp.mrc
using 79986 points
correlation = 0.5681, correlation about mean = 0.2736, overlap = 1.989e+04
steps = 380, shift = 15.9, angle = 14.3 degrees
Position of J249_emready.mrc (#2) relative to
cryosparc_P10_J246_011_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87701038 -0.41340009 0.24485335 44.45969679
0.46089951 0.86781507 -0.18565736 -23.85739196
-0.13573666 0.27567622 0.95161872 -34.88278091
Axis 0.43551558 0.35929073 0.82537043
Axis point 68.19479235 106.22096025 0.00000000
Rotation angle (degrees) 31.98118332
Shift along axis -18.00006490
> view matrix models
> #2,-0.1772,-0.97924,0.098453,342.23,0.97621,-0.16218,0.14393,3.288,-0.12498,0.12162,0.98468,-16.795
> view matrix models
> #2,-0.87712,0.48017,-0.0095549,238.09,-0.47245,-0.86626,-0.16245,418.05,-0.086281,-0.13798,0.98667,19.238
> fitmap #2 inMap #1
Fit map J249_emready.mrc in map cryosparc_P10_J246_011_volume_map_sharp.mrc
using 79986 points
correlation = 0.7824, correlation about mean = 0.5728, overlap = 3.306e+04
steps = 188, shift = 19, angle = 6.11 degrees
Position of J249_emready.mrc (#2) relative to
cryosparc_P10_J246_011_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.87820164 0.47359430 -0.06686043 252.12634888
-0.46907864 -0.88013414 -0.07300093 407.45989194
-0.09341897 -0.03274674 0.99508821 19.87214841
Axis 0.04264641 0.02813686 -0.99869395
Axis point 177.64589326 172.36179438 0.00000000
Rotation angle (degrees) 151.83886402
Shift along axis 2.37073121
> view matrix models
> #2,-0.84042,-0.53326,0.09661,384.74,0.52801,-0.84586,-0.075705,232.52,0.12209,-0.012613,0.99244,-19.697
> fitmap #2 inMap #1
Fit map J249_emready.mrc in map cryosparc_P10_J246_011_volume_map_sharp.mrc
using 79986 points
correlation = 0.8112, correlation about mean = 0.6118, overlap = 3.468e+04
steps = 108, shift = 6.6, angle = 6.99 degrees
Position of J249_emready.mrc (#2) relative to
cryosparc_P10_J246_011_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.84670232 -0.52828234 0.06334788 392.04792878
0.53111981 -0.84628402 0.04141387 211.04189658
0.03173208 0.06871053 0.99713186 -25.05347095
Axis 0.02574610 0.02981989 0.99922366
Axis point 166.01553161 162.20358657 0.00000000
Rotation angle (degrees) 147.98693528
Shift along axis -8.64707096
> volume #1 level 0.07297
> volume #1 level 0.06752
> close #1
> show #!2 models
> select subtract #2
Nothing selected
> volume #2 level 1.52
> volume #2 color #62a0ea
> open /home/azinas/Projects/ClpG_Y541A/j214_open/J214_emready-coot-3.pdb
Chain information for J214_emready-coot-3.pdb #1
---
Chain | Description
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Af | No description available
S | No description available
> select add #2
2 models selected
> view matrix models
> #2,-0.69178,-0.70909,0.1365,383.2,0.69374,-0.70509,-0.14689,191.79,0.2004,-0.006925,0.97969,-38.333
> undo
> select add #1
57419 atoms, 57793 bonds, 3636 residues, 3 models selected
> select subtract #2
57419 atoms, 57793 bonds, 3636 residues, 1 model selected
> view matrix models
> #1,0.64037,0.74701,-0.17859,-32.98,-0.32138,0.4718,0.82105,6.3341,0.69759,-0.46838,0.5422,34.609
> view matrix models
> #1,-0.41296,0.74702,-0.52099,204.3,-0.76793,0.021937,0.64016,187.7,0.48964,0.66444,0.5646,-121.94
> show sel cartoons
> hide sel atoms
> view matrix models
> #1,-0.64764,-0.76083,-0.041171,416.15,0.33279,-0.33106,0.88298,18.286,-0.68543,0.55816,0.46761,112.54
> view matrix models
> #1,-0.91989,-0.39151,0.023024,390.49,0.3878,-0.91679,-0.095488,268.48,0.058492,-0.07891,0.99516,4.258
> view matrix models
> #1,-0.87712,-0.47973,-0.022701,405.45,0.47563,-0.87425,0.097294,214.47,-0.066521,0.074542,0.995,0.074739
> fitmap #1 inMap #2
Fit molecule J214_emready-coot-3.pdb (#1) to map J249_emready.mrc (#2) using
57419 atoms
average map value = 6.775, steps = 104
shifted from previous position = 9.03
