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Opened 3 years ago
Closed 3 years ago
#8624 closed defect (duplicate)
modeller refine: KeyError for seq.match_maps[chain]
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-3.10.0-1160.83.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/smissour/Downloads/cryosparc_P8_J893_002_volume_map_sharp.mrc
Opened cryosparc_P8_J893_002_volume_map_sharp.mrc as #1, grid size
288,288,288, pixel 1.2, shown at level 0.0425, step 2, values float32
> volume #1 step 1
> volume #1 level 0.1337
> volume style mesh
> open /home/smissour/Downloads/cryosparc_P8_J884_001_volume_map_sharp.mrc
Opened cryosparc_P8_J884_001_volume_map_sharp.mrc as #2, grid size
288,288,288, pixel 1.2, shown at level 0.0338, step 2, values float32
> close #1
> volume #2 step 1
> volume #2 level 0.07881
> volume style mesh
> volume showOutlineBox true
> transparency 50
> volume #2 level 0.1388
> volume #2 level 0.1199
> volume #2 level 0.1294
> open "/home/smissour/Downloads/cryosparc_P8_J958_004_volume_map_sharp
> (1).mrc"
Opened cryosparc_P8_J958_004_volume_map_sharp (1).mrc as #1, grid size
200,200,200, pixel 1.2, shown at level 0.0977, step 1, values float32
> close #2
> volume #1 level 0.09769
> volume #1 level 0.1052
> volume #1 level 0.1126
> volume #1 level 0.1294
> volume #1 level 0.1444
> volume #1 level 0.1463
> volume #1 level 0.15
> volume #1 level 0.1537
> volume #1 level 0.1575
> volume #1 level 0.1631
> volume #1 level 0.178
> volume #1 level 0.1836
> volume #1 level 0.1911
> volume #1 level 0.2098
> volume #1 level 0.2135
> volume #1 level 0.2116
> volume #1 level 0.2023
> volume #1 level 0.1892
> volume #1 level 0.178
> volume #1 level 0.1687
> volume #1 level 0.1593
> volume #1 level 0.15
> volume #1 level 0.1463
> volume #1 level 0.06033
> open "/home/smissour/Downloads/cryosparc_P8_J997_004_volume_map_sharp
> (1).mrc"
Opened cryosparc_P8_J997_004_volume_map_sharp (1).mrc as #2, grid size
224,224,224, pixel 1.2, shown at level 0.0981, step 1, values float32
> volume #2 level 0.1137
[Repeated 1 time(s)]
> volume #2 level 0.1038
> volume #2 level 0.09812
> open /home/smissour/Downloads/cryosparc_P8_J1028_002_volume_map_sharp.mrc
Opened cryosparc_P8_J1028_002_volume_map_sharp.mrc as #3, grid size
224,224,224, pixel 1.2, shown at level 0.101, step 1, values float32
> volume #3 level 0.1246
> volume #!2 style mesh
> open /home/smissour/Downloads/cryosparc_P8_J1085_004_volume_map_sharp.mrc
Opened cryosparc_P8_J1085_004_volume_map_sharp.mrc as #4, grid size
224,224,224, pixel 1.2, shown at level 0.0923, step 1, values float32
> open /home/smissour/Desktop/DNAP01-YERA41/titan-DNAP-WT-T35-P15/molrep.pdb
molrep.pdb title:
MOLREP --- /Vers 11.9.02; 28.02.2022/ [more info...]
Chain information for molrep.pdb #5
---
Chain | Description
A | No description available
> transparency #4.1 50
> volume #!4 style mesh
> open /home/smissour/Desktop/DNAP01-YERA41/titan-DNAP-WT-T35-P15/molrep.pdb
Summary of feedback from opening /home/smissour/Desktop/DNAP01-YERA41/titan-
DNAP-WT-T35-P15/molrep.pdb
---
warning | Ignored bad PDB record found on line 10246
#MOLECULE 1
molrep.pdb title:
MOLREP --- /Vers 11.9.02; 28.02.2022/ [more info...]
Chain information for molrep.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open /home/smissour/Desktop/DNAP01-YERA41/titan-DNAP-WT-T35-P15/molrep.pdb
Summary of feedback from opening /home/smissour/Desktop/DNAP01-YERA41/titan-
DNAP-WT-T35-P15/molrep.pdb
---
warning | Ignored bad PDB record found on line 10246
#MOLECULE 1
molrep.pdb title:
MOLREP --- /Vers 11.9.02; 28.02.2022/ [more info...]
Chain information for molrep.pdb #7
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!6 models
> open /home/smissour/Desktop/DNAP01-YERA41/titan-DNAP-WT-T35-P15/molrep.pdb
Summary of feedback from opening /home/smissour/Desktop/DNAP01-YERA41/titan-
DNAP-WT-T35-P15/molrep.pdb
---
warning | Ignored bad PDB record found on line 10246
#MOLECULE 1
molrep.pdb title:
MOLREP --- /Vers 11.9.02; 28.02.2022/ [more info...]
Chain information for molrep.pdb #8
---
Chain | Description
A | No description available
B | No description available
C | No description available
> select #8 /C /B
717 atoms, 803 bonds, 35 residues, 1 model selected
> ui mousemode right select
> hide #!7 models
Drag select of 2 residues, 1 shapes
> select #8 /C /B
717 atoms, 803 bonds, 35 residues, 1 model selected
Drag select of 4 cryosparc_P8_J1085_004_volume_map_sharp.mrc , 3 residues, 6
shapes
> select clear
> select #8 /C /B
717 atoms, 803 bonds, 35 residues, 1 model selected
Drag select of 4 cryosparc_P8_J1085_004_volume_map_sharp.mrc , 2 residues
> select clear
> select #8 /C /B
717 atoms, 803 bonds, 35 residues, 1 model selected
> ui mousemode right rotate
> ui mousemode right "translate selected atoms"
> save /home/smissour/Desktop/DNAP01-YERA41/titan-DNAP-WT-T35-P15/molrep-DNA-
> short.pdb models #8
> select #8 /A:196
5 atoms, 4 bonds, 1 residue, 1 model selected
> ui tool show "Build Structure"
> volume #3 level 0.15
> volume #!4 style surface
> volume #4 level 0.15
> OPEN 1ssP
Unknown command: OPEN 1ssP
> OPEN 1SSP
Unknown command: OPEN 1SSP
> open 1SSP
1ssp title:
Wild-type uracil-DNA glycosylase bound to uracil-containing DNA [more info...]
