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Opened 5 years ago
Closed 5 years ago
#4354 closed defect (fixed)
ISOLDE: merge_fragment() got an unexpected keyword argument 'update_style'
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.18362
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:\Users\LocalAdmin\Desktop\Test ChimeraX\4c2m_1_monomers.cif" format
> mmcif
Chain information for 4c2m_1_monomers.cif #1
---
Chain | Description
A | DNA-directed RNA polymerase I subunit RPA190
B | DNA-directed RNA polymerase I subunit RPA135
C | DNA-directed RNA polymerases I and III subunit RPAC1
D | DNA-directed RNA polymerase I subunit RPA14
E | DNA-directed RNA polymerases I, II, and III subunit rpabc 1
F | DNA-directed RNA polymerases I, II, and III subunit rpabc 2
G O | DNA-directed RNA polymerase I subunit RPA43
H | DNA-directed RNA polymerases I, II, and III subunit rpabc 3
I | DNA-directed RNA polymerase I subunit RPA12
J | DNA-directed RNA polymerases I, II, and III subunit rpabc 5
K | DNA-directed RNA polymerases I and III subunit RPAC2
L | DNA-directed RNA polymerases I, II, and III subunit rpabc 4
M | DNA-directed RNA polymerase I subunit RPA49
N | DNA-directed RNA polymerase I subunit RPA34
4c2m_1_monomers.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> open "C:/Users/LocalAdmin/Desktop/Test ChimeraX/script-
> domainssattributionpolI-030720envoyeMichael.cxc"
> hide atoms
> show cartoons
> select all
34700 atoms, 35175 bonds, 42 pseudobonds, 4541 residues, 3 models selected
> color sel grey
> select clear
> name rpa190 #1/A
> name rpa135 #1/B
> name rpb5 #1/E
> name rpb6 #1/F
> name rpb8 #1/H
> name rpb10 #1/J
> name rpb12 #1/L
> name ac40 #1/C
> name ac19 #1/K
> name rpa12 #1/I
> name rpa14 #1/D
> name rpa43 #1/G
> name rpa34 #1/N
> name rpa49 #1/M
> name a++clamp #1/A:01-90 #1/A:356-477 #1/A:1608-1664 #1/A:126-303
> #1/B:1170-1203
> name a++jaw #1/A:1285-1320 #1/A:1456-1500 #1/E:1-145 #1/I:1-39
> name a++stalk #1/D #1/G
> name a++shelf #1/A:477-506 #1/A:581-654 #1/A:506-581 #1/A:1060-1137
> #1/A:991-1053 #1/A:1180-1261 #1/A:1514-1608 #1/E #1/F #1/B:1068-1092
> name a++core #1/B:647-698 #1/H #1/A:709-827 #1/A:827-991 #1/B:469-553
> #1/B:698-800 #1/C #1/J #1/K #1/B:43-209 #1/B:400-469 #1/L #1/B:800-910
> name rpa190++clampcore++engel #1/A:01-90 #1/A:356-477 #1/A:1608-1664
> name rpa190++clampcore++tornero #1/A:01-90 #1/A:350-477 #1/A:1608-1664
> name rpa190++clamphead++engel #1/A:126-303
> name rpa190++clamphead++tornero #1/A:90-350
> name rpa190++activesite #1/A:477-506 #1/A:581-654
> name rpa190++dock #1/A:506-581
> name rpa190++pore++engel #1/A:709-827
> name rpa190++pore++tornero #1/A:654-828
> name rpa190++funnel #1/A:827-991
> name rpa190++cleft++engel #1/A:991-1053 #1/A:1180-1261 #1/A:1514-1608
> name rpa190++cleft++tornero #1/A:991-1051 #1/A:1180-1260 #1/A:1499-1607
> name rpa190++foot #1/A:1060-1137
> name rpa190++jaw++engel #1/A:1285-1320 #1/A:1456-1500
> name rpa190++jaw++tornero #1/A:1260-1360 #1/A:1400-1499
> name rpa190++expander++engel #1/A:1337-1440
> name rpa190++mimickingloop++tornero #1/A:1360-1400
