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Opened 5 years ago
Closed 5 years ago
#4381 closed defect (duplicate)
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: Linux-3.10.0-1062.18.1.el7.x86_64-x86_64-with-redhat-7.9-Nitrogen
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 /home/michael/NLRP3/iNext_202101/run_class001_j99_C1.mrc
> /home/michael/NLRP3/iNext_202101/run_class001_j100_D5.mrc
Opened run_class001_j99_C1.mrc, grid size 240,240,240, pixel 1.29, shown at
level 0.0151, step 1, values float32
> open 6npy
Summary of feedback from opening 6npy fetched from pdb
---
notes | Fetching compressed mmCIF 6npy from
http://files.rcsb.org/download/6npy.cif
Fetching CCD ADP from http://ligand-expo.rcsb.org/reports/A/ADP/ADP.cif
6npy title:
Cryo-EM structure of NLRP3 bound to NEK7 [more info...]
Chain information for 6npy #2
---
Chain | Description
A | NACHT, LRR and PYD domains-containing protein 3
B | Protein kinase R,Serine/threonine-protein kinase Nek7
Non-standard residues in 6npy #2
---
ADP — adenosine-5'-diphosphate
> open 6npy
6npy title:
Cryo-EM structure of NLRP3 bound to NEK7 [more info...]
Chain information for 6npy #3
---
Chain | Description
A | NACHT, LRR and PYD domains-containing protein 3
B | Protein kinase R,Serine/threonine-protein kinase Nek7
Non-standard residues in 6npy #3
---
ADP — adenosine-5'-diphosphate
> delete 7b
Missing or invalid "atoms" argument: invalid atoms specifier
> delete /b
> fitmap #2 inMap #1.1
Fit molecule 6npy (#2) to map run_class001_j99_C1.mrc (#1.1) using 6219 atoms
average map value = 0.00951, steps = 344
shifted from previous position = 34.4
rotated from previous position = 78.9 degrees
atoms outside contour = 5777, contour level = 0.015105
Position of 6npy (#2) relative to run_class001_j99_C1.mrc (#1.1) coordinates:
Matrix rotation and translation
0.45840180 0.58635826 0.66787108 -62.10618693
-0.88831745 0.27898096 0.36477627 157.26476348
0.02756627 -0.76049564 0.64875765 120.96114749
Axis -0.57342498 0.32629160 -0.75147694
Axis point 51.07825651 156.98215151 0.00000000
Rotation angle (degrees) 78.86798786
Shift along axis -3.97210198
> fitmap #2 inMap #1.1 search 50
Found 40 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (42 of 50).
Average map values and times found:
0.01312 (1), 0.01216 (1), 0.01214 (1), 0.01045 (1), 0.01041 (1), 0.01039 (1),
0.01038 (1), 0.01035 (1), 0.01031 (1), 0.0103 (1), 0.01027 (1), 0.01022 (1),
0.01019 (1), 0.01013 (2), 0.01006 (1), 0.01004 (1), 0.01003 (1), 0.009973 (1),
0.009954 (1), 0.009932 (1), 0.009914 (1), 0.009861 (2), 0.00979 (1), 0.009788
(1), 0.009777 (1), 0.009662 (1), 0.009622 (1), 0.009601 (1), 0.0096 (1),
0.009481 (1), 0.009352 (1), 0.009296 (1), 0.009222 (1), 0.009031 (1), 0.00896
(1), 0.008916 (1), 0.008786 (1), 0.008577 (1), 0.008541 (1), 0.008141 (1)
Best fit found:
Fit molecule 6npy (#2) to map run_class001_j99_C1.mrc (#1.1) using 6219 atoms
average map value = 0.01312, steps = 380
shifted from previous position = 50.1
rotated from previous position = 90.3 degrees
atoms outside contour = 4123, contour level = 0.015105
Position of 6npy (#2) relative to run_class001_j99_C1.mrc (#1.1) coordinates:
Matrix rotation and translation
-0.48695936 0.14807972 0.86078043 132.83515008
0.64423804 -0.60456742 0.46846084 154.66255035
0.58976936 0.78266893 0.19900118 -31.88586128
Axis 0.48579063 0.41900461 0.76710012
Axis point 64.52229288 94.90861021 0.00000000
Rotation angle (degrees) 161.13141261
Shift along axis 104.87474597
Found 40 fits. List window not yet implemented.
> fitmap #2 inMap #1.2 search 50
Found 43 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (45 of 50).
Average map values and times found:
0.01225 (1), 0.01223 (1), 0.01016 (1), 0.01004 (1), 0.01002 (1), 0.009911 (1),
0.009866 (1), 0.009832 (1), 0.009704 (1), 0.009665 (1), 0.009659 (1), 0.009596
(1), 0.00959 (1), 0.009587 (1), 0.009586 (1), 0.009581 (1), 0.00958 (1),
0.009577 (2), 0.009577 (1), 0.009522 (1), 0.009512 (1), 0.009507 (1), 0.009492
(1), 0.009489 (1), 0.009471 (1), 0.009471 (1), 0.009373 (1), 0.009361 (1),
0.009343 (1), 0.009182 (2), 0.009163 (1), 0.009127 (1), 0.009053 (1), 0.009014
(1), 0.00898 (1), 0.008883 (1), 0.008823 (1), 0.008776 (1), 0.008652 (1),
0.008333 (1), 0.008146 (1), 0.005524 (1), 0.005363 (1)
Best fit found:
Fit molecule 6npy (#2) to map run_class001_j100_D5.mrc (#1.2) using 6219 atoms
average map value = 0.01225, steps = 316
shifted from previous position = 50
rotated from previous position = 49.3 degrees
atoms outside contour = 4380, contour level = 0.014331
Position of 6npy (#2) relative to run_class001_j100_D5.mrc (#1.2) coordinates:
Matrix rotation and translation
-0.51026281 0.13887152 0.84873238 139.08441594
0.62117747 -0.62300842 0.47539363 159.03657150
0.59478602 0.76978912 0.23163419 -34.94913088
Axis 0.47521701 0.40992349 0.77854449
Axis point 68.34187687 97.85823242 0.00000000
Rotation angle (degrees) 161.95592636
Shift along axis 104.07865257
Found 43 fits. List window not yet implemented.