Chain information for 1ssp #9
---
Chain | Description | UniProt
A | 5'-D(*CP*TP*GP*TP*(D1P)P*ap*TP*CP*TP*T)-3' |
B | 5'-D(*ap*ap*ap*GP*ap*TP*ap*ap*CP*ap*G)-3' |
E | uracil-DNA glycosylase | UNG_HUMAN
Non-standard residues in 1ssp #9
---
ORP — 2-deoxy-5-phosphono-ribose
> ui tool show Matchmaker
> matchmaker #!9 to #8
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 molrep.pdb, chain A (#8) with 1ssp, chain E (#9), sequence
alignment score = 55.3
RMSD between 7 pruned atom pairs is 1.479 angstroms; (across all 188 pairs:
21.645)
> close #5-7
> select #8 /A:1-200
1287 atoms, 1315 bonds, 1 pseudobond, 157 residues, 2 models selected
> matchmaker #!9 to #8 & sel
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 molrep.pdb, chain A (#8) with 1ssp, chain E (#9), sequence
alignment score = 52.3
RMSD between 6 pruned atom pairs is 1.620 angstroms; (across all 138 pairs:
18.012)
> select clear
> select #9
2498 atoms, 2344 bonds, 21 pseudobonds, 510 residues, 2 models selected
> matchmaker #!9 to #8 & sel
No 'to' model specified
> select clear
> select #8 /A:1-200
1287 atoms, 1315 bonds, 1 pseudobond, 157 residues, 2 models selected
> matchmaker #!9 to #8 & sel
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 molrep.pdb, chain A (#8) with 1ssp, chain E (#9), sequence
alignment score = 52.3
RMSD between 6 pruned atom pairs is 1.620 angstroms; (across all 138 pairs:
18.012)
> matchmaker #!9 to #8 & sel matrix BLOSUM-45
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-45
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 molrep.pdb, chain A (#8) with 1ssp, chain E (#9), sequence
alignment score = 89.3
RMSD between 5 pruned atom pairs is 1.496 angstroms; (across all 149 pairs:
19.873)
> matchmaker #!9 to #8 & sel matrix BLOSUM-90
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-90
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 molrep.pdb, chain A (#8) with 1ssp, chain E (#9), sequence
alignment score = 9.6
RMSD between 16 pruned atom pairs is 1.387 angstroms; (across all 69 pairs:
14.347)
> open /home/smissour/Desktop/DNAP01-YERA41/titan-DNAP-
> WT-T35-P15/imodfit_fitted.pdb
Summary of feedback from opening /home/smissour/Desktop/DNAP01-YERA41/titan-
DNAP-WT-T35-P15/imodfit_fitted.pdb
---
warning | Ignored bad PDB record found on line 10961
TER 10951 DG C 20
Chain information for imodfit_fitted.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!5 models
> show #!5 models
> hide #!8 models
> select #8
10956 atoms, 11290 bonds, 1 pseudobond, 1274 residues, 2 models selected
> hide #!9 models
> ~select #8
Nothing selected
> show #!8 models
> hide #!8 models
> volume #4 level 0.1234
> hide #!5 models
> show #!5 models
> hide #!4 models
> select #5 /b /c
717 atoms, 803 bonds, 35 residues, 1 model selected
> ui mousemode right "translate selected atoms"
> fitmap #5 inMap #4
Fit molecule imodfit_fitted.pdb (#5) to map
cryosparc_P8_J1085_004_volume_map_sharp.mrc (#4) using 10959 atoms
average map value = 0.1562, steps = 52
shifted from previous position = 0.232
rotated from previous position = 1.08 degrees
atoms outside contour = 3983, contour level = 0.12343
Position of imodfit_fitted.pdb (#5) relative to
cryosparc_P8_J1085_004_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99982250 -0.00706021 0.01746798 -1.50227845
0.00705273 0.99997501 0.00049001 -0.84379969
-0.01747100 -0.00036673 0.99984730 2.49982626
Axis -0.02273026 0.92697494 0.37443396
Axis point 138.29363424 0.00000000 87.16252075
Rotation angle (degrees) 1.07984300
Shift along axis 0.18798588
> fitmap #5 inMap #4
Fit molecule imodfit_fitted.pdb (#5) to map
cryosparc_P8_J1085_004_volume_map_sharp.mrc (#4) using 10959 atoms
average map value = 0.1547, steps = 40
shifted from previous position = 0.0588
rotated from previous position = 0.339 degrees
atoms outside contour = 4062, contour level = 0.12343
Position of imodfit_fitted.pdb (#5) relative to
cryosparc_P8_J1085_004_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99979175 -0.00275123 0.02022107 -2.37816291
0.00268320 0.99999065 0.00339052 -0.64190597
-0.02023021 -0.00333556 0.99978978 3.26534579
Axis -0.16260241 0.97790623 0.13137676
Axis point 158.96533051 0.00000000 117.73384509
Rotation angle (degrees) 1.18511018
Shift along axis 0.18796174
> show #!9 models
> select #5 /A:1-200
1290 atoms, 1318 bonds, 1 pseudobond, 157 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #!9 to #5 & sel matrix BLOSUM-90
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-90
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 imodfit_fitted.pdb, chain A (#5) with 1ssp, chain E (#9), sequence
alignment score = 9.6
RMSD between 16 pruned atom pairs is 1.416 angstroms; (across all 69 pairs:
14.333)
> matchmaker #!9 to #5 & sel matrix BLOSUM-90
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-90
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 imodfit_fitted.pdb, chain A (#5) with 1ssp, chain E (#9), sequence
alignment score = 9.6
RMSD between 16 pruned atom pairs is 1.416 angstroms; (across all 69 pairs:
14.333)
> matchmaker #!9 to #5 & sel matrix BLOSUM-85
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-85
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 imodfit_fitted.pdb, chain A (#5) with 1ssp, chain E (#9), sequence
alignment score = 10.5
RMSD between 7 pruned atom pairs is 1.333 angstroms; (across all 104 pairs:
17.815)
> select #5
10959 atoms, 11293 bonds, 1 pseudobond, 1274 residues, 2 models selected
> ~select #5
Nothing selected
> OPEN 6IOD
Unknown command: OPEN 6IOD
> open 6IOD
6iod title:
The structure of UdgX in complex with single-stranded DNA [more info...]