rotated from previous position = 6.7 degrees
atoms outside contour = 3546, contour level = 1.5197
Position of J214_emready-coot-3.pdb (#1) relative to J249_emready.mrc (#2)
coordinates:
Matrix rotation and translation
0.99999996 -0.00030371 -0.00009231 0.06662657
0.00030371 0.99999996 -0.00002837 -0.05128028
0.00009232 0.00002834 1.00000000 -0.04109634
Axis 0.08897705 -0.28966730 0.95298265
Axis point 186.41406638 224.73005332 0.00000000
Rotation angle (degrees) 0.01825974
Shift along axis -0.01838165
> color zone #2 near sel & #1 distance 5.08
> open
> /home/azinas/Projects/ClpG_Y541A/J249_emready/entropy_scores/J249_emready.cif
Summary of feedback from opening
/home/azinas/Projects/ClpG_Y541A/J249_emready/entropy_scores/J249_emready.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for J249_emready.cif #3
---
Chain | Description
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Af | No description available
Ag | No description available
Ah | No description available
Ai | No description available
Aj | No description available
Ak | No description available
Al | No description available
Am | No description available
> select subtract #1
Nothing selected
> hide #!1 models
> hide #!2 models
> open
> /home/azinas/Projects/ClpG_Y541A/J249_emready/entropy_scores/J249_emready_raw.cif
Summary of feedback from opening
/home/azinas/Projects/ClpG_Y541A/J249_emready/entropy_scores/J249_emready_raw.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for J249_emready_raw.cif #4
---
Chain | Description
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
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 r | No description available
n | No description available
o | No description available
p | No description available
q | No description available
> hide #!3 models
> close #3
> show #4 cartoons
> hide #4 atoms
> show #!2 models
> hide #4 models
> lighting soft
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> lighting flat
> lighting soft
> close #1
> open /home/azinas/Projects/ClpG_Y541A/j214_open/J214_emready-coot-5.pdb
Summary of feedback from opening
/home/azinas/Projects/ClpG_Y541A/j214_open/J214_emready-coot-5.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU a 280
GLU a 286 1 7
Start residue of secondary structure not found: HELIX 2 2 ALA a 296 LEU a 306
1 11
Start residue of secondary structure not found: HELIX 3 3 LYS a 324 ALA a 337
1 14
Start residue of secondary structure not found: HELIX 4 4 GLU a 342 LEU a 344
1 3
Start residue of secondary structure not found: HELIX 5 5 ILE a 354 VAL a 358
1 5
312 messages similar to the above omitted
Cannot find LINK/SSBOND residue ARG (638 )
Chain information for J214_emready-coot-5.pdb #1
---
Chain | Description
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Af | No description available
S | No description available
> hide #!1 atoms
> show #!1 cartoons
> show #!2 models
> select add #1
28803 atoms, 29199 bonds, 3676 residues, 1 model selected
> view matrix models
> #1,0.91761,-0.39411,-0.051586,88.328,0.38758,0.91598,-0.10379,-34.857,0.088155,0.075243,0.99326,-26.461
> view matrix models
> #1,-0.79096,-0.58975,0.16302,376.81,0.60342,-0.79596,0.048247,188.14,0.10131,0.13653,0.98544,-37.613
> fitmap #1 inMap #2
Fit molecule J214_emready-coot-5.pdb (#1) to map J249_emready.mrc (#2) using
28803 atoms
average map value = 10.37, steps = 124
shifted from previous position = 9.1
rotated from previous position = 7.5 degrees
atoms outside contour = 684, contour level = 1.5197
Position of J214_emready-coot-5.pdb (#1) relative to J249_emready.mrc (#2)
coordinates:
Matrix rotation and translation
0.99999999 0.00004603 0.00011246 -0.02214279
-0.00004602 0.99999999 -0.00007611 0.01584409
-0.00011247 0.00007610 0.99999999 0.00776308
Axis 0.53079546 0.78435810 -0.32099619
Axis point 63.82285558 0.00000000 188.31651887
Rotation angle (degrees) 0.00821523