> name rpa190++BH++engel #1/A:991-1051
> name rpa190++BH++Darriere #1/A:1012-1016
> name rpa135++extendedprotrusion #1/B:1-43
> name rpa135++nter #1/B:1-42
> name rpa135++protrusion++engel #1/B:43-209 #1/B:400-469
> name rpa135++protrusion++tornero #1/B:42-210 #1/B:399-470
> name rpa135++lobe++engel #1/B:209-400
> name rpa135++lobe++tornero #1/B:210-399
> name rpa135++fork++engel #1/B:469-553
> name rpa135++fork++tornero #1/B:470-553
> name rpa135++external1++engel #1/B:647-698
> name rpa135++external1++tornero #1/B:649-697
> name rpa135++external2++engel #1/B:553-647
> name rpa135++external2++tornero #1/B:553-649
> name rpa135++hybridbinding++engel #1/B:698-800
> name rpa135++hybridbinding++tornero #1/B:697-800
> name rpa135++wall++engel #1/B:800-910
> name rpa135++wall++tornero #1/B:800-911
> name rpa135++anchor++engel #1/B:1068-1092
> name rpa135++anchor++tornero #1/B:1069-1095
> name rpa135++stalkbinding++tornero #1/B:1095-1170
> name rpa135++clamp++engel #1/B:1092-1203
> name rpa135++clamp++tornero #1/B:1170-1203
> name rpb5++jaw #1/E:1-145
> name rpb5++assembly #1/E:145-215
> name rpb6++tail #1/F:01-72
> name rpb6++assembly #1/F:72-155
> name rpb6++nter++tornero #1/F:55-71
> name rpb8++betabarrel #1/H:01-63 #1/H:96-146
> name rpb8++loop #1/H:63-96
> name rpb10++zincbundle #1/J:1-53
> name rpb10++tail #1/J:53-70
> name rpb12++zincribbon #1/L:1-60
> name rpb12++tail #1/L:60-70
> name ac19++tail #1/K:1-48
> name ac19++dimerization #1/K:49-142
> name ac40++nterextension #1/C:1-31
> name ac40++dimerization #1/C:31-75 #1/C:220-230 #1/C:297-335
> name ac40++domain2 #1/C:75-143 #1/C:168-220
> name ac40++zincloop #1/C:143-168
> name ac40++looptoe #1/C:230-297
> name rpa12++jaw++zincbindingribbon1 #1/I:1-40
> name rpa12++linkerflexible #1/I:40-65
> name rpa12++zincbindingribbon2 #1/I:65-125
> name rpa43++nter #1/G:1-37
> name rpa43++tipdomain #1/G:38-91
> name rpa43++tiploop #1/G:92-113
> name rpa43++obdomain #1/G:114-248
> name rpa43++ctail #1/G:249-326
> name rpa43++connector #1/G:270-313
> name rpa14++nter #1/D:1-21
> name rpa14++tipassociateddomain #1/D:22-96
> name rpa14++linker #1/D:97-137
> name rpa49++nterdimerization #1/M:1-101
> name rpa49++linkerdomain #1/M:102-184
> name rpa49++twh #1/M:185-403
> name rpa49++wh1 #1/M:255-320
> name rpa49++wh2 #1/M:321-403
> name rpa49++cter #1/M:403-415
> name rpa34++nter #1/N:1-22
> name rpa34++dimerizationdomain #1/N:23-144
> name rpa34++ctail #1/N:145-233
executed script-domainssattributionpolI-030720envoyeMichael.cxc
> open "C:/Users/LocalAdmin/Desktop/Test ChimeraX/3tj1.cif"
3tj1.cif title:
Crystal Structure of RNA Polymerase I Transcription Initiation Factor Rrn3
[more info...]
Chain information for 3tj1.cif #2
---
Chain | Description
A B | RNA polymerase I-specific transcription initiation factor RRN3
> open "C:/Users/LocalAdmin/Desktop/Test ChimeraX/polI-Rrn3.mrc"
Opened polI-Rrn3.mrc, grid size 128,128,128, pixel 2.16, shown at level 0.142,
step 1, values float32
> fitmap #1 inMap #3 search 100
Found 87 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (98 of 100).