Chain information for 6iod #6
---
Chain | Description | UniProt
A B | Phage SPO1 DNA polymerase-related protein | I7F541_MYCS2
C D | DNA |
Non-standard residues in 6iod #6
---
ORP — 2-deoxy-5-phosphono-ribose
SF4 — iron/sulfur cluster
6iod mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> select clear
> select add #6/B:119
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #6/D:12
24 atoms, 24 bonds, 2 residues, 1 model selected
> select add #6/B:173
32 atoms, 31 bonds, 3 residues, 1 model selected
> select up
325 atoms, 352 bonds, 24 residues, 1 model selected
> select up
1738 atoms, 1714 bonds, 289 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 46 atoms, 223 residues, 4 pseudobonds, 47 bonds, 30 shapes
> ui tool show Matchmaker
> matchmaker #!6 to #9 matrix BLOSUM-85
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-85
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 1ssp, chain E (#9) with 6iod, chain A (#6), sequence alignment
score = 55.9
RMSD between 47 pruned atom pairs is 0.982 angstroms; (across all 168 pairs:
8.301)
> select #6
2023 atoms, 1839 bonds, 4 pseudobonds, 467 residues, 2 models selected
> hide #!9 models
> select clear
[Repeated 1 time(s)]
> hide #!5 models
> select #6/C:8@C3
1 atom, 1 residue, 1 model selected
> select add #6/A:180
7 atoms, 5 bonds, 2 residues, 1 model selected
> select up
17 atoms, 16 bonds, 2 residues, 1 model selected
> ui tool show Contacts
> contacts select true
204595 contacts
> contacts select true
204595 contacts
> select clear
[Repeated 2 time(s)]
> select #7
204595 pseudobonds, 1 model selected
> hide #7 models
> ~select #7
Nothing selected
> show #!5 models
> hide #!5 models
> open
> /home/smissour/Desktop/DNAP01-YERA41/RealSpaceRefine_172/imodfit_fitted_real_space_refined_172.pdb
Chain information for imodfit_fitted_real_space_refined_172.pdb #10
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!6 models
> hide #!10 models
> show #!5 models
> show #!10 models
> hide #!10 models
> close #7
> show #!6 models
> hide #!5 models
> hide #!4 models
> show #!5 models
> show #!4 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> hide #!4 models
> hide #!6 models
> show #!9 models
> show #!5 models
> hide #!9 models
> fitmap #5 inMap #4
Fit molecule imodfit_fitted.pdb (#5) to map
cryosparc_P8_J1085_004_volume_map_sharp.mrc (#4) using 10959 atoms
average map value = 0.1509, steps = 52
shifted from previous position = 0.375
rotated from previous position = 0.957 degrees
atoms outside contour = 4306, contour level = 0.12343
Position of imodfit_fitted.pdb (#5) relative to
cryosparc_P8_J1085_004_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99961940 0.01244922 0.02461848 -4.97477226
-0.01265899 0.99988473 0.00838323 0.38424937
-0.02451128 -0.00869168 0.99966177 4.44916379
Axis -0.29564077 0.85064945 -0.43473215
Axis point 176.24380142 0.00000000 206.43969748
Rotation angle (degrees) 1.65480561
Shift along axis -0.13658749
> fitmap #5 inMap #4
Fit molecule imodfit_fitted.pdb (#5) to map
cryosparc_P8_J1085_004_volume_map_sharp.mrc (#4) using 10959 atoms
average map value = 0.1509, steps = 40
shifted from previous position = 0.0213
rotated from previous position = 0.00789 degrees
atoms outside contour = 4310, contour level = 0.12343
Position of imodfit_fitted.pdb (#5) relative to
cryosparc_P8_J1085_004_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99962246 0.01242183 0.02450804 -4.97464432
-0.01263254 0.99988441 0.00846141 0.36947993
-0.02440010 -0.00876782 0.99966382 4.43276510
Axis -0.29917202 0.84925151 -0.43504940
Axis point 176.56065365 0.00000000 207.24317478
Rotation angle (degrees) 1.65005146
Shift along axis -0.12641603
> open /home/smissour/Desktop/DNAP01-YERA41/titan-DNAP-
> WT-T35-P15/sharpened_map_P8_J1085.ccp4
Opened sharpened_map_P8_J1085.ccp4 as #7, grid size 224,224,224, pixel 1.2,
shown at level 3.66, step 1, values float32
> surface dust #4 size 12
> surface dust #7 size 12
> volume #7 level 4.144
> volume #7 level 5.75
> volume #!7 style mesh
> open /home/smissour/Desktop/DNAP01-YERA41/T20-P15.pdb
Chain information for T20-P15.pdb #11
---
Chain | Description
A | No description available
B | No description available
> open
> /home/smissour/Desktop/DNAP01-YERA41/RealSpaceRefine_176/imodfit_fitted_real_space_refined_176.pdb
Chain information for imodfit_fitted_real_space_refined_176.pdb #12
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #11 models
> hide #!5 models
> color #12 #fcaf3e transparency 0
> volume #!7 style surface
> transparency #7.1 50
> close #7
> close #4
> close #3
> close #2
> close #1
> open /home/smissour/Desktop/DNAP01-YERA41/titan-DNAP-
> WT-T35-P15/sharpened_map_P8_J1085.ccp4
Opened sharpened_map_P8_J1085.ccp4 as #1, grid size 224,224,224, pixel 1.2,