Shift along axis -0.00181777
> select subtract #1
Nothing selected
> select add #1
28803 atoms, 29199 bonds, 3676 residues, 1 model selected
> select subtract #1
Nothing selected
> volume #2 level 4.543
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #2 level 7.278
> show #4 models
> select add #4
31260 atoms, 31725 bonds, 3919 residues, 1 model selected
> fitmap #4 inMap #2
Fit molecule J249_emready_raw.cif (#4) to map J249_emready.mrc (#2) using
31260 atoms
average map value = 1.776, steps = 108
shifted from previous position = 5.01
rotated from previous position = 4.88 degrees
atoms outside contour = 29586, contour level = 7.2784
Position of J249_emready_raw.cif (#4) relative to J249_emready.mrc (#2)
coordinates:
Matrix rotation and translation
-0.86140319 0.49674569 0.10596347 219.52418549
-0.49459371 -0.86782096 0.04757985 389.00183047
0.11559241 -0.01142343 0.99323104 -11.84236357
Axis -0.05941081 -0.00969544 -0.99818653
Axis point 161.90625259 165.36681833 0.00000000
Rotation angle (degrees) 150.22665466
Shift along axis -4.99276773
> view matrix models
> #4,-0.75336,-0.62509,-0.20426,432.9,0.64669,-0.76057,-0.057621,194.64,-0.11933,-0.1755,0.97722,49.582
> fitmap #4 inMap #2
Fit molecule J249_emready_raw.cif (#4) to map J249_emready.mrc (#2) using
31260 atoms
average map value = 9.515, steps = 172
shifted from previous position = 6.65
rotated from previous position = 18.3 degrees
atoms outside contour = 15722, contour level = 7.2784
Position of J249_emready_raw.cif (#4) relative to J249_emready.mrc (#2)
coordinates:
Matrix rotation and translation
1.00000000 -0.00002895 0.00001140 -0.00308151
0.00002895 1.00000000 -0.00003868 0.00683037
-0.00001140 0.00003868 0.99999999 -0.00134717
Axis 0.77918772 0.22969431 0.58318695
Axis point 0.00000000 10.43925000 186.17955979
Rotation angle (degrees) 0.00284447
Shift along axis -0.00161783
> select subtract #4
Nothing selected
> volume #2 level 1.772
> hide #!1 models
> open /home/azinas/Projects/ClpG_Y541A/j214_open/J214_emready-coot-6.pdb
Summary of feedback from opening
/home/azinas/Projects/ClpG_Y541A/j214_open/J214_emready-coot-6.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU a 280
GLU a 286 1 7
Start residue of secondary structure not found: HELIX 2 2 ALA a 296 LEU a 306
1 11
Start residue of secondary structure not found: HELIX 3 3 LYS a 324 ALA a 337
1 14
Start residue of secondary structure not found: HELIX 4 4 GLU a 342 LEU a 344
1 3
Start residue of secondary structure not found: HELIX 5 5 ILE a 354 VAL a 358
1 5
312 messages similar to the above omitted
Cannot find LINK/SSBOND residue ARG (638 )
Chain information for J214_emready-coot-6.pdb #3
---
Chain | Description
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Af | No description available
S | No description available
> select add #3
29277 atoms, 29681 bonds, 3735 residues, 1 model selected
> hide #4 models
> view matrix models
> #3,-0.97709,-0.21249,-0.011993,376.01,0.20162,-0.94224,0.26747,244.18,-0.068133,0.25892,0.96349,-25.344
> fitmap #3 inMap #2
Fit molecule J214_emready-coot-6.pdb (#3) to map J249_emready.mrc (#2) using
29277 atoms
average map value = 10.3, steps = 236
shifted from previous position = 9.23
rotated from previous position = 23.7 degrees
atoms outside contour = 885, contour level = 1.7716
Position of J214_emready-coot-6.pdb (#3) relative to J249_emready.mrc (#2)
coordinates:
Matrix rotation and translation
0.99999999 0.00007360 0.00005727 -0.02302656
-0.00007360 0.99999999 -0.00002007 0.02317597
-0.00005727 0.00002006 0.99999999 0.01211014
Axis 0.21035275 0.60033128 -0.77159191
Axis point 317.10309761 312.07565847 0.00000000
Rotation angle (degrees) 0.00546558
Shift along axis -0.00027453
> show sel cartoons
> hide sel atoms
> color sel bychain
> color zone #2 near sel & #3 distance 5.08
> volume #2 level 5.443
> select subtract #3