Average map values and times found:
0.1112 (5), 0.06616 (2), 0.06495 (1), 0.06494 (1), 0.06381 (1), 0.06258 (1),
0.0619 (2), 0.06181 (1), 0.06164 (1), 0.06155 (2), 0.06144 (1), 0.0614 (1),
0.06137 (1), 0.06135 (2), 0.06123 (1), 0.06098 (1), 0.06095 (1), 0.06094 (2),
0.06094 (1), 0.06093 (1), 0.06089 (1), 0.06084 (1), 0.06082 (1), 0.06073 (1),
0.06059 (1), 0.06025 (1), 0.06015 (2), 0.06009 (1), 0.06003 (1), 0.05983 (1),
0.0598 (1), 0.05974 (1), 0.05971 (2), 0.05967 (1), 0.05959 (1), 0.05928 (1),
0.0591 (1), 0.05908 (1), 0.05907 (1), 0.05893 (1), 0.0589 (1), 0.05881 (1),
0.05862 (1), 0.05861 (1), 0.05845 (1), 0.05837 (1), 0.05834 (1), 0.05831 (1),
0.05828 (1), 0.05824 (1), 0.05812 (1), 0.05808 (1), 0.05806 (1), 0.05804 (1),
0.05799 (1), 0.05791 (1), 0.05789 (1), 0.05773 (1), 0.05745 (1), 0.05738 (1),
0.05735 (1), 0.05721 (1), 0.05719 (1), 0.05711 (1), 0.05705 (1), 0.05694 (1),
0.05685 (1), 0.05678 (1), 0.05667 (1), 0.05647 (1), 0.05646 (1), 0.05599 (1),
0.05597 (1), 0.05582 (1), 0.0558 (1), 0.05574 (1), 0.05567 (1), 0.05534 (1),
0.05514 (1), 0.05509 (1), 0.05508 (1), 0.05434 (1), 0.05298 (1), 0.05298 (1),
0.05286 (1), 0.05282 (1), 0.04999 (1)
Best fit found:
Fit molecule 4c2m_1_monomers.cif (#1) to map polI-Rrn3.mrc (#3) using 34700
atoms
average map value = 0.1112, steps = 608
shifted from previous position = 89.2
rotated from previous position = 51.9 degrees
atoms outside contour = 23408, contour level = 0.14213
Position of 4c2m_1_monomers.cif (#1) relative to polI-Rrn3.mrc (#3)
coordinates:
Matrix rotation and translation
-0.08718624 -0.17721780 0.98030222 221.93767268
-0.19595359 0.96787513 0.15754349 212.72089314
-0.97672967 -0.17835814 -0.11911186 249.28945454
Axis -0.16915709 0.98554394 -0.00943518
Axis point 242.14127478 0.00000000 12.85352634
Rotation angle (degrees) 96.84659701
Shift along axis 169.75136672
Found 87 fits. List window not yet implemented.
> select #1
34700 atoms, 35175 bonds, 42 pseudobonds, 4541 residues, 3 models selected
> view sel
> delete #2/b
> open 5g5l
5g5l title:
RNA polymerase I-Rrn3 complex at 4.8 A resolution [more info...]