shown at level 3.66, step 1, values float32
> surface dust #1 size 12
> transparency 50
> volume #1 color #babdb6
> volume #1 color #d3d7cf
> transparency 50
> volume #1 color #d3d7cf
> transparency 50
> set bgColor white
> volume #1 level 4.601
> volume #1 level 5.697
> open
> /home/smissour/Desktop/DNAP01-YERA41/RealSpaceRefine_178/imodfit_fitted_real_space_refined_176-coot-1_real_space_refined_178.pdb
Chain information for
imodfit_fitted_real_space_refined_176-coot-1_real_space_refined_178.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!12 models
> select #2 /b /c
717 atoms, 803 bonds, 35 residues, 1 model selected
> fitmap #2 inMap #1
Fit molecule
imodfit_fitted_real_space_refined_176-coot-1_real_space_refined_178.pdb (#2)
to map sharpened_map_P8_J1085.ccp4 (#1) using 10959 atoms
average map value = 7.464, steps = 48
shifted from previous position = 0.044
rotated from previous position = 0.0903 degrees
atoms outside contour = 3762, contour level = 5.6971
Position of
imodfit_fitted_real_space_refined_176-coot-1_real_space_refined_178.pdb (#2)
relative to sharpened_map_P8_J1085.ccp4 (#1) coordinates:
Matrix rotation and translation
0.99999876 -0.00065165 -0.00143404 0.23675364
0.00065157 0.99999979 -0.00005209 -0.08962613
0.00143407 0.00005115 0.99999897 -0.20857880
Axis 0.03275250 -0.90993417 0.41345748
Axis point 146.44849722 0.00000000 164.89889543
Rotation angle (degrees) 0.09029815
Shift along axis 0.00306968
> select clear
> save
> /home/smissour/Desktop/DNAP01-YERA41/RealSpaceRefine_178/imodfit_fitted_real_space_refined_176-coot-1_real_space_refined_178coot1.pdb
> models #2
> close #2,5
> close #11#10,12
> close #8
> open /home/smissour/Downloads/cryosparc_P8_J1085_004_volume_map_half_B.mrc
> /home/smissour/Downloads/cryosparc_P8_J1085_004_volume_map_half_A.mrc
Opened cryosparc_P8_J1085_004_volume_map_half_B.mrc as #2.1, grid size
224,224,224, pixel 1.2, shown at level 0.175, step 1, values float32
Opened cryosparc_P8_J1085_004_volume_map_half_A.mrc as #2.2, grid size
224,224,224, pixel 1.2, shown at level 0.168, step 1, values float32
> surface dust #1 size 12
> surface dust #2.1 size 12
> surface dust #2.2 size 12
> volume #2.1 level 0.2116
> transparency #2.1.1 50
> open /home/smissour/Downloads/cryosparc_P8_J1356_map_sharp.mrc
Opened cryosparc_P8_J1356_map_sharp.mrc as #3, grid size 224,224,224, pixel
1.2, shown at level 0.0928, step 1, values float32
> volume #3 level 0.1458
> volume #3 level 0.1028
> volume #3 level 0.08178
> volume #3 level 0.1358
> volume #3 level 0.09778
> open 2C2P
2c2p title:
The crystal structure of mismatch specific uracil-DNA glycosylase (MUG) from
Deinococcus radiodurans [more info...]
Chain information for 2c2p #4
---
Chain | Description | UniProt
A | G/U mismatch-specific DNA glycosylase | Q9RWF4_DEIRA
Non-standard residues in 2c2p #4
---
ACT — acetate ion
> select #4
1582 atoms, 1473 bonds, 336 residues, 1 model selected
> show #!1 models
> fitmap #4 inMap #1
Fit molecule 2c2p (#4) to map sharpened_map_P8_J1085.ccp4 (#1) using 1582
atoms
average map value = 4.827, steps = 92
shifted from previous position = 5.75
rotated from previous position = 14 degrees
atoms outside contour = 943, contour level = 5.6971
Position of 2c2p (#4) relative to sharpened_map_P8_J1085.ccp4 (#1)
coordinates:
Matrix rotation and translation
0.99417756 -0.09025639 -0.05886225 16.46755884
0.10090787 0.97143773 0.21477044 -37.18135880
0.03779660 -0.21945961 0.97488917 26.83316627
Axis -0.89681271 -0.19962894 0.39481039
Axis point 0.00000000 95.50912180 182.80396210
Rotation angle (degrees) 14.01029792
Shift along axis 3.24817221
> close #2.2
> close #2.1
> close #3
> show #!6 models
> ui tool show Matchmaker
> matchmaker #4 to #6 matrix BLOSUM-85
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-85
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 6iod, chain A (#6) with 2c2p, chain A (#4), sequence alignment
score = 108.6
RMSD between 71 pruned atom pairs is 1.148 angstroms; (across all 167 pairs:
6.863)
> fitmap #4 inMap #1
Fit molecule 2c2p (#4) to map sharpened_map_P8_J1085.ccp4 (#1) using 1582
atoms
average map value = 5.131, steps = 112
shifted from previous position = 5.78
rotated from previous position = 21.4 degrees
atoms outside contour = 890, contour level = 5.6971
Position of 2c2p (#4) relative to sharpened_map_P8_J1085.ccp4 (#1)
coordinates:
Matrix rotation and translation
0.95249956 0.13870826 0.27111733 -48.99550381
-0.11782641 -0.65307090 0.74807442 168.21264572
0.28082294 -0.74448534 -0.60570625 261.56736960
Axis -0.98552855 -0.00640856 -0.16938836
Axis point 0.00000000 145.16642023 95.89840190
Rotation angle (degrees) 130.77867354
Shift along axis 2.90200015
> hide #4 models
> hide #!6 models
> ~select #4
Nothing selected
