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Opened 21 months ago
Closed 21 months ago
#14677 closed defect (fixed)
Combine: Structure object is None
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.3.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202402290246 (2024-02-29 02:46:47 UTC)
Description
Repeated errors wehn trying to use the Combine command
Log:
UCSF ChimeraX version: 1.8.dev202402290246 (2024-02-29)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Compositor returned null texture
> open /Users/matthias.vorlaender/Library/CloudStorage/OneDrive-
> VBC/ILS_manuscript/FinalMaps/PRP43bound/composite/ce_ILS_PRP43_bound_composite_201207.mrc
Opened ce_ILS_PRP43_bound_composite_201207.mrc as #1, grid size 199,231,236,
pixel 1.3,1.3,1.3, shown at level 1.45, step 1, values float32
> open /Users/matthias.vorlaender/Library/CloudStorage/OneDrive-
> VBC/ILS_manuscript/FinalMaps/PRP43bound/Map16_ILS''/PRP43bound_ILS''_J2242__localfilter.mrc
Opened PRP43bound_ILS''_J2242__localfilter.mrc as #2, grid size 448,448,448,
pixel 1.3, shown at level 0.0993, step 2, values float32
> volume #2 step 1
> open /Users/matthias.vorlaender/Library/CloudStorage/OneDrive-
> VBC/ILS_manuscript/FinalMaps/PRP43bound/Map16_ILS''/PRP43bound_ILS''_J1902_007_volume_map_sharp.mrc
Opened PRP43bound_ILS''_J1902_007_volume_map_sharp.mrc as #3, grid size
448,448,448, pixel 1.3, shown at level 0.116, step 2, values float32
> open /Users/matthias.vorlaender/Library/CloudStorage/OneDrive-
> VBC/ILS_manuscript/FinalMaps/PRP43bound/Map16_ILS''/PRP43bound_ILS''_J1902_007_volume_map_sharp.mrc
Opened PRP43bound_ILS''_J1902_007_volume_map_sharp.mrc as #4, grid size
448,448,448, pixel 1.3, shown at level 0.116, step 2, values float32
> volume #3 step 1
> volume #3 level 0.4264
> close #4
> open /Users/matthias.vorlaender/Library/CloudStorage/OneDrive-
> VBC/ILS_manuscript/Models/For_Deposition/ceILS_doubleprime_SYF1_assigned.pdb
Summary of feedback from opening
/Users/matthias.vorlaender/Library/CloudStorage/OneDrive-
VBC/ILS_manuscript/Models/For_Deposition/ceILS_doubleprime_SYF1_assigned.pdb
---
warnings | Cannot find LINK/SSBOND residue ZN (900 )
Cannot find LINK/SSBOND residue ZN (900 )
Cannot find LINK/SSBOND residue ZN (900 )
Cannot find LINK/SSBOND residue ZN (900 )
Chain information for ceILS_doubleprime_SYF1_assigned.pdb #4
---
Chain | Description
2 | No description available
5 | No description available
6 | No description available
A | No description available
C | No description available
DX | No description available
E | No description available
F | No description available
I | No description available
In | No description available
J | No description available
K | No description available
L | No description available
L1 | No description available
L2 | No description available
M | No description available
N | No description available
O | No description available
P | No description available
PX | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
TF | No description available
W | No description available
X | No description available
Z | No description available
a h | No description available
b | No description available
c j | No description available
d | No description available
e l | No description available
f m | No description available
g n | No description available
i | No description available
k | 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
y | No description available
> hide
> show nucleic cartoons,atoms
> volume #3 level 0.2562
> fitmap #4 inMap #2
Fit molecule ceILS_doubleprime_SYF1_assigned.pdb (#4) to map