Chain information for 5g5l #4
---
Chain | Description
A | DNA-directed RNA polymerase I subunit RPA190
B | DNA-directed RNA polymerase I subunit RPA135
C | DNA-directed RNA polymerases I and III subunit RPAC1
D | DNA-directed RNA polymerase I subunit RPA14
E | DNA-directed RNA polymerases I, II, and III subunit rpabc 1
F | DNA-directed RNA polymerases I, II, and III subunit rpabc 2
G | DNA-directed RNA polymerase I subunit RPA43
H | DNA-directed RNA polymerases I, II, and III subunit rpabc 3
I | DNA-directed RNA polymerase I subunit RPA12
J | DNA-directed RNA polymerases I, II, and III subunit rpabc 5
K | DNA-directed RNA polymerases I and III subunit RPAC2
L | DNA-directed RNA polymerases I, II, and III subunit rpabc 4
M | DNA-directed RNA polymerase I subunit RPA49
N | DNA-directed RNA polymerase I subunit RPA34
O | RNA polymerase I-specific transcription initiation factor RRN3
Non-standard residues in 5g5l #4
---
ZN — zinc ion
> mmaker #4 to #1
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 4c2m_1_monomers.cif, chain A (#1) with 5g5l, chain A (#4), sequence
alignment score = 8187
RMSD between 1384 pruned atom pairs is 1.008 angstroms; (across all 1480
pairs: 1.209)
> mmaker #2 to #4
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 5g5l, chain O (#4) with 3tj1.cif, chain A (#2), sequence alignment
score = 2914.7
RMSD between 413 pruned atom pairs is 1.207 angstroms; (across all 463 pairs:
1.412)
> transparency 50
> hide sel cartoons
> hide sel atoms
> select #2
4048 atoms, 4078 bonds, 2 pseudobonds, 543 residues, 2 models selected
> select #3
2 models selected
> select #4
37349 atoms, 38087 bonds, 48 pseudobonds, 4693 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> volume #3 level 0.1056
> show sel cartoons
> hide #!4 models
> fitmap #2 inMap #3
Fit molecule 3tj1.cif (#2) to map polI-Rrn3.mrc (#3) using 4048 atoms
average map value = 0.1083, steps = 44
shifted from previous position = 2.75
rotated from previous position = 2.11 degrees
atoms outside contour = 1874, contour level = 0.10564
Position of 3tj1.cif (#2) relative to polI-Rrn3.mrc (#3) coordinates:
Matrix rotation and translation
0.33384165 0.73669868 0.58806871 -12.93002872
-0.04243988 -0.61148057 0.79012048 82.08504610
0.94167330 -0.28873269 -0.17287228 170.06584903
Axis -0.78350396 -0.25680103 -0.56583988
Axis point 0.00000000 71.02670837 75.80710911
Rotation angle (degrees) 136.49011476
Shift along axis -107.17883568
> show #!4 models
> close #4
> close #3
> show cartoons
> ui tool show ISOLDE
> set selectionWidth 4
Chain information for 4c2m_1_monomers.cif
---
Chain | Description
1.2/A | DNA-directed RNA polymerase I subunit RPA190
1.2/B | DNA-directed RNA polymerase I subunit RPA135
1.2/C | DNA-directed RNA polymerases I and III subunit RPAC1
1.2/D | DNA-directed RNA polymerase I subunit RPA14
1.2/E | DNA-directed RNA polymerases I, II, and III subunit rpabc 1
1.2/F | DNA-directed RNA polymerases I, II, and III subunit rpabc 2
1.2/G 1.2/O | DNA-directed RNA polymerase I subunit RPA43
1.2/H | DNA-directed RNA polymerases I, II, and III subunit rpabc 3
1.2/I | DNA-directed RNA polymerase I subunit RPA12
1.2/J | DNA-directed RNA polymerases I, II, and III subunit rpabc 5
1.2/K | DNA-directed RNA polymerases I and III subunit RPAC2
1.2/L | DNA-directed RNA polymerases I, II, and III subunit rpabc 4
1.2/M | DNA-directed RNA polymerase I subunit RPA49
1.2/N | DNA-directed RNA polymerase I subunit RPA34
4c2m_1_monomers.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
Done loading forcefield
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> close #1.3
> close #1.1
> close #1.1
> hide cartoons
> hide atoms
> select #1-2
38748 atoms, 39253 bonds, 44 pseudobonds, 5084 residues, 11 models selected
> select #1-2
38748 atoms, 39253 bonds, 44 pseudobonds, 5084 residues, 11 models selected
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "C:\Users\LocalAdmin\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\menu\menu.py", line 58, in f
module.run_script(session)
File "C:\Users\LocalAdmin\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\menu\model_building\merge_models.py", line 25, in
run_script
merge_fragment(target, m.residues[m.residues.chain_ids==cid],
chain_id=new_cid, transform=m.position, update_style=False)
TypeError: merge_fragment() got an unexpected keyword argument 'update_style'
TypeError: merge_fragment() got an unexpected keyword argument 'update_style'
File "C:\Users\LocalAdmin\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\menu\model_building\merge_models.py", line 25, in
run_script
merge_fragment(target, m.residues[m.residues.chain_ids==cid],
chain_id=new_cid, transform=m.position, update_style=False)
See log for complete Python traceback.