> show #4 models
> fitmap #4 inMap #1
Fit molecule 2c2p (#4) to map sharpened_map_P8_J1085.ccp4 (#1) using 1582
atoms
average map value = 5.132, steps = 40
shifted from previous position = 0.0221
rotated from previous position = 0.0467 degrees
atoms outside contour = 893, contour level = 5.6971
Position of 2c2p (#4) relative to sharpened_map_P8_J1085.ccp4 (#1)
coordinates:
Matrix rotation and translation
0.95261388 0.13794881 0.27110314 -48.88180523
-0.11835213 -0.65293365 0.74811124 168.26566227
0.28021342 -0.74474678 -0.60566712 261.69780736
Axis -0.98556235 -0.00601447 -0.16920602
Axis point 0.00000000 145.22558416 95.92858446
Rotation angle (degrees) 130.76767691
Shift along axis 2.88319395
> show #!9 models
> hide #!9 models
> select #4
1582 atoms, 1473 bonds, 336 residues, 1 model selected
> fitmap #4 inMap #1
Fit molecule 2c2p (#4) to map sharpened_map_P8_J1085.ccp4 (#1) using 1582
atoms
average map value = 5.131, steps = 40
shifted from previous position = 0.0224
rotated from previous position = 0.0758 degrees
atoms outside contour = 888, contour level = 5.6971
Position of 2c2p (#4) relative to sharpened_map_P8_J1085.ccp4 (#1)
coordinates:
Matrix rotation and translation
0.95234892 0.13914082 0.27142471 -49.07043387
-0.11775926 -0.65315606 0.74801064 168.22221976
0.28136150 -0.74432990 -0.60564734 261.45424028
Axis -0.98548310 -0.00656187 -0.16964672
Axis point 0.00000000 145.14247235 95.85680731
Rotation angle (degrees) 130.78536628
Shift along axis 2.89937572
> fitmap #4 inMap #1
Fit molecule 2c2p (#4) to map sharpened_map_P8_J1085.ccp4 (#1) using 1582
atoms
average map value = 5.125, steps = 92
shifted from previous position = 8.5
rotated from previous position = 12.2 degrees
atoms outside contour = 913, contour level = 5.6971
Position of 2c2p (#4) relative to sharpened_map_P8_J1085.ccp4 (#1)
coordinates:
Matrix rotation and translation
0.93535894 0.02213674 0.35300653 -45.30472946
-0.20773769 -0.77338022 0.59893913 218.71937562
0.28626683 -0.63355583 -0.71878947 252.61079133
Axis -0.98165790 0.05315685 -0.18309045
Axis point 0.00000000 153.87507951 91.30012674
Rotation angle (degrees) 141.11480411
Shift along axis 9.84955681
> fitmap #4 inMap #1
Fit molecule 2c2p (#4) to map sharpened_map_P8_J1085.ccp4 (#1) using 1582
atoms
average map value = 5.247, steps = 108
shifted from previous position = 5.36
rotated from previous position = 14.3 degrees
atoms outside contour = 908, contour level = 5.6971
Position of 2c2p (#4) relative to sharpened_map_P8_J1085.ccp4 (#1)
coordinates:
Matrix rotation and translation
0.87128956 0.21602067 0.44066947 -72.83060303
-0.18283849 -0.69039516 0.69994614 188.21852370
0.45543891 -0.69042710 -0.56203720 208.33062114
Axis -0.96117934 -0.01021027 -0.27573544
Axis point 0.00000000 141.51298621 72.69949819
Rotation angle (degrees) 133.67535760
Shift along axis 10.63737305
> hide #4 models
> hide #2 models
> open /home/smissour/Desktop/DNAP01-YERA41/titan-DNAP-
> WT-T35-P15/imodfit_fitted_real_space_refined_176-coot-6.pdb
Chain information for imodfit_fitted_real_space_refined_176-coot-6.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open /home/smissour/Desktop/DNAP01-YERA41/titan-DNAP-
> WT-T35-P15/imodfit_fitted_real_space_refined_176-coot-8.pdb
Chain information for imodfit_fitted_real_space_refined_176-coot-8.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!3 models
> ~select #4
Nothing selected
> volume #1 level 6.48
> volume #1 level 5.854
> volume #1 level 5.071
> volume #1 level 4.523
> open
> /home/smissour/Desktop/DNAP01-YERA41/RealSpaceRefine_185/imodfit_fitted_real_space_refined_176-coot-8_real_space_refined_185.pdb
Chain information for
imodfit_fitted_real_space_refined_176-coot-8_real_space_refined_185.pdb #7
---
Chain | Description
A | No description available
B | No description available
C | No description available
> close #5
> volume #1 level 4.914
> select #7/A:174
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:177
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #7/A:176
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:175
12 atoms, 12 bonds, 1 residue, 1 model selected
> open /home/smissour/Desktop/DNAP01-YERA41/titan-DNAP-
> WT-T35-P15/imodfit_fitted_real_space_refined_176-coot-9.pdb
Chain information for imodfit_fitted_real_space_refined_176-coot-9.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!7 models
> select #7
10851 atoms, 11187 bonds, 2 pseudobonds, 1257 residues, 2 models selected
> ~select #7
Nothing selected
> fitmap #5 inMap #1
Fit molecule imodfit_fitted_real_space_refined_176-coot-9.pdb (#5) to map
sharpened_map_P8_J1085.ccp4 (#1) using 10851 atoms
average map value = 7.789, steps = 44
shifted from previous position = 0.0293
rotated from previous position = 0.0227 degrees