PRP43bound_ILS''_J2242__localfilter.mrc (#2) using 237437 atoms
average map value = 0.1833, steps = 212
shifted from previous position = 3.83
rotated from previous position = 1.55 degrees
atoms outside contour = 50511, contour level = 0.099295
Position of ceILS_doubleprime_SYF1_assigned.pdb (#4) relative to
PRP43bound_ILS''_J2242__localfilter.mrc (#2) coordinates:
Matrix rotation and translation
0.99965418 -0.02196119 -0.01446498 6.74034275
0.02205114 0.99973831 0.00608815 -6.75111886
0.01432749 -0.00640501 0.99987684 -1.97884220
Axis -0.23111049 -0.53263071 0.81418209
Axis point 299.48442214 306.69765355 0.00000000
Rotation angle (degrees) 1.54881077
Shift along axis 0.42695140
> hide #!4 models
> open /Users/matthias.vorlaender/Library/CloudStorage/OneDrive-
> VBC/ILS_manuscript/Models/For_Deposition/ILSprime_branch_helix_replaced_old_protein.pdb
Chain information for ILSprime_branch_helix_replaced_old_protein.pdb #5
---
Chain | Description
2 | No description available
5 | No description available
6 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | 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
O | No description available
P | No description available
PX | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
TF | No description available
W | No description available
Z | No description available
a h | No description available
b | No description available
c j | No description available
d | No description available
e l | No description available
f m | No description available
g n | No description available
i | No description available
k | 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
y | No description available
> open /Users/matthias.vorlaender/Library/CloudStorage/OneDrive-
> VBC/ILS_manuscript/Models/For_Deposition/old/Ce_ILS_doubleprime.pdb
Summary of feedback from opening
/Users/matthias.vorlaender/Library/CloudStorage/OneDrive-
VBC/ILS_manuscript/Models/For_Deposition/old/Ce_ILS_doubleprime.pdb
---
warnings | Cannot find LINK/SSBOND residue ZN (900 )
Cannot find LINK/SSBOND residue ZN (900 )
Cannot find LINK/SSBOND residue ZN (900 )
Cannot find LINK/SSBOND residue ZN (900 )
Chain information for Ce_ILS_doubleprime.pdb #6
---
Chain | Description
2 | No description available
5 | No description available
6 | No description available
A | No description available
C | No description available
D | No description available
Dx | No description available
E | No description available
I | No description available
In | No description available
J | No description available
K | No description available
L | No description available
L1 | No description available
L2 | No description available
M | No description available
N | No description available
O | No description available
P | No description available
PX | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
TF | No description available
W | No description available
X | No description available
Z | No description available
a h | No description available
b | No description available
c j | No description available
d | No description available
e l | No description available
f m | No description available
g n | No description available
i | No description available
k | 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
xx | No description available
y | No description available
> hide #!5 models
> hide protein
> transparency 50
> hide #!6 models
> show #!4 models
> open /Users/matthias.vorlaender/Downloads/D_1292135564_model_P1.cif
D_1292135564_model_P1.cif title:
Structure of the c. elegans Intron Lariat Spliceosome double-primed for
disassembly (ILS'') [more info...]