Must specify one map, got 0
> fitmap #3 inMap #1.1 search 50
Found 34 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (37 of 50).
Average map values and times found:
0.01216 (1), 0.01214 (1), 0.01212 (3), 0.01055 (1), 0.01053 (1), 0.01049 (1),
0.01044 (1), 0.01042 (1), 0.0104 (1), 0.01032 (1), 0.0103 (1), 0.01026 (1),
0.01013 (1), 0.01013 (1), 0.01008 (1), 0.01002 (1), 0.01 (1), 0.009954 (1),
0.009768 (1), 0.009712 (1), 0.009692 (1), 0.009678 (1), 0.009672 (1), 0.009634
(1), 0.00942 (1), 0.009402 (1), 0.009359 (1), 0.009296 (1), 0.009223 (2),
0.009137 (1), 0.009048 (1), 0.00883 (1), 0.006608 (1), 0.006597 (1)
Best fit found:
Fit molecule 6npy (#3) to map run_class001_j99_C1.mrc (#1.1) using 6219 atoms
average map value = 0.01216, steps = 376
shifted from previous position = 60
rotated from previous position = 62.9 degrees
atoms outside contour = 4827, contour level = 0.015105
Position of 6npy (#3) relative to run_class001_j99_C1.mrc (#1.1) coordinates:
Matrix rotation and translation
0.03355135 0.24324371 -0.96938471 167.86907323
-0.81497590 0.56810185 0.11434437 147.33066690
0.57852277 0.78618877 0.21729834 -36.01909129
Axis 0.33730711 -0.77714452 -0.53129117
Axis point 149.16310601 0.00000000 37.93840427
Rotation angle (degrees) 95.19376687
Shift along axis -38.73716392
Found 34 fits. List window not yet implemented.
> volume #1.1 level 0.01285
> volume #1.1 level 0.01346
> ui tool show ISOLDE
> set selectionWidth 4
6npy title:
Cryo-EM structure of NLRP3 bound to NEK7 [more info...]
Chain information for 6npy
---
Chain | Description
2.2/A | NACHT, LRR and PYD domains-containing protein 3
Non-standard residues in 6npy #2.2
---
ADP — adenosine-5'-diphosphate
Done loading forcefield
> select #2.1
5 models selected
> ~select #2.1
Nothing selected
> select #2
6219 atoms, 6336 bonds, 7 pseudobonds, 799 residues, 13 models selected
> volume #2.1.1.1 level 0.01627
> volume #2.1.1.1 level 0.01505
> select #2.1:137-697
Nothing selected
> select #2.1:137-697
Nothing selected
> select #2.1/a:137-697
Nothing selected
> select #2/a:137-697
3621 atoms, 3698 bonds, 7 pseudobonds, 457 residues, 2 models selected
> volume #2.1.1.1 level 0.01316
Loading residue template for ADP from internal database
> addh
Summary of feedback from adding hydrogens to multiple structures
---
warnings | Not adding hydrogens to 6npy #3/A HIS 175 CB because it is missing
heavy-atom bond partners
Not adding hydrogens to 6npy #3/A ARG 176 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to 6npy #3/A ILE 201 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to 6npy #3/A THR 245 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to 6npy #3/A LEU 246 CB because it is missing heavy-atom
bond partners
61 messages similar to the above omitted
notes | Termini for 6npy (#3) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: 6npy #3/A ILE 133, 6npy
#3/A SER 161, 6npy #3/A ILE 201, 6npy #3/A GLY 459, 6npy #3/A ASN 543, 6npy
#3/A GLU 561, 6npy #3/A ALA 614, 6npy #3/A GLY 680
Chain-final residues that are actual C termini: 6npy #3/A TRP 1034
Chain-final residues that are not actual C termini: 6npy #3/A GLU 150, 6npy
#3/A ARG 176, 6npy #3/A GLY 453, 6npy #3/A GLU 535, 6npy #3/A ARG 554, 6npy
#3/A THR 587, 6npy #3/A ILE 653
489 hydrogen bonds
Adding 'H' to 6npy #3/A ILE 133
Adding 'H' to 6npy #3/A SER 161
Adding 'H' to 6npy #3/A ILE 201
Adding 'H' to 6npy #3/A GLY 459
Adding 'H' to 6npy #3/A ASN 543
3 messages similar to the above omitted
Termini for 6npy (#2.2) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: 6npy #2.2/A ILE 133,
6npy #2.2/A SER 161, 6npy #2.2/A ILE 201, 6npy #2.2/A GLY 459, 6npy #2.2/A ASN
543, 6npy #2.2/A GLU 561, 6npy #2.2/A ALA 614, 6npy #2.2/A GLY 680
Chain-final residues that are actual C termini: 6npy #2.2/A TRP 1034
Chain-final residues that are not actual C termini: 6npy #2.2/A GLU 150, 6npy
#2.2/A ARG 176, 6npy #2.2/A GLY 453, 6npy #2.2/A GLU 535, 6npy #2.2/A ARG 554,
6npy #2.2/A THR 587, 6npy #2.2/A ILE 653
489 hydrogen bonds
Adding 'H' to 6npy #2.2/A ILE 133
Adding 'H' to 6npy #2.2/A SER 161
Adding 'H' to 6npy #2.2/A ILE 201
Adding 'H' to 6npy #2.2/A GLY 459
Adding 'H' to 6npy #2.2/A ASN 543
3 messages similar to the above omitted
12228 hydrogens added
> addh
Summary of feedback from adding hydrogens to multiple structures
---
warnings | Not adding hydrogens to 6npy #3/A HIS 175 CB because it is missing
heavy-atom bond partners
Not adding hydrogens to 6npy #3/A ARG 176 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to 6npy #3/A ILE 201 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to 6npy #3/A THR 245 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to 6npy #3/A LEU 246 CB because it is missing heavy-atom