atoms outside contour = 2431, contour level = 4.9145
Position of imodfit_fitted_real_space_refined_176-coot-9.pdb (#5) relative to
sharpened_map_P8_J1085.ccp4 (#1) coordinates:
Matrix rotation and translation
0.99999999 0.00011735 0.00008960 -0.02719549
-0.00011738 0.99999993 0.00036686 -0.04321432
-0.00008955 -0.00036687 0.99999993 0.03288905
Axis -0.92769058 0.22650967 -0.29678874
Axis point 0.00000000 94.21873883 121.32109767
Rotation angle (degrees) 0.02265818
Shift along axis 0.00567944
> select #5
10851 atoms, 11187 bonds, 2 pseudobonds, 1257 residues, 2 models selected
> fitmap #5 inMap #1
Fit molecule imodfit_fitted_real_space_refined_176-coot-9.pdb (#5) to map
sharpened_map_P8_J1085.ccp4 (#1) using 10851 atoms
average map value = 7.79, steps = 28
shifted from previous position = 0.0189
rotated from previous position = 0.00587 degrees
atoms outside contour = 2427, contour level = 4.9145
Position of imodfit_fitted_real_space_refined_176-coot-9.pdb (#5) relative to
sharpened_map_P8_J1085.ccp4 (#1) coordinates:
Matrix rotation and translation
0.99999998 0.00010191 0.00018418 -0.03341725
-0.00010197 0.99999994 0.00033056 -0.04092216
-0.00018415 -0.00033058 0.99999993 0.05900109
Axis -0.84350301 0.46993198 -0.26012806
Axis point 0.00000000 173.42523073 114.74292434
Rotation angle (degrees) 0.02245414
Shift along axis -0.00639092
> ~select #5
Nothing selected
> hide #!5 models
> show #!5 models
> show #!6 models
> show #4 models
> hide #4 models
> show #!9 models
> hide #!6 models
> ui tool show Matchmaker
> matchmaker #!9 to #5 matrix BLOSUM-85
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-85
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 imodfit_fitted_real_space_refined_176-coot-9.pdb, chain A (#5) with
1ssp, chain E (#9), sequence alignment score = 25.3
RMSD between 8 pruned atom pairs is 1.178 angstroms; (across all 144 pairs:
24.876)
> hide #!9 models
> volume #1 level 4.993
> volume #1 level 5.306
> volume #1 level 5.619
> open /home/smissour/Desktop/DNAP01-YERA41/titan-DNAP-
> WT-T35-P15/imodfit_fitted_real_space_refined_176-coot-10.pdb
Chain information for imodfit_fitted_real_space_refined_176-coot-10.pdb #8
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!5 models
> select #8/C:7
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #8/B:10
41 atoms, 44 bonds, 2 residues, 1 model selected
> select up
757 atoms, 847 bonds, 37 residues, 1 model selected
> select up
10851 atoms, 11187 bonds, 1257 residues, 1 model selected
> select up
49507 atoms, 50404 bonds, 6341 residues, 10 models selected
> select down
10851 atoms, 11187 bonds, 1257 residues, 1 model selected
> select down
757 atoms, 847 bonds, 37 residues, 1 model selected
> addh select
Expected a keyword
> addh sel
Summary of feedback from adding hydrogens to
imodfit_fitted_real_space_refined_176-coot-10.pdb #8
---
warnings | Not adding hydrogens to
imodfit_fitted_real_space_refined_176-coot-10.pdb #8/C DT -1 P because it is
missing heavy-atom bond partners
Not adding hydrogens to imodfit_fitted_real_space_refined_176-coot-10.pdb #8/B
DC 2 P because it is missing heavy-atom bond partners
notes | No usable SEQRES records for
imodfit_fitted_real_space_refined_176-coot-10.pdb (#8) chain A; guessing
termini instead
No usable SEQRES records for imodfit_fitted_real_space_refined_176-coot-10.pdb
(#8) chain B; guessing termini instead
No usable SEQRES records for imodfit_fitted_real_space_refined_176-coot-10.pdb
(#8) chain C; guessing termini instead
Chain-initial residues that are actual N termini:
imodfit_fitted_real_space_refined_176-coot-10.pdb #8/A VAL 4
Chain-initial residues that are not actual N termini:
imodfit_fitted_real_space_refined_176-coot-10.pdb #8/A VAL 148,
imodfit_fitted_real_space_refined_176-coot-10.pdb #8/A ALA 618
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
imodfit_fitted_real_space_refined_176-coot-10.pdb #8/A GLY 1282,
imodfit_fitted_real_space_refined_176-coot-10.pdb #8/A THR 107,
imodfit_fitted_real_space_refined_176-coot-10.pdb #8/A ILE 598
882 hydrogen bonds
Adding 'H' to imodfit_fitted_real_space_refined_176-coot-10.pdb #8/A VAL 148
Adding 'H' to imodfit_fitted_real_space_refined_176-coot-10.pdb #8/A ALA 618
imodfit_fitted_real_space_refined_176-coot-10.pdb #8/A GLY 1282 is not
terminus, removing H atom from 'C'
10333 hydrogens added
> isolde start
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 52 residues in model #3 to IUPAC-IUB
standards.
Chain information for imodfit_fitted_real_space_refined_176-coot-6.pdb
---
Chain | Description
3.2/A | No description available
3.2/B | No description available
3.2/C | No description available
Done loading forcefield
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 52 residues in model #8 to IUPAC-IUB
standards.