Chain information for D_1292135564_model_P1.cif #7
---
Chain | Description
2 | U2 snRNA
5 | U5 snRNA
6 | U6 snRNA
A | PRP8
C | SNU114
D | ISY1
DX | DHX15
E | SNR40
I | SYF1
In | Intron lariat RNA
J | SYF3
K | SPF27
L | CDC5L
L1 | C19L1
L2 | C19L2
M | SYF2
N | BUD31
O | RMB22
P | CWC15
PX | PAXBP1
Q | AQR
R | SNW1
S | PPIL1
T | PLRG1
TF | TFIP11
W | PRP17
X | SDE2
Z | CCD12
a h | SMD3
b i | RSMB
c j | SMD1
d k | SMD2
e l | RUXE
f m | RUXF
g n | RUXG
o | RU2A
p | RU2B
q r s t | PRP19
xx | Unknown
y | PPIE
Non-standard residues in D_1292135564_model_P1.cif #7
---
GTP — guanosine-5'-triphosphate
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)
MG — magnesium ion
N — any 5'-monophosphate nucleotide (1-deoxy-ribofuranose-5'-phosphate)
ZN — zinc ion
> hide #!4 models
> hide #!2 models
> hide
> show nucleic
> show @N
> undo
> select :N
1867 atoms, 1950 bonds, 124 residues, 2 models selected
> select clear
> select #7/In:164@O3'
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
467 atoms, 511 bonds, 33 residues, 1 model selected
> open /Users/matthias.vorlaender/Library/CloudStorage/OneDrive-
> VBC/ILS_manuscript/Models/Modelling_temp/6id1_BP_helix_aligned.pdb
Chain information for 6id1_BP_helix_aligned.pdb #8
---
Chain | Description
G | No description available
H | No description available
> fitmap #8 inMap #2
Fit molecule 6id1_BP_helix_aligned.pdb (#8) to map
PRP43bound_ILS''_J2242__localfilter.mrc (#2) using 607 atoms
average map value = 0.1505, steps = 384
shifted from previous position = 7.18
rotated from previous position = 50.8 degrees
atoms outside contour = 60, contour level = 0.099295
Position of 6id1_BP_helix_aligned.pdb (#8) relative to
PRP43bound_ILS''_J2242__localfilter.mrc (#2) coordinates:
Matrix rotation and translation
0.64976975 -0.41298779 0.63815387 12.48952404
0.53424245 0.84532564 0.00309422 -122.92880537
-0.54072570 0.33891836 0.76990263 153.67039006
Axis 0.21678349 0.76099837 0.61146251
Axis point 233.91092427 0.00000000 109.86391636
Rotation angle (degrees) 50.76526360
Shift along axis 3.12258567
> select add #8
1074 atoms, 1185 bonds, 62 residues, 2 models selected
> select add #7
120906 atoms, 123995 bonds, 39 pseudobonds, 14442 residues, 3 models selected
> select clear
> select add #8
607 atoms, 674 bonds, 29 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.64977,-0.41299,0.63815,10.622,0.53424,0.84533,0.0030942,-131.2,-0.54073,0.33892,0.7699,150.71
> view matrix models
> #8,0.56687,-0.62902,0.53197,116.47,0.79144,0.59506,-0.13974,-110.88,-0.22866,0.50023,0.83515,-0.69069
> color /G black
> set bgColor white
> view matrix models
> #8,0.56573,-0.69383,0.44559,156.84,0.81217,0.56228,-0.15563,-105.09,-0.14257,0.44994,0.88161,-29.087
> view matrix models
> #8,0.79127,-0.49146,0.36382,65.556,0.57602,0.79874,-0.17382,-81.593,-0.20517,0.34711,0.91511,3.7582
> view matrix models
> #8,0.79127,-0.49146,0.36382,66.055,0.57602,0.79874,-0.17382,-81.685,-0.20517,0.34711,0.91511,5.1268
> view matrix models
> #8,0.79127,-0.49146,0.36382,69.388,0.57602,0.79874,-0.17382,-79.806,-0.20517,0.34711,0.91511,-2.8402
> color /IN black
> color /In black
> color /H,2 green
> color /F,6 crimson
> color /B,5 blue
> fitmap #7 inMap #2
Fit molecule D_1292135564_model_P1.cif (#7) to map
PRP43bound_ILS''_J2242__localfilter.mrc (#2) using 120299 atoms
average map value = 0.2202, steps = 76
shifted from previous position = 4.13
rotated from previous position = 1.32 degrees
atoms outside contour = 19182, contour level = 0.099295
Position of D_1292135564_model_P1.cif (#7) relative to
PRP43bound_ILS''_J2242__localfilter.mrc (#2) coordinates:
Matrix rotation and translation
0.99977001 -0.01173680 -0.01794898 4.80880405
0.01188468 0.99989613 0.00815422 -3.79097091
0.01785141 -0.00836566 0.99980565 -2.16426598
Axis -0.35942110 -0.77890487 0.51392964
Axis point 127.38966954 0.00000000 268.52839985
Rotation angle (degrees) 1.31684388
Shift along axis 0.11213966
> fitmap #7 inMap #2
Fit molecule D_1292135564_model_P1.cif (#7) to map
PRP43bound_ILS''_J2242__localfilter.mrc (#2) using 120299 atoms
average map value = 0.2202, steps = 48
shifted from previous position = 0.0206
rotated from previous position = 0.00404 degrees