bond partners
61 messages similar to the above omitted
notes | Termini for 6npy (#3) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: 6npy #3/A ILE 133, 6npy
#3/A SER 161, 6npy #3/A ILE 201, 6npy #3/A GLY 459, 6npy #3/A ASN 543, 6npy
#3/A GLU 561, 6npy #3/A ALA 614, 6npy #3/A GLY 680
Chain-final residues that are actual C termini: 6npy #3/A TRP 1034
Chain-final residues that are not actual C termini: 6npy #3/A GLU 150, 6npy
#3/A ARG 176, 6npy #3/A GLY 453, 6npy #3/A GLU 535, 6npy #3/A ARG 554, 6npy
#3/A THR 587, 6npy #3/A ILE 653
440 hydrogen bonds
Termini for 6npy (#2.2) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: 6npy #2.2/A ILE 133,
6npy #2.2/A SER 161, 6npy #2.2/A ILE 201, 6npy #2.2/A GLY 459, 6npy #2.2/A ASN
543, 6npy #2.2/A GLU 561, 6npy #2.2/A ALA 614, 6npy #2.2/A GLY 680
Chain-final residues that are actual C termini: 6npy #2.2/A TRP 1034
Chain-final residues that are not actual C termini: 6npy #2.2/A GLU 150, 6npy
#2.2/A ARG 176, 6npy #2.2/A GLY 453, 6npy #2.2/A GLU 535, 6npy #2.2/A ARG 554,
6npy #2.2/A THR 587, 6npy #2.2/A ILE 653
439 hydrogen bonds
0 hydrogens added
> select #2
12333 atoms, 12450 bonds, 7 pseudobonds, 799 residues, 19 models selected
> addh
Summary of feedback from adding hydrogens to multiple structures
---
warnings | Not adding hydrogens to 6npy #3/A HIS 175 CB because it is missing
heavy-atom bond partners
Not adding hydrogens to 6npy #3/A ARG 176 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to 6npy #3/A ILE 201 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to 6npy #3/A THR 245 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to 6npy #3/A LEU 246 CB because it is missing heavy-atom
bond partners
61 messages similar to the above omitted
notes | Termini for 6npy (#3) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: 6npy #3/A ILE 133, 6npy
#3/A SER 161, 6npy #3/A ILE 201, 6npy #3/A GLY 459, 6npy #3/A ASN 543, 6npy
#3/A GLU 561, 6npy #3/A ALA 614, 6npy #3/A GLY 680
Chain-final residues that are actual C termini: 6npy #3/A TRP 1034
Chain-final residues that are not actual C termini: 6npy #3/A GLU 150, 6npy
#3/A ARG 176, 6npy #3/A GLY 453, 6npy #3/A GLU 535, 6npy #3/A ARG 554, 6npy
#3/A THR 587, 6npy #3/A ILE 653
440 hydrogen bonds
Termini for 6npy (#2.2) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: 6npy #2.2/A ILE 133,
6npy #2.2/A SER 161, 6npy #2.2/A ILE 201, 6npy #2.2/A GLY 459, 6npy #2.2/A ASN
543, 6npy #2.2/A GLU 561, 6npy #2.2/A ALA 614, 6npy #2.2/A GLY 680
Chain-final residues that are actual C termini: 6npy #2.2/A TRP 1034
Chain-final residues that are not actual C termini: 6npy #2.2/A GLU 150, 6npy
#2.2/A ARG 176, 6npy #2.2/A GLY 453, 6npy #2.2/A GLU 535, 6npy #2.2/A ARG 554,
6npy #2.2/A THR 587, 6npy #2.2/A ILE 653
439 hydrogen bonds
0 hydrogens added
> select #2/a:137-697
7144 atoms, 7221 bonds, 7 pseudobonds, 457 residues, 2 models selected
> volume #2.1.1.1 level 0.01215
> select #2/a:138-438
4200 atoms, 4244 bonds, 2 pseudobonds, 267 residues, 2 models selected
> volume #2.1.1.1 level 0.01145
> select #2/a:439-697
2922 atoms, 2954 bonds, 5 pseudobonds, 189 residues, 2 models selected
> volume #2.1.1.1 level 0.01022
> select #2/a:697-1034
5113 atoms, 5149 bonds, 338 residues, 1 model selected
> volume #2.1.1.1 level 0.01167
> volume #2.1.1.1 level 0.01221
> select #2
12333 atoms, 12450 bonds, 7 pseudobonds, 799 residues, 19 models selected
> open 6npy
6npy title:
Cryo-EM structure of NLRP3 bound to NEK7 [more info...]
Chain information for 6npy #4
---
Chain | Description
A | NACHT, LRR and PYD domains-containing protein 3
B | Protein kinase R,Serine/threonine-protein kinase Nek7
Non-standard residues in 6npy #4
---
ADP — adenosine-5'-diphosphate
> open 6npy
6npy title:
Cryo-EM structure of NLRP3 bound to NEK7 [more info...]
Chain information for 6npy #5
---
Chain | Description
A | NACHT, LRR and PYD domains-containing protein 3
B | Protein kinase R,Serine/threonine-protein kinase Nek7
Non-standard residues in 6npy #5
---
ADP — adenosine-5'-diphosphate
> open 6npy
6npy title:
Cryo-EM structure of NLRP3 bound to NEK7 [more info...]
Chain information for 6npy #6
---
Chain | Description
A | NACHT, LRR and PYD domains-containing protein 3
B | Protein kinase R,Serine/threonine-protein kinase Nek7
Non-standard residues in 6npy #6
---
ADP — adenosine-5'-diphosphate
> open 6npy
6npy title:
Cryo-EM structure of NLRP3 bound to NEK7 [more info...]
Chain information for 6npy #7
---
Chain | Description
A | NACHT, LRR and PYD domains-containing protein 3
B | Protein kinase R,Serine/threonine-protein kinase Nek7
Non-standard residues in 6npy #7
---
ADP — adenosine-5'-diphosphate
> open 6npy
6npy title:
Cryo-EM structure of NLRP3 bound to NEK7 [more info...]