Chain information for imodfit_fitted_real_space_refined_176-coot-10.pdb
---
Chain | Description
8.2/A | No description available
8.2/B | No description available
8.2/C | No description available
Opened sharpened_map_P8_J1085.ccp4 as #8.1.1.1, grid size 224,224,224, pixel
1.2, shown at step 1, values float32
> select clear
> select up
1173 atoms, 1263 bonds, 37 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> clipper spotlight radius 20.00
[Repeated 1 time(s)]
> clipper spotlight radius 5.00
> clipper spotlight radius 50.00
[Repeated 1 time(s)]
> volume #8.1.1.1 level 7.618
> volume #8.1.1.1 level 5.035
> volume #8.1.1.1 color #eeeeec
> clipper spotlight radius 12.00
[Repeated 1 time(s)]
> clipper spotlight radius 5.00
> clipper spotlight radius 50.00
[Repeated 1 time(s)]reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #8.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> close #7
> close #8.1
> close #8
> open /home/smissour/Desktop/DNAP01-YERA41/titan-DNAP-
> WT-T35-P15/imodfit_fitted_real_space_refined_176-coot-10.pdb
Chain information for imodfit_fitted_real_space_refined_176-coot-10.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> select clear
[Repeated 5 time(s)]
> ui mousemode right "translate selected models"
> ui mousemode right select
> close #3
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 52 residues in model #1 to IUPAC-IUB
standards.
Chain information for imodfit_fitted_real_space_refined_176-coot-10.pdb
---
Chain | Description
1.2/A | No description available
1.2/B | No description available
1.2/C | No description available
> select up
205 atoms, 229 bonds, 10 residues, 1 model selected
> open /home/smissour/Desktop/DNAP01-YERA41/titan-DNAP-
> WT-T35-P15/sharpened_map_P8_J1085.ccp4
Opened sharpened_map_P8_J1085.ccp4 as #3, grid size 224,224,224, pixel 1.2,
shown at level 3.66, step 1, values float32
> volume #3 level 5.384
> transparency 50
> surface dust #3 size 12
> addh sel
Summary of feedback from adding hydrogens to
imodfit_fitted_real_space_refined_176-coot-10.pdb #1.2
---
warnings | Not adding hydrogens to
imodfit_fitted_real_space_refined_176-coot-10.pdb #1.2/C DT -1 P because it is
missing heavy-atom bond partners
Not adding hydrogens to imodfit_fitted_real_space_refined_176-coot-10.pdb
#1.2/B DC 2 P because it is missing heavy-atom bond partners
notes | No usable SEQRES records for
imodfit_fitted_real_space_refined_176-coot-10.pdb (#1.2) chain A; guessing
termini instead
No usable SEQRES records for imodfit_fitted_real_space_refined_176-coot-10.pdb
(#1.2) chain B; guessing termini instead
No usable SEQRES records for imodfit_fitted_real_space_refined_176-coot-10.pdb
(#1.2) chain C; guessing termini instead
Chain-initial residues that are actual N termini:
imodfit_fitted_real_space_refined_176-coot-10.pdb #1.2/A VAL 4
Chain-initial residues that are not actual N termini:
imodfit_fitted_real_space_refined_176-coot-10.pdb #1.2/A VAL 148,
imodfit_fitted_real_space_refined_176-coot-10.pdb #1.2/A ALA 618
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
imodfit_fitted_real_space_refined_176-coot-10.pdb #1.2/A GLY 1282,
imodfit_fitted_real_space_refined_176-coot-10.pdb #1.2/A THR 107,
imodfit_fitted_real_space_refined_176-coot-10.pdb #1.2/A ILE 598
882 hydrogen bonds
Adding 'H' to imodfit_fitted_real_space_refined_176-coot-10.pdb #1.2/A VAL 148
Adding 'H' to imodfit_fitted_real_space_refined_176-coot-10.pdb #1.2/A ALA 618
imodfit_fitted_real_space_refined_176-coot-10.pdb #1.2/A GLY 1282 is not
terminus, removing H atom from 'C'
10333 hydrogens added
Opened sharpened_map_P8_J1085.ccp4 as #1.1.1.1, grid size 224,224,224, pixel
1.2, shown at step 1, values float32
> volume #1.1.1.1 level 7.115
> clipper spotlight radius 50.00
> volume #1.1.1.1 level 5.706
> isolde sim start sel
ISOLDE: started sim
> transparency 50
ISOLDE: paused sim
> close #1.3#1#1.1-2
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/home/smissour/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1020, in
_sim_end_cb
self._pr_sim_end_cb()
File "/home/smissour/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1077, in
_pr_sim_end_cb
restraints =
self.position_restraint_mgr.get_restraints(self.sim_construct.all_atoms)
File "/home/smissour/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/molobject.py", line 2375, in get_restraints
return self._get_restraints(atoms)
File "/home/smissour/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/molobject.py", line 2328, in _get_restraints
num = f(self._c_pointer, atoms._c_pointers, create, n, pointer(ret))
AttributeError: 'PositionRestraintMgr' object has no attribute '_c_pointer'
Error processing trigger "sim terminated":
AttributeError: 'PositionRestraintMgr' object has no attribute '_c_pointer'
File "/home/smissour/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/molobject.py", line 2328, in _get_restraints
num = f(self._c_pointer, atoms._c_pointers, create, n, pointer(ret))
See log for complete Python traceback.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> open /home/smissour/Desktop/DNAP01-YERA41/titan-DNAP-
> WT-T35-P15/imodfit_fitted_real_space_refined_176-coot-10.pdb
Chain information for imodfit_fitted_real_space_refined_176-coot-10.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 52 residues in model #1 to IUPAC-IUB
standards.