atoms outside contour = 19186, contour level = 0.099295
Position of D_1292135564_model_P1.cif (#7) relative to
PRP43bound_ILS''_J2242__localfilter.mrc (#2) coordinates:
Matrix rotation and translation
0.99976908 -0.01172174 -0.01801079 4.82661041
0.01186959 0.99989655 0.00812424 -3.77472062
0.01791369 -0.00833614 0.99980479 -2.21027569
Axis -0.35766005 -0.78058643 0.51260522
Axis point 128.80152285 0.00000000 268.06490164
Rotation angle (degrees) 1.31856164
Shift along axis 0.08721111
> hide #!7 models
> hide #8 models
> open 6id1
6id1 title:
Cryo-EM structure of a human intron lariat spliceosome after Prp43 loaded
(ILS2 complex) at 2.9 angstrom resolution [more info...]
Chain information for 6id1 #9
---
Chain | Description | UniProt
A | Pre-mRNA-processing-splicing factor 8 | PRP8_HUMAN 1-2335
B | U5snRNA |
C | 116 kDa U5 small nuclear ribonucleoprotein component | U5S1_HUMAN 1-972
E | U5 small nuclear ribonucleoprotein 40 kDa protein | SNR40_HUMAN 1-357
F | U6snRNA |
G | pre-mRNA |
H | U2snRNA |
I | Pre-mRNA-splicing factor SYF1 | SYF1_HUMAN 1-855
J | Crooked neck-like protein 1 | CRNL1_HUMAN 1-848
K | Pre-mRNA-splicing factor SPF27 | SPF27_HUMAN 1-225
L | Cell division cycle 5-like protein | CDC5L_HUMAN 1-802
M | Pre-mRNA-splicing factor SYF2 | SYF2_HUMAN 1-243
N | Protein BUD31 homolog | BUD31_HUMAN 1-144
O | Pre-mRNA-splicing factor RBM22 | RBM22_HUMAN 1-420
P | Spliceosome-associated protein CWC15 homolog | CWC15_HUMAN 1-229
Q | RNA helicase aquarius | AQR_HUMAN 1-1485
R | SNW domain-containing protein 1 | SNW1_HUMAN 1-536
S | Peptidyl-prolyl cis-trans isomerase-like 1 | PPIL1_HUMAN 1-166
T | Pleiotropic regulator 1 | PLRG1_HUMAN 1-514
U | CWF19-like protein 2 | C19L2_HUMAN 1-894
V | Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 | DHX15_HUMAN
1-795
W | Pre-mRNA-processing factor 17 | PRP17_HUMAN 1-579
a h | Small nuclear ribonucleoprotein Sm D3 | SMD3_HUMAN 1-126
b i | Small nuclear ribonucleoprotein-associated protein | Q66K91_HUMAN 1-231
c j | Small nuclear ribonucleoprotein Sm D1 | SMD1_HUMAN 1-119
d k | Small nuclear ribonucleoprotein Sm D2 | SMD2_HUMAN 1-118
e l | Small nuclear ribonucleoprotein E | RUXE_HUMAN 1-92
f m | Small nuclear ribonucleoprotein F | RUXF_HUMAN 1-86
g n | Small nuclear ribonucleoprotein G | RUXG_HUMAN 1-76
o | U2 small nuclear ribonucleoprotein A' | RU2A_HUMAN 1-255
p | U2 small nuclear ribonucleoprotein B'' | RU2B_HUMAN 1-225
q r s t | Pre-mRNA-processing factor 19 | PRP19_HUMAN 1-504
y | Peptidyl-prolyl cis-trans isomerase E | PPIE_HUMAN 1-301
Non-standard residues in 6id1 #9
---
GTP — guanosine-5'-triphosphate
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)
MG — magnesium ion
ZN — zinc ion
> mmaker #9/A to #7/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker D_1292135564_model_P1.cif, chain A (#7) with 6id1, chain A (#9),
sequence alignment score = 10265.7
RMSD between 883 pruned atom pairs is 1.053 angstroms; (across all 1961 pairs:
3.736)
> close #4
> close #6
> hide
> show cartoons
> fitmap #9 inMap #2
Fit molecule 6id1 (#9) to map PRP43bound_ILS''_J2242__localfilter.mrc (#2)
using 79882 atoms
average map value = 0.1923, steps = 72
shifted from previous position = 0.567
rotated from previous position = 1.29 degrees
atoms outside contour = 27002, contour level = 0.099295
Position of 6id1 (#9) relative to PRP43bound_ILS''_J2242__localfilter.mrc (#2)
coordinates:
Matrix rotation and translation
0.98391371 -0.14631230 0.10250129 36.77084318
0.07117976 -0.20517840 -0.97613281 573.45906380
0.16385129 0.96772648 -0.19146337 51.15524688
Axis 0.99331036 -0.03134980 0.11113825
Axis point 0.00000000 267.52375612 257.96171011
Rotation angle (degrees) 101.90935980
Shift along axis 24.23233939
> hide #!9 models
> show #8 models
> mmaker #8 to #9
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6id1, chain Q (#9) with 6id1_BP_helix_aligned.pdb, chain H (#8),
sequence alignment score = 1.53934e+216
Fewer than 3 residues aligned; cannot match 6id1, chain Q with
6id1_BP_helix_aligned.pdb, chain H
> mmaker #8 to #9/G
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6id1, chain G (#9) with 6id1_BP_helix_aligned.pdb, chain G (#8),
sequence alignment score = 778.4