Chain information for 6npy #8
---
Chain | Description
A | NACHT, LRR and PYD domains-containing protein 3
B | Protein kinase R,Serine/threonine-protein kinase Nek7
Non-standard residues in 6npy #8
---
ADP — adenosine-5'-diphosphate
> open 6npy
6npy title:
Cryo-EM structure of NLRP3 bound to NEK7 [more info...]
Chain information for 6npy #9
---
Chain | Description
A | NACHT, LRR and PYD domains-containing protein 3
B | Protein kinase R,Serine/threonine-protein kinase Nek7
Non-standard residues in 6npy #9
---
ADP — adenosine-5'-diphosphate
> open 6npy
6npy title:
Cryo-EM structure of NLRP3 bound to NEK7 [more info...]
Chain information for 6npy #10
---
Chain | Description
A | NACHT, LRR and PYD domains-containing protein 3
B | Protein kinase R,Serine/threonine-protein kinase Nek7
Non-standard residues in 6npy #10
---
ADP — adenosine-5'-diphosphate
> open 6npy
6npy title:
Cryo-EM structure of NLRP3 bound to NEK7 [more info...]
Chain information for 6npy #11
---
Chain | Description
A | NACHT, LRR and PYD domains-containing protein 3
B | Protein kinase R,Serine/threonine-protein kinase Nek7
Non-standard residues in 6npy #11
---
ADP — adenosine-5'-diphosphate
> delete /b
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> show #!1.2 models
> volume #1.2 level 0.01174
> fitmap #3 inMap #1.2 search 50
Found 45 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.01163 (1), 0.01162 (1), 0.01162 (1), 0.01162 (2), 0.01161 (1), 0.0101 (1),
0.00997 (1), 0.009954 (1), 0.009919 (1), 0.009919 (1), 0.009915 (1), 0.009864
(1), 0.009859 (3), 0.009828 (2), 0.009798 (1), 0.009663 (1), 0.00965 (1),
0.00965 (1), 0.009621 (1), 0.009618 (1), 0.009618 (1), 0.009617 (1), 0.009599
(1), 0.009592 (1), 0.009568 (1), 0.009566 (2), 0.009566 (1), 0.009559 (1),
0.009559 (1), 0.009559 (1), 0.009557 (1), 0.009508 (1), 0.009488 (1), 0.009469
(1), 0.009454 (1), 0.009388 (1), 0.009309 (1), 0.009245 (1), 0.009101 (1),
0.008945 (1), 0.008686 (1), 0.008387 (1), 0.007423 (1), 0.006786 (1), 0.00649
(1)
Best fit found:
Fit molecule 6npy (#3) to map run_class001_j100_D5.mrc (#1.2) using 12333
atoms
average map value = 0.01163, steps = 296
shifted from previous position = 41.2
rotated from previous position = 31.4 degrees
atoms outside contour = 6363, contour level = 0.011736
Position of 6npy (#3) relative to run_class001_j100_D5.mrc (#1.2) coordinates:
Matrix rotation and translation
0.77944428 -0.47888709 -0.40389838 169.62915976
-0.19995925 0.42081946 -0.88483171 160.86403357
0.59370278 0.77044022 0.23224742 -34.96681700
Axis 0.84769517 -0.51088988 0.14284407
Axis point 0.00000000 163.18322143 107.67655381
Rotation angle (degrees) 77.51079987
Shift along axis 56.61520978
Found 45 fits. List window not yet implemented.
> transparency 50
> fitmap #4 inMap #1.2 search 50
Found 49 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.01225 (2), 0.01017 (1), 0.01015 (1), 0.01003 (1), 0.009962 (1), 0.009955
(1), 0.009955 (1), 0.009954 (1), 0.00995 (1), 0.009906 (1), 0.009873 (1),
0.009844 (1), 0.009815 (1), 0.009707 (1), 0.009677 (1), 0.009673 (1), 0.009633
(1), 0.009627 (1), 0.009596 (1), 0.009596 (1), 0.009596 (1), 0.009583 (1),
0.009577 (1), 0.009526 (1), 0.00951 (1), 0.009502 (1), 0.009489 (1), 0.009488
(1), 0.009426 (1), 0.009425 (1), 0.009421 (1), 0.009375 (1), 0.009272 (1),
0.009222 (1), 0.009206 (1), 0.009204 (1), 0.009202 (1), 0.009052 (1), 0.008983
(1), 0.008901 (1), 0.008725 (1), 0.008692 (1), 0.008615 (1), 0.008398 (1),
0.008044 (1), 0.008041 (1), 0.006877 (1), 0.0062 (1), 0.005363 (1)
Best fit found:
Fit molecule 6npy (#4) to map run_class001_j100_D5.mrc (#1.2) using 6219 atoms
average map value = 0.01225, steps = 184
shifted from previous position = 25.5
rotated from previous position = 31.1 degrees
atoms outside contour = 2900, contour level = 0.011736
Position of 6npy (#4) relative to run_class001_j100_D5.mrc (#1.2) coordinates:
Matrix rotation and translation
0.77827997 -0.47870485 -0.40635198 169.88367887
0.20095640 -0.42321685 0.88346141 149.25833940
-0.59489224 -0.76923931 -0.23318238 344.69431228
Axis -0.91974298 0.10492437 0.37823766
Axis point 0.00000000 202.62245890 156.25567764
Rotation angle (degrees) 116.04389718
Shift along axis -10.21211207
Found 49 fits. List window not yet implemented.