> close #1
3tj1.cif title:
Crystal Structure of RNA Polymerase I Transcription Initiation Factor Rrn3
[more info...]
Chain information for 3tj1.cif
---
Chain | Description
1.2/A | RNA polymerase I-specific transcription initiation factor RRN3
> open "C:/Users/LocalAdmin/Desktop/Test ChimeraX/4c2m_1_monomers.cif"
Chain information for 4c2m_1_monomers.cif #2
---
Chain | Description
A | DNA-directed RNA polymerase I subunit RPA190
B | DNA-directed RNA polymerase I subunit RPA135
C | DNA-directed RNA polymerases I and III subunit RPAC1
D | DNA-directed RNA polymerase I subunit RPA14
E | DNA-directed RNA polymerases I, II, and III subunit rpabc 1
F | DNA-directed RNA polymerases I, II, and III subunit rpabc 2
G O | DNA-directed RNA polymerase I subunit RPA43
H | DNA-directed RNA polymerases I, II, and III subunit rpabc 3
I | DNA-directed RNA polymerase I subunit RPA12
J | DNA-directed RNA polymerases I, II, and III subunit rpabc 5
K | DNA-directed RNA polymerases I and III subunit RPAC2
L | DNA-directed RNA polymerases I, II, and III subunit rpabc 4
M | DNA-directed RNA polymerase I subunit RPA49
N | DNA-directed RNA polymerase I subunit RPA34
4c2m_1_monomers.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> view
> open "C:/Users/LocalAdmin/Desktop/Test ChimeraX/polI-Rrn3.mrc"
Opened polI-Rrn3.mrc, grid size 128,128,128, pixel 2.16, shown at level 0.142,
step 1, values float32
> open 5g5l
5g5l title:
RNA polymerase I-Rrn3 complex at 4.8 A resolution [more info...]
Chain information for 5g5l #4
---
Chain | Description
A | DNA-directed RNA polymerase I subunit RPA190
B | DNA-directed RNA polymerase I subunit RPA135
C | DNA-directed RNA polymerases I and III subunit RPAC1
D | DNA-directed RNA polymerase I subunit RPA14
E | DNA-directed RNA polymerases I, II, and III subunit rpabc 1
F | DNA-directed RNA polymerases I, II, and III subunit rpabc 2
G | DNA-directed RNA polymerase I subunit RPA43
H | DNA-directed RNA polymerases I, II, and III subunit rpabc 3
I | DNA-directed RNA polymerase I subunit RPA12
J | DNA-directed RNA polymerases I, II, and III subunit rpabc 5
K | DNA-directed RNA polymerases I and III subunit RPAC2
L | DNA-directed RNA polymerases I, II, and III subunit rpabc 4
M | DNA-directed RNA polymerase I subunit RPA49
N | DNA-directed RNA polymerase I subunit RPA34
O | RNA polymerase I-specific transcription initiation factor RRN3
Non-standard residues in 5g5l #4
---
ZN — zinc ion
> fitmap #4 inMap #3
Fit molecule 5g5l (#4) to map polI-Rrn3.mrc (#3) using 37349 atoms
average map value = 0.04949, steps = 156
shifted from previous position = 38
rotated from previous position = 25.3 degrees
atoms outside contour = 33208, contour level = 0.14213
Position of 5g5l (#4) relative to polI-Rrn3.mrc (#3) coordinates:
Matrix rotation and translation
0.90607210 -0.38747104 -0.16999869 96.00090452
0.39799180 0.91684752 0.03151442 -78.49756049
0.14365195 -0.09621242 0.98494025 -29.82242100
Axis -0.14932505 -0.36668795 0.91828208
Axis point 247.34912436 182.81665254 0.00000000
Rotation angle (degrees) 25.32045417
Shift along axis -12.93662479
> volume #3 level 0.09956
> fitmap #4 inMap #3 search 50
Found 39 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (49 of 50).