Nothing selected
> volume #2 level 10.16
> volume #2 level 4.507
> toolshed show
Downloading bundle ChimeraX_ISOLDE-1.7-cp311-cp311-manylinux_2_28_x86_64.whl
[Repeated 5 time(s)]
> devel install /home/azinas/Downloads/Isolde.whl
[Errno 20] Not a directory: '/home/azinas/Downloads/Isolde.whl/pyproject.toml'
> devel install /home/azinas/Downloads/Isolde
[Errno 2] No such file or directory:
'/home/azinas/Downloads/Isolde/pyproject.toml'
> devel install /home/azinas/Downloads/Isolde
[Errno 2] No such file or directory:
'/home/azinas/Downloads/Isolde/pyproject.toml'
> devel install /home/azinas/Downloads/Isolde
[Errno 2] No such file or directory:
'/home/azinas/Downloads/Isolde/pyproject.toml'
> toolshed install /home/azinas/Downloads/Isolde.whl
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/toolshed.py", line 312, in toolshed_install
ts.install_bundle(bundles, logger, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 927, in install_bundle
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/toolshed_utils/__init__.py", line 222, in _install_bundle
bundle_version = parse_wheel_filename(bundle).version
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/wheel_filename/__init__.py", line 100, in parse_wheel_filename
raise InvalidFilenameError(basename)
wheel_filename.InvalidFilenameError: Invalid wheel filename: 'Isolde.whl'
wheel_filename.InvalidFilenameError: Invalid wheel filename: 'Isolde.whl'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/wheel_filename/__init__.py", line 100, in parse_wheel_filename
raise InvalidFilenameError(basename)
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 535.146.02
OpenGL renderer: NVIDIA GeForce RTX 4090/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=:0
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7D67
OS: Ubuntu 23.10 Mantic Minotaur
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 AMD Ryzen 9 7950X 16-Core Processor
Cache Size: 1024 KB
Memory:
total used free shared buff/cache available
Mem: 124Gi 29Gi 22Gi 990Mi 74Gi 95Gi
Swap: 9Gi 0B 9Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation AD102 [GeForce RTX 4090] [10de:2684] (rev a1)
Subsystem: NVIDIA Corporation AD102 [GeForce RTX 4090] [10de:16f3]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.13.1
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: 1.5.12
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: 12.1.2
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: 0.22.2
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: 1.7rc202311220128
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: 1.1.2
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: 1.7rc1
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-NIHPresets: 1.1.17
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.2.1
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-QScore: 1.1
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: 4.45.0
funcparserlib: 2.0.0a0
glfw: 2.6.3
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.4
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: 5.5.0
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: 2.8.7
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.0.0
prompt-toolkit: 3.0.41
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: 25.1.1
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: 6.3.3
traitlets: 5.9.0
typing-extensions: 4.8.0
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 , 22 months ago
| Component: | Unassigned → Tool Shed |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Invalid wheel filename: 'Isolde.whl' |
comment:2 by , 22 months ago
| Resolution: | → not a bug |
|---|---|
| Status: | assigned → closed |
Wheel names must follow PEP 427 so the platform and abi tags are present.
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Not sure what the user was trying to accomplish here.