> fitmap #5 inMap #1.2 search 50
Found 50 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.01225 (1), 0.01224 (1), 0.01223 (1), 0.01017 (1), 0.01015 (1), 0.01015 (1),
0.009995 (1), 0.009979 (1), 0.009869 (1), 0.009866 (1), 0.009838 (1), 0.009832
(1), 0.009707 (1), 0.009701 (1), 0.009691 (1), 0.009685 (1), 0.009678 (1),
0.009662 (1), 0.009632 (1), 0.00962 (1), 0.009596 (1), 0.00959 (1), 0.00959
(1), 0.009584 (1), 0.009534 (1), 0.009446 (1), 0.009277 (1), 0.009267 (1),
0.00916 (1), 0.009133 (1), 0.009067 (1), 0.009008 (1), 0.009 (1), 0.008918
(1), 0.008906 (1), 0.008872 (1), 0.008872 (1), 0.008813 (1), 0.008787 (1),
0.008689 (1), 0.008684 (1), 0.008621 (1), 0.008615 (1), 0.008549 (1), 0.0083
(1), 0.008155 (1), 0.008145 (1), 0.006877 (1), 0.006875 (1), 0.006261 (1)
Best fit found:
Fit molecule 6npy (#5) to map run_class001_j100_D5.mrc (#1.2) using 6219 atoms
average map value = 0.01225, steps = 328
shifted from previous position = 33
rotated from previous position = 52 degrees
atoms outside contour = 2902, contour level = 0.011736
Position of 6npy (#5) relative to run_class001_j100_D5.mrc (#1.2) coordinates:
Matrix rotation and translation
0.77828928 -0.47863925 -0.40641145 169.88013122
-0.20096284 0.42332499 -0.88340809 160.32612154
0.59487791 0.76922064 0.23328060 -35.10384270
Axis 0.84657111 -0.51291777 0.14224177
Axis point 0.00000000 163.41597768 107.66636164
Rotation angle (degrees) 77.44084720
Shift along axis 56.58826067
Found 50 fits. List window not yet implemented.
> fitmap #6 inMap #1.2 search 50
Found 50 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.01224 (1), 0.01224 (1), 0.01017 (1), 0.009954 (1), 0.009943 (1), 0.009906
(1), 0.009898 (1), 0.009849 (1), 0.009838 (1), 0.009707 (1), 0.009706 (1),
0.009599 (1), 0.009596 (1), 0.00959 (1), 0.00959 (1), 0.009586 (1), 0.009581
(1), 0.009577 (1), 0.009515 (1), 0.009499 (1), 0.009499 (1), 0.009498 (1),
0.009489 (1), 0.009471 (1), 0.009465 (1), 0.00945 (1), 0.009421 (1), 0.009411
(1), 0.009375 (1), 0.00936 (1), 0.009356 (1), 0.009339 (1), 0.009336 (1),
0.009263 (1), 0.009263 (1), 0.009249 (1), 0.009206 (1), 0.009184 (1), 0.009004
(1), 0.009 (1), 0.008862 (1), 0.008801 (1), 0.008759 (1), 0.008728 (1),
0.008568 (1), 0.008544 (1), 0.008309 (1), 0.00687 (1), 0.006236 (1), 0.006031
(1)
Best fit found:
Fit molecule 6npy (#6) to map run_class001_j100_D5.mrc (#1.2) using 6219 atoms
average map value = 0.01224, steps = 344
shifted from previous position = 31.8
rotated from previous position = 67.4 degrees
atoms outside contour = 2906, contour level = 0.011736
Position of 6npy (#6) relative to run_class001_j100_D5.mrc (#1.2) coordinates:
Matrix rotation and translation
0.43127872 -0.55054513 0.71477176 154.21418465
0.67804959 -0.32485030 -0.65933370 170.89893345
0.59518673 0.76900733 0.23319592 -35.11340469
Axis 0.75660453 0.06334522 0.65079718
Axis point 0.00000000 127.39886440 -6.84746312
Rotation angle (degrees) 109.28017710
Shift along axis 104.65307549
Found 50 fits. List window not yet implemented.
> fitmap #7 inMap #1.2 search 50
Found 47 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (49 of 50).
Average map values and times found:
0.01225 (1), 0.01224 (1), 0.01001 (1), 0.009995 (1), 0.009979 (1), 0.009979
(1), 0.009955 (1), 0.009955 (1), 0.009754 (1), 0.009707 (1), 0.009707 (1),
0.00968 (1), 0.009665 (1), 0.009638 (1), 0.009637 (1), 0.009635 (1), 0.009619
(1), 0.009596 (1), 0.009596 (3), 0.00959 (1), 0.009586 (1), 0.009586 (1),
0.009584 (1), 0.009581 (1), 0.00958 (1), 0.009539 (1), 0.009499 (1), 0.009485
(1), 0.009467 (1), 0.009446 (1), 0.009411 (1), 0.009366 (1), 0.009348 (1),
0.009271 (1), 0.009213 (1), 0.009093 (1), 0.009001 (1), 0.00898 (1), 0.008907
(1), 0.008824 (1), 0.008452 (1), 0.008428 (1), 0.008312 (1), 0.008303 (1),
0.007777 (1), 0.006875 (1), 0.006393 (1)
Best fit found:
Fit molecule 6npy (#7) to map run_class001_j100_D5.mrc (#1.2) using 6219 atoms
average map value = 0.01225, steps = 248
shifted from previous position = 24
rotated from previous position = 48.4 degrees
atoms outside contour = 2901, contour level = 0.011736
Position of 6npy (#7) relative to run_class001_j100_D5.mrc (#1.2) coordinates:
Matrix rotation and translation
-0.51016116 0.13889280 0.84878994 139.05194779
-0.62099056 0.62331201 -0.47523987 150.48820817
-0.59506836 -0.76953947 -0.23173844 344.58436126
Axis -0.17750930 0.87087540 -0.45833011
Axis point 182.82673263 0.00000000 172.24313952
Rotation angle (degrees) 124.00697326
Shift along axis -51.55992216
Found 47 fits. List window not yet implemented.
> fitmap #8 inMap #1.2 search 50
Found 49 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (49 of 50).