Average map values and times found:
0.1168 (9), 0.06189 (1), 0.06103 (1), 0.06048 (1), 0.05959 (1), 0.05954 (1),
0.05936 (1), 0.05853 (1), 0.05841 (1), 0.0582 (1), 0.05813 (1), 0.05772 (1),
0.05711 (1), 0.05649 (2), 0.05575 (1), 0.05574 (1), 0.05573 (1), 0.055 (1),
0.05496 (1), 0.05488 (1), 0.05474 (1), 0.05474 (1), 0.05472 (1), 0.0546 (2),
0.05385 (1), 0.05371 (1), 0.05362 (1), 0.05347 (1), 0.05138 (1), 0.05137 (1),
0.05127 (1), 0.05049 (1), 0.05036 (1), 0.04981 (1), 0.04937 (1), 0.04933 (1),
0.04903 (1), 0.0481 (1), 0.04454 (1)
Best fit found:
Fit molecule 5g5l (#4) to map polI-Rrn3.mrc (#3) using 37349 atoms
average map value = 0.1168, steps = 420
shifted from previous position = 76.4
rotated from previous position = 78 degrees
atoms outside contour = 14603, contour level = 0.09956
Position of 5g5l (#4) relative to polI-Rrn3.mrc (#3) coordinates:
Matrix rotation and translation
-0.13614417 -0.19773272 0.97075566 28.54599622
-0.23013330 0.95938698 0.16314187 -9.04784700
-0.96358885 -0.20119238 -0.17611984 350.96158892
Axis -0.18507057 0.98258740 -0.01645850
Axis point 162.70561798 0.00000000 164.82328271
Rotation angle (degrees) 100.16238158
Shift along axis -19.94962430
Found 39 fits. List window not yet implemented.
> mmaker #2 to #4
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 5g5l, chain A (#4) with 4c2m_1_monomers.cif, chain A (#2), sequence
alignment score = 8187
RMSD between 1384 pruned atom pairs is 1.008 angstroms; (across all 1480
pairs: 1.209)
> hide cartoons
> hide atoms
> select #4
37349 atoms, 38087 bonds, 48 pseudobonds, 4693 residues, 3 models selected
> view sel
> ~select #4
Nothing selected
> volume #3 color black
> volume #3 color #bababa
> lighting soft
> lighting full
> lighting soft
> transparency 50
> open "C:/Users/LocalAdmin/Desktop/Test ChimeraX/3tj1.cif"
3tj1.cif title:
Crystal Structure of RNA Polymerase I Transcription Initiation Factor Rrn3
[more info...]
Chain information for 3tj1.cif #5
---
Chain | Description
A B | RNA polymerase I-specific transcription initiation factor RRN3
> mmaker #5 to #1
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 3tj1.cif, chain A (#1.2) with 3tj1.cif, chain A (#5), sequence
alignment score = 3171.1
RMSD between 483 pruned atom pairs is 0.000 angstroms; (across all 483 pairs:
0.000)
> delete #5/b
> select #4
37349 atoms, 38087 bonds, 48 pseudobonds, 4693 residues, 3 models selected
> ~select #4
Nothing selected
> show cartoons
> hide #!4 models
> hide #!2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> select #1.2
4048 atoms, 4078 bonds, 2 pseudobonds, 543 residues, 6 models selected
> show sel cartoons
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> fitmap #5 inMap #3
Fit molecule 3tj1.cif (#5) to map polI-Rrn3.mrc (#3) using 4048 atoms
average map value = 0.1083, steps = 44
shifted from previous position = 0.0477
rotated from previous position = 0.0456 degrees
atoms outside contour = 1677, contour level = 0.09956
Position of 3tj1.cif (#5) relative to polI-Rrn3.mrc (#3) coordinates:
Matrix rotation and translation
0.33334730 0.73659564 0.58847807 -12.98107315
-0.04300865 -0.61164812 0.78996002 82.14816900
0.94182261 -0.28864069 -0.17221127 169.95137074
Axis -0.78332115 -0.25661234 -0.56617849
Axis point 0.00000000 71.04000646 75.74485628
Rotation angle (degrees) 136.49015164
Shift along axis -107.13469544
> show #!4 models
> close #4
> show #!2 models
> close #1
3tj1.cif title:
Crystal Structure of RNA Polymerase I Transcription Initiation Factor Rrn3
[more info...]