RMSD between 14 pruned atom pairs is 0.001 angstroms; (across all 14 pairs:
0.001)
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> mmaker #8 to #7/2
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker D_1292135564_model_P1.cif, chain 2 (#7) with
6id1_BP_helix_aligned.pdb, chain H (#8), sequence alignment score = 233
RMSD between 10 pruned atom pairs is 1.087 angstroms; (across all 14 pairs:
2.265)
> hide #!9 models
> show #8/G
> volume #2 level 0.1345
> show #!9 models
> hide #8 models
> hide #!2 models
> hide #9
> hide #9 cartoons
> show #9/G cartoons,atoms
> color /G black
> color /2 black
> color /H black
> color /H green
> show #9/H cartoons,atoms
Drag select of 396 atoms, 27 residues
> hide sek
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide sel
> hide sel cartoons
Drag select of 1364 atoms, 89 residues, 50 pseudobonds
> hide sel cartoons,atoms
> show #!7 models
> hide protein cartoons
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!9 models
> show #8 models
> select #7/In:151
12 atoms, 12 bonds, 1 residue, 1 model selected
> sequence chain #7/IN
Chains must have same sequence
> sequence chain #7/sel
Chains must have same sequence
> sequence chain sel
Alignment identifier is 7/In
> select #7/In:9
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #7/In:9-164
300 atoms, 324 bonds, 25 residues, 1 model selected
> select #7/In:164
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #7/In:157-164
96 atoms, 103 bonds, 8 residues, 1 model selected
> show #7/In
> select #7/In:164
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #7/In:153-164
144 atoms, 155 bonds, 12 residues, 1 model selected
> select #7/In:164
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #7/In:151-164
168 atoms, 181 bonds, 14 residues, 1 model selected
> select #7/In:152-153
24 atoms, 25 bonds, 2 residues, 1 model selected
> select #7/In:152-164
156 atoms, 168 bonds, 13 residues, 1 model selected
> select #7/In:151
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #7/In:151-164
168 atoms, 181 bonds, 14 residues, 1 model selected
> select #7/In:19
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #7/In:19-164
180 atoms, 194 bonds, 15 residues, 1 model selected
> hide #8 models
> select #7/In:164
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #7/In:152-164
156 atoms, 168 bonds, 13 residues, 1 model selected
> select #7/In:164
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #7/In:19-164
180 atoms, 194 bonds, 15 residues, 1 model selected
> select #7/In:19
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #7/In:19-164
180 atoms, 194 bonds, 15 residues, 1 model selected
> select #7/In:151
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #7/In:151-164
168 atoms, 181 bonds, 14 residues, 1 model selected
> delete sel
> show #8 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #8 models
> show #!7 models
> show #8 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> select #8/H:33
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
318 atoms, 354 bonds, 15 residues, 1 model selected
> delete sel
> hide #8 models
> show #8 models
> combine #7,8
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2904, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/cmd.py", line 65, in combine_cmd
combination = structures[0].copy(name)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 162, in copy
m._copy_custom_attrs(self)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 176, in _copy_custom_attrs
py_objs = [py_obj for py_obj in python_instances_of_class(class_obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 61, in python_instances_of_class
return [x for x in instances if filt(x)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 61, in <listcomp>
return [x for x in instances if filt(x)]
^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 52, in <lambda>
filt = lambda x: open_structure(x.structure)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 48, in open_structure
return s.session is not None and s.session.models.have_model(s)
^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'session'
AttributeError: 'NoneType' object has no attribute 'session'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 48, in open_structure