Average map values and times found:
0.01225 (1), 0.01016 (1), 0.01013 (1), 0.009955 (1), 0.009949 (1), 0.009922
(1), 0.009905 (1), 0.009902 (1), 0.009844 (1), 0.009707 (1), 0.009691 (1),
0.009684 (1), 0.00968 (1), 0.00959 (1), 0.00959 (1), 0.00959 (1), 0.009587
(1), 0.009581 (1), 0.009581 (1), 0.00958 (1), 0.009579 (1), 0.009578 (1),
0.009502 (1), 0.009501 (1), 0.009497 (1), 0.009495 (1), 0.009475 (1), 0.009467
(1), 0.009436 (1), 0.009423 (1), 0.009387 (1), 0.009346 (1), 0.009298 (1),
0.009237 (1), 0.009204 (1), 0.009112 (1), 0.009 (1), 0.00892 (1), 0.008906
(1), 0.008823 (1), 0.008801 (1), 0.008711 (1), 0.008497 (1), 0.008298 (1),
0.008156 (1), 0.007481 (1), 0.006875 (1), 0.006631 (1), 0.006198 (1)
Best fit found:
Fit molecule 6npy (#8) to map run_class001_j100_D5.mrc (#1.2) using 6219 atoms
average map value = 0.01225, steps = 312
shifted from previous position = 52.6
rotated from previous position = 22.8 degrees
atoms outside contour = 2903, contour level = 0.011736
Position of 6npy (#8) relative to run_class001_j100_D5.mrc (#1.2) coordinates:
Matrix rotation and translation
-0.51046067 0.13908847 0.84857779 139.10162990
0.62110199 -0.62284099 0.47571141 158.98917730
0.59469506 0.76988530 0.23154774 -34.93908660
Axis 0.47513467 0.41005845 0.77852367
Axis point 68.35933861 97.83211315 0.00000000
Rotation angle (degrees) 161.96674379
Shift along axis 104.08595680
Found 49 fits. List window not yet implemented.
> fitmap #9 inMap #1.2 search 50
Found 50 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.01018 (1), 0.01016 (1), 0.01016 (1), 0.01012 (1), 0.01011 (1), 0.01002 (1),
0.009955 (1), 0.009902 (1), 0.009684 (1), 0.009684 (1), 0.009673 (1), 0.009654
(1), 0.009646 (1), 0.009633 (1), 0.009609 (1), 0.009589 (1), 0.009579 (1),
0.009578 (1), 0.009557 (1), 0.009532 (1), 0.009494 (1), 0.009492 (1), 0.009478
(1), 0.009446 (1), 0.009429 (1), 0.009378 (1), 0.009375 (1), 0.009361 (1),
0.009279 (1), 0.009261 (1), 0.009216 (1), 0.009183 (1), 0.009065 (1), 0.00905
(1), 0.008986 (1), 0.008775 (1), 0.00874 (1), 0.008708 (1), 0.008684 (1),
0.008513 (1), 0.00831 (1), 0.008103 (1), 0.007203 (1), 0.006893 (1), 0.006877
(1), 0.00632 (1), 0.006313 (1), 0.006205 (1), 0.00604 (1), 0.005996 (1)
Best fit found:
Fit molecule 6npy (#9) to map run_class001_j100_D5.mrc (#1.2) using 6219 atoms
average map value = 0.01018, steps = 352
shifted from previous position = 48.9
rotated from previous position = 70.3 degrees
atoms outside contour = 3868, contour level = 0.011736
Position of 6npy (#9) relative to run_class001_j100_D5.mrc (#1.2) coordinates:
Matrix rotation and translation
0.15682854 0.43616607 0.88609479 15.37954712
0.56410073 -0.77600795 0.28213827 87.61450866
0.81067575 0.45559939 -0.36774181 45.00528270
Axis 0.75962575 0.33027716 0.56025504
Axis point 0.00000000 40.15765300 19.31441915
Rotation angle (degrees) 173.44393549
Shift along axis 65.83420768
Found 50 fits. List window not yet implemented.
> fitmap #10 inMap #1.2 search 50
Found 48 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (49 of 50).
Average map values and times found:
0.01224 (1), 0.01017 (1), 0.01013 (1), 0.01002 (1), 0.009991 (1), 0.009907
(1), 0.009902 (1), 0.009838 (1), 0.009832 (2), 0.009707 (1), 0.009679 (1),
0.009678 (1), 0.009678 (1), 0.009677 (1), 0.009635 (1), 0.009607 (1), 0.009596
(1), 0.009596 (1), 0.009591 (1), 0.00959 (1), 0.009587 (1), 0.009584 (1),
0.009582 (1), 0.009581 (1), 0.009549 (1), 0.00952 (1), 0.009493 (1), 0.009492
(1), 0.009485 (1), 0.009471 (1), 0.00945 (1), 0.009423 (1), 0.009419 (1),
0.009323 (1), 0.009256 (1), 0.009204 (1), 0.009116 (1), 0.00898 (1), 0.008919
(1), 0.008906 (1), 0.008884 (1), 0.008869 (1), 0.008839 (1), 0.008836 (1),
0.008812 (1), 0.008692 (1), 0.008491 (1), 0.007876 (1)
Best fit found:
Fit molecule 6npy (#10) to map run_class001_j100_D5.mrc (#1.2) using 6219
atoms
average map value = 0.01224, steps = 248
shifted from previous position = 31.1
rotated from previous position = 41.2 degrees
atoms outside contour = 2904, contour level = 0.011736
Position of 6npy (#10) relative to run_class001_j100_D5.mrc (#1.2)
coordinates:
Matrix rotation and translation
-0.74852426 0.63551827 -0.18928266 145.83965744
0.29282316 0.06068162 -0.95423915 168.48422389
-0.59495044 -0.76969750 -0.23151613 344.56765319
Axis 0.32825271 0.72157991 -0.60956755
Axis point 66.38583742 0.00000000 227.62909192
Rotation angle (degrees) 163.67431701
Shift along axis -40.59016452
Found 48 fits. List window not yet implemented.