Chain information for 3tj1.cif
---
Chain | Description
1.2/A | RNA polymerase I-specific transcription initiation factor RRN3
Chain information for 4c2m_1_monomers.cif
---
Chain | Description
2.2/A | DNA-directed RNA polymerase I subunit RPA190
2.2/B | DNA-directed RNA polymerase I subunit RPA135
2.2/C | DNA-directed RNA polymerases I and III subunit RPAC1
2.2/D | DNA-directed RNA polymerase I subunit RPA14
2.2/E | DNA-directed RNA polymerases I, II, and III subunit rpabc 1
2.2/F | DNA-directed RNA polymerases I, II, and III subunit rpabc 2
2.2/G 2.2/O | DNA-directed RNA polymerase I subunit RPA43
2.2/H | DNA-directed RNA polymerases I, II, and III subunit rpabc 3
2.2/I | DNA-directed RNA polymerase I subunit RPA12
2.2/J | DNA-directed RNA polymerases I, II, and III subunit rpabc 5
2.2/K | DNA-directed RNA polymerases I and III subunit RPAC2
2.2/L | DNA-directed RNA polymerases I, II, and III subunit rpabc 4
2.2/M | DNA-directed RNA polymerase I subunit RPA49
2.2/N | DNA-directed RNA polymerase I subunit RPA34
4c2m_1_monomers.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> select #1,2
38748 atoms, 39253 bonds, 44 pseudobonds, 5084 residues, 19 models selected
> ~select #2.3
38748 atoms, 39253 bonds, 44 pseudobonds, 5084 residues, 18 models selected
> hide #2.3 models
> hide #!3 models
> ~select #1.3
38748 atoms, 39253 bonds, 44 pseudobonds, 5084 residues, 17 models selected
> hide #1.3 models
> ~select #1.1
38748 atoms, 39253 bonds, 44 pseudobonds, 5084 residues, 16 models selected
> hide #1.1 models
> ~select #2.1
38748 atoms, 39253 bonds, 44 pseudobonds, 5084 residues, 15 models selected
> hide #2.1 models
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "C:\Users\LocalAdmin\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\menu\menu.py", line 58, in f
module.run_script(session)
File "C:\Users\LocalAdmin\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\menu\model_building\merge_models.py", line 25, in
run_script
merge_fragment(target, m.residues[m.residues.chain_ids==cid],
chain_id=new_cid, transform=m.position, update_style=False)
TypeError: merge_fragment() got an unexpected keyword argument 'update_style'
TypeError: merge_fragment() got an unexpected keyword argument 'update_style'
File "C:\Users\LocalAdmin\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\menu\model_building\merge_models.py", line 25, in
run_script
merge_fragment(target, m.residues[m.residues.chain_ids==cid],
chain_id=new_cid, transform=m.position, update_style=False)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "C:\Users\LocalAdmin\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\menu\menu.py", line 58, in f
module.run_script(session)
File "C:\Users\LocalAdmin\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\menu\model_building\merge_models.py", line 25, in
run_script
merge_fragment(target, m.residues[m.residues.chain_ids==cid],
chain_id=new_cid, transform=m.position, update_style=False)
TypeError: merge_fragment() got an unexpected keyword argument 'update_style'
TypeError: merge_fragment() got an unexpected keyword argument 'update_style'
File "C:\Users\LocalAdmin\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\menu\model_building\merge_models.py", line 25, in
run_script
merge_fragment(target, m.residues[m.residues.chain_ids==cid],
chain_id=new_cid, transform=m.position, update_style=False)
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 23.20.16.4973
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Manufacturer: HP
Model: HP EliteBook 850 G5
OS: Microsoft Windows 10 Education (Build 18363)
Memory: 8,425,529,344
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-Clipper: 0.15.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.0
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-ISOLDE: 1.1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
gdcm: 2.8.8
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5+mkl
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pywin32: 228
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
WMI: 1.5.1
Change History (2)
comment:1 by , 5 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ISOLDE: merge_fragment() got an unexpected keyword argument 'update_style' |
comment:2 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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Known bug, fixed in my local version. I guess it's time I put out another incremental build to cover this and a few other bug-fixes I've made. Will try to do so tomorrow.