return s.session is not None and s.session.models.have_model(s)
^^^^^^^^^
See log for complete Python traceback.
> hide #!7 models
> show #!7 models
> hide #8 models
> changechains #8/G In
Chain IDs of 14 residues changed
> combine #7,8
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2904, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/cmd.py", line 65, in combine_cmd
combination = structures[0].copy(name)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 162, in copy
m._copy_custom_attrs(self)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 176, in _copy_custom_attrs
py_objs = [py_obj for py_obj in python_instances_of_class(class_obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 61, in python_instances_of_class
return [x for x in instances if filt(x)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 61, in <listcomp>
return [x for x in instances if filt(x)]
^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 52, in <lambda>
filt = lambda x: open_structure(x.structure)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 48, in open_structure
return s.session is not None and s.session.models.have_model(s)
^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'session'
AttributeError: 'NoneType' object has no attribute 'session'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 48, in open_structure
return s.session is not None and s.session.models.have_model(s)
^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: Z1AU002HPD/A
Chip: Apple M3 Pro
Total Number of Cores: 11 (5 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 10151.81.1
OS Loader Version: 10151.81.1
Software:
System Software Overview:
System Version: macOS 14.3.1 (23D60)
Kernel Version: Darwin 23.3.0
Time since boot: 1 day, 12 hours, 40 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP Z32:
Resolution: 6016 x 3384
UI Looks like: 3008 x 1692 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.0.3
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.53.1
ChimeraX-AtomicLibrary: 12.1.15
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
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: 2.12
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: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.4
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: 1.8.dev202402290246
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4.2
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: 1.7.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.2
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
ChimeraX-ModelPanel: 1.5
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-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.3
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
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: 1.2.1
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-Segmentations: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.15
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.4
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: 1.36
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: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.8
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.49.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.2
matplotlib-inline: 0.1.6
msgpack: 1.0.7
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.2.0
pip: 24.0
pkginfo: 1.9.6
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.2
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.1
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.8.2
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.1.0
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.0
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.42.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 21 months ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Combine: Structure object is None |
comment:2 by , 21 months ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
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Hi Matthias,
--Eric
Fix: https://github.com/RBVI/ChimeraX/commit/22e55013de923eb304e1377d692fa224ef1461c0