> fitmap #11 inMap #1.2 search 50
Found 50 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Average map values and times found:
0.01224 (1), 0.01015 (1), 0.009847 (1), 0.009838 (1), 0.009746 (1), 0.009744
(1), 0.009707 (1), 0.009706 (1), 0.009677 (1), 0.009659 (1), 0.009637 (1),
0.009634 (1), 0.009591 (1), 0.009591 (1), 0.009588 (1), 0.009586 (1), 0.00958
(1), 0.009579 (1), 0.009579 (1), 0.009577 (1), 0.009534 (1), 0.009505 (1),
0.009502 (1), 0.009498 (1), 0.009494 (1), 0.009493 (1), 0.009411 (1), 0.009323
(1), 0.009211 (1), 0.009209 (1), 0.009183 (1), 0.009133 (1), 0.009129 (1),
0.009102 (1), 0.009037 (1), 0.009022 (1), 0.008992 (1), 0.008969 (1), 0.008911
(1), 0.008909 (1), 0.008906 (1), 0.008775 (1), 0.00877 (1), 0.008711 (1),
0.008509 (1), 0.006307 (1), 0.006275 (1), 0.005998 (1), 0.005976 (1), 0.005516
(1)
Best fit found:
Fit molecule 6npy (#11) to map run_class001_j100_D5.mrc (#1.2) using 6219
atoms
average map value = 0.01224, steps = 516
shifted from previous position = 50.5
rotated from previous position = 103 degrees
atoms outside contour = 2911, contour level = 0.011736
Position of 6npy (#11) relative to run_class001_j100_D5.mrc (#1.2)
coordinates:
Matrix rotation and translation
0.43151022 -0.55035213 0.71478066 154.16904961
-0.67813949 0.32463622 0.65934679 138.74329573
-0.59491660 -0.76923589 -0.23313167 344.68156644
Axis -0.73551515 0.67430621 -0.06579216
Axis point 0.00000000 322.28306124 76.20651930
Rotation angle (degrees) 103.79759044
Shift along axis -42.51554989
Found 50 fits. List window not yet implemented.
> ui mousemode right "translate selected models"
> select #9
6219 atoms, 6336 bonds, 7 pseudobonds, 799 residues, 2 models selected
> select #3
12333 atoms, 12450 bonds, 7 pseudobonds, 799 residues, 2 models selected
> fitmap #3 inMap #1.2 search3
Expected a keyword
> fitmap #3 inMap #1.2
Fit molecule 6npy (#3) to map run_class001_j100_D5.mrc (#1.2) using 12333
atoms
average map value = 0.009458, steps = 584
shifted from previous position = 63.1
rotated from previous position = 58.9 degrees
atoms outside contour = 8408, contour level = 0.011736
Position of 6npy (#3) relative to run_class001_j100_D5.mrc (#1.2) coordinates:
Matrix rotation and translation
0.45850340 -0.80738182 0.37136129 202.36730975
0.00942917 -0.41343060 -0.91048680 331.35131922
0.88864267 0.42096287 -0.18194641 55.59693863
Axis 0.80916864 -0.31437003 0.49640468
Axis point 0.00000000 200.99325400 82.00930480
Rotation angle (degrees) 124.64129089
Shift along axis 87.18093638
> select #9
6219 atoms, 6336 bonds, 7 pseudobonds, 799 residues, 2 models selected
> ui mousemode right "rotate selected models"
> fitmap #9 inMap #1.2
Fit molecule 6npy (#9) to map run_class001_j100_D5.mrc (#1.2) using 6219 atoms
average map value = 0.009695, steps = 148
shifted from previous position = 2.53
rotated from previous position = 22.9 degrees
atoms outside contour = 4066, contour level = 0.011736
Position of 6npy (#9) relative to run_class001_j100_D5.mrc (#1.2) coordinates:
Matrix rotation and translation
0.28106902 0.35175589 -0.89289865 127.00945963
-0.33790162 0.90709931 0.25098465 58.87470227
0.89823309 0.23116790 0.37381641 -17.15204172
Axis -0.01032434 -0.93316301 -0.35930516
Axis point 88.31709811 0.00000000 70.55496583
Rotation angle (degrees) 73.68055828
Shift along axis -50.08816686
> ui mousemode right "translate selected models"
> fitmap #9 inMap #1.2
Fit molecule 6npy (#9) to map run_class001_j100_D5.mrc (#1.2) using 6219 atoms
average map value = 0.009815, steps = 196
shifted from previous position = 10.4
rotated from previous position = 27.8 degrees
atoms outside contour = 3982, contour level = 0.011736
Position of 6npy (#9) relative to run_class001_j100_D5.mrc (#1.2) coordinates:
Matrix rotation and translation
0.53845503 0.24592045 -0.80597104 105.67339552
-0.77666297 0.51588420 -0.36146660 184.85792482
0.32689571 0.82060136 0.46877776 -27.56274071
Axis 0.61235139 -0.58686349 -0.52973298
Axis point 0.00000000 188.97764248 210.94177581
Rotation angle (degrees) 74.83744228
Shift along axis -29.17622381
> select #3
12333 atoms, 12450 bonds, 7 pseudobonds, 799 residues, 2 models selected
> fitmap #3 inMap #1.2
Fit molecule 6npy (#3) to map run_class001_j100_D5.mrc (#1.2) using 12333
atoms
average map value = 0.01005, steps = 348
shifted from previous position = 34.2
rotated from previous position = 45.9 degrees
atoms outside contour = 7589, contour level = 0.011736
Position of 6npy (#3) relative to run_class001_j100_D5.mrc (#1.2) coordinates:
Matrix rotation and translation
0.09740105 -0.95819733 -0.26901851 221.42290389
-0.41444915 0.20670076 -0.88628810 309.07707900
0.90484530 0.19781981 -0.37699121 69.84537524
Axis 0.64229313 -0.69547013 0.32215033
Axis point 219.46127045 0.00000000 206.68760738
Rotation angle (degrees) 122.44194076
Shift along axis -50.23475528
> ui mousemode right "rotate selected models"
> fitmap #3 inMap #1.2
Fit molecule 6npy (#3) to map run_class001_j100_D5.mrc (#1.2) using 12333
atoms
average map value = 0.01162, steps = 236
shifted from previous position = 18.1
rotated from previous position = 47.1 degrees
atoms outside contour = 6380, contour level = 0.011736
Position of 6npy (#3) relative to run_class001_j100_D5.mrc (#1.2) coordinates:
Matrix rotation and translation
-0.74884154 0.63432817 -0.19200045 146.33545897
-0.29417305 -0.05853199 0.95395815 140.81269493
0.59388436 0.77084484 0.23043344 -34.82672058
Axis -0.14885491 -0.63885474 -0.75478926
Axis point 96.24430250 54.70502214 0.00000000
Rotation angle (degrees) 142.04276398
Shift along axis -85.45477474
> ~select #3
Nothing selected
> select #9
6219 atoms, 6336 bonds, 7 pseudobonds, 799 residues, 2 models selected
> ui mousemode right "translate selected models"
> fitmap #9 inMap #1.2
Fit molecule 6npy (#9) to map run_class001_j100_D5.mrc (#1.2) using 6219 atoms
average map value = 0.01003, steps = 268
shifted from previous position = 21.5
rotated from previous position = 55.8 degrees
atoms outside contour = 3930, contour level = 0.011736
Position of 6npy (#9) relative to run_class001_j100_D5.mrc (#1.2) coordinates:
Matrix rotation and translation
0.23690916 0.22810249 -0.94437456 146.64348470
-0.18542830 0.96479406 0.18651738 46.43587501
0.95367205 0.13092611 0.27086521 -4.38655185
Axis -0.02860564 -0.97667896 -0.21279079
Axis point 82.23684628 0.00000000 87.35798105
Rotation angle (degrees) 76.33266529
Shift along axis -48.61435459
> ui mousemode right "rotate selected models"
> fitmap #9 inMap #1.2
Fit molecule 6npy (#9) to map run_class001_j100_D5.mrc (#1.2) using 6219 atoms
average map value = 0.01223, steps = 164
shifted from previous position = 19.5
rotated from previous position = 18.7 degrees
atoms outside contour = 2911, contour level = 0.011736
Position of 6npy (#9) relative to run_class001_j100_D5.mrc (#1.2) coordinates:
Matrix rotation and translation
0.04805936 0.25475923 -0.96580952 164.85237436
-0.80253380 0.58551404 0.11451105 142.12844529
0.59466780 0.76959145 0.23259233 -35.03361248
Axis 0.32827602 -0.78199147 -0.52983412
Axis point 145.39276367 0.00000000 40.45719968
Rotation angle (degrees) 93.83693676
Shift along axis -38.46414690
> ~select #9
Nothing selected
> select #8
6219 atoms, 6336 bonds, 7 pseudobonds, 799 residues, 2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> fitmap #8 inMap #1.2
Fit molecule 6npy (#8) to map run_class001_j100_D5.mrc (#1.2) using 6219 atoms
average map value = 0.009995, steps = 344
shifted from previous position = 66.8
rotated from previous position = 57.4 degrees
atoms outside contour = 3968, contour level = 0.011736
Position of 6npy (#8) relative to run_class001_j100_D5.mrc (#1.2) coordinates:
Matrix rotation and translation
0.56809808 0.28245860 -0.77296939 95.18385127
0.79260895 -0.44052446 0.42155572 109.41304506
-0.22143992 -0.85214742 -0.47414036 332.36426178
Axis -0.86132663 -0.37296526 0.34498312
Axis point 0.00000000 120.07269582 157.95638768
Rotation angle (degrees) 132.32098653
Shift along axis -8.13158991
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> fitmap #8 inMap #1.2
Fit molecule 6npy (#8) to map run_class001_j100_D5.mrc (#1.2) using 6219 atoms
average map value = 0.01224, steps = 92
shifted from previous position = 7.36
rotated from previous position = 12.9 degrees
atoms outside contour = 2914, contour level = 0.011736
Position of 6npy (#8) relative to run_class001_j100_D5.mrc (#1.2) coordinates:
Matrix rotation and translation
0.04823300 0.25470675 -0.96581469 164.84790392
0.80237553 -0.58575165 -0.11440490 167.50859803
-0.59486730 -0.76942795 -0.23262306 344.66261698
Axis -0.70363539 -0.39847714 0.58831387
Axis point 0.00000000 95.48305178 210.45540731
Rotation angle (degrees) 152.26024290
Shift along axis 20.02863001
> select add
74418 atoms, 75588 bonds, 70 pseudobonds, 7990 residues, 42 models selected
> hide #!1.2 models
> hide #!1 models
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/ui/gui.py", line
1574, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "/home/michael/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/menu/menu.py", line 58, in f
module.run_script(session)
File "/home/michael/.local/share/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 "/home/michael/.local/share/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.
> save /home/michael/NLRP3/iNext_202101/Decamer_mmcif.cif
> volume #1.2 level 0.006826
> volume #1.2 level 0.00374
> volume #1.2 level 0.00395
> show #!1 models
> volume #1.2 level 0.01223
> volume #1.2 level 0.009211
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/ui/gui.py", line
1574, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "/home/michael/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/menu/menu.py", line 58, in f
module.run_script(session)
File "/home/michael/.local/share/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 "/home/michael/.local/share/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 NVIDIA 440.64
OpenGL renderer: Quadro RTX 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7A95
OS: Scientific Linux 7.9 Nitrogen
Architecture: 64bit ELF
CPU: 32 Intel(R) Core(TM) i9-9960X CPU @ 3.10GHz
Cache Size: 22528 KB
Memory:
total used free shared buff/cache available
Mem: 125G 4.8G 108G 111M 12G 119G
Swap: 4.0G 0B 4.0G
Graphics:
65:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104GL [Quadro RTX 4000] [10de:1eb1] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:12a0]
Kernel driver in use: nvidia
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: 2.1.3
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-LinuxSupport: 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-Phenix: 0.1
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-TestManager: 0.2.1
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.1
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
distro: 1.5.0
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
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
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
ptyprocess: 0.6.0
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
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
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: | → duplicate |
|---|---|
| Status: | assigned → closed |
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