Chain information for imodfit_fitted_real_space_refined_176-coot-10.pdb
---
Chain | Description
1.2/A | No description available
1.2/B | No description available
1.2/C | No description available
> open /home/smissour/Desktop/DNAP01-YERA41/titan-DNAP-
> WT-T35-P15/sharpened_map_P8_J1085.ccp4
Opened sharpened_map_P8_J1085.ccp4 as #3, grid size 224,224,224, pixel 1.2,
shown at level 3.66, step 1, values float32
> transparency 50
> volume style mesh
> select up
164 atoms, 183 bonds, 8 residues, 1 model selected
> addh sel
Summary of feedback from adding hydrogens to
imodfit_fitted_real_space_refined_176-coot-10.pdb #1.2
---
warnings | Not adding hydrogens to
imodfit_fitted_real_space_refined_176-coot-10.pdb #1.2/C DT -1 P because it is
missing heavy-atom bond partners
Not adding hydrogens to imodfit_fitted_real_space_refined_176-coot-10.pdb
#1.2/B DC 2 P because it is missing heavy-atom bond partners
notes | No usable SEQRES records for
imodfit_fitted_real_space_refined_176-coot-10.pdb (#1.2) chain A; guessing
termini instead
No usable SEQRES records for imodfit_fitted_real_space_refined_176-coot-10.pdb
(#1.2) chain B; guessing termini instead
No usable SEQRES records for imodfit_fitted_real_space_refined_176-coot-10.pdb
(#1.2) chain C; guessing termini instead
Chain-initial residues that are actual N termini:
imodfit_fitted_real_space_refined_176-coot-10.pdb #1.2/A VAL 4
Chain-initial residues that are not actual N termini:
imodfit_fitted_real_space_refined_176-coot-10.pdb #1.2/A VAL 148,
imodfit_fitted_real_space_refined_176-coot-10.pdb #1.2/A ALA 618
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
imodfit_fitted_real_space_refined_176-coot-10.pdb #1.2/A GLY 1282,
imodfit_fitted_real_space_refined_176-coot-10.pdb #1.2/A THR 107,
imodfit_fitted_real_space_refined_176-coot-10.pdb #1.2/A ILE 598
882 hydrogen bonds
Adding 'H' to imodfit_fitted_real_space_refined_176-coot-10.pdb #1.2/A VAL 148
Adding 'H' to imodfit_fitted_real_space_refined_176-coot-10.pdb #1.2/A ALA 618
imodfit_fitted_real_space_refined_176-coot-10.pdb #1.2/A GLY 1282 is not
terminus, removing H atom from 'C'
10333 hydrogens added
Opened sharpened_map_P8_J1085.ccp4 as #1.1.1.1, grid size 224,224,224, pixel
1.2, shown at step 1, values float32
> clipper spotlight radius 50.00
> volume #1.1.1.1 level 6.522
> isolde sim start sel
ISOLDE: started sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1.2
21184 atoms, 21520 bonds, 2 pseudobonds, 1257 residues, 12 models selected
> select #1.2
21184 atoms, 21520 bonds, 2 pseudobonds, 1257 residues, 12 models selected
> select #1
21184 atoms, 21520 bonds, 2 pseudobonds, 1257 residues, 19 models selected
> save /home/smissour/Desktop/DNAP01-YERA41/titan-DNAP-
> WT-T35-P15/imodfit_fitted_real_space_refined_176-coot-10-isolde.pdb models
> #1
> open
> /home/smissour/Desktop/DNAP01-YERA41/RealSpaceRefine_186/imodfit_fitted_real_space_refined_176-coot-10-isolde_real_space_refined_186.pdb
Chain information for
imodfit_fitted_real_space_refined_176-coot-10-isolde_real_space_refined_186.pdb
#3
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!1 models
> select #1
21184 atoms, 21520 bonds, 2 pseudobonds, 1257 residues, 19 models selected
> hide #!1.1 models
> ~select #1.1
21184 atoms, 21520 bonds, 2 pseudobonds, 1257 residues, 14 models selected
> hide #!1.2 models
> select #1.2
21184 atoms, 21520 bonds, 2 pseudobonds, 1257 residues, 12 models selected
> hide #1.3 models
> open /home/smissour/Desktop/DNAP01-YERA41/titan-DNAP-
> WT-T35-P15/sharpened_map_P8_J1085.ccp4
Opened sharpened_map_P8_J1085.ccp4 as #7, grid size 224,224,224, pixel 1.2,
shown at level 3.66, step 1, values float32
> surface dust #7 size 12
> transparency #7.1 50
> volume #7 color #d3d7cf
> transparency #7.1 50
> volume #7 level 4.993
> ui tool show ViewDockX
No suitable models found for ViewDockX
> open
> /home/smissour/Desktop/DNAP01-YERA41/RealSpaceRefine_190/imodfit_fitted_real_space_refined_176-coot-11_real_space_refined_190.pdb
Chain information for
imodfit_fitted_real_space_refined_176-coot-11_real_space_refined_190.pdb #8
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!8 models
> show #!8 models
> hide #!3 models
> hide #!8 models
> open
> /home/smissour/Desktop/DNAP01-YERA41/RealSpaceRefine_190/imodfit_fitted_real_space_refined_176-coot-11_real_space_refined_190.pdb
Chain information for
imodfit_fitted_real_space_refined_176-coot-11_real_space_refined_190.pdb #10
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open /home/smissour/Desktop/DNAP01-YERA41/titan-DNAP-
> WT-T35-P15/imodfit_fitted_real_space_refined_176-coot-11.pdb
Chain information for imodfit_fitted_real_space_refined_176-coot-11.pdb #11
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!10 models
> volume #7 level 5.854
> open /home/smissour/Desktop/DNAP01-YERA41/titan-DNAP-
> WT-T35-P15/imodfit_fitted_real_space_refined_176-coot-12.pdb
Chain information for imodfit_fitted_real_space_refined_176-coot-12.pdb #12
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!11 models
> close #11
> close #10
> close #8
> show #!9 models
> select #12 /A :1-200
2552 atoms, 2580 bonds, 1 pseudobond, 157 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #4 to #12 & sel matrix BLOSUM-85
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-85
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 imodfit_fitted_real_space_refined_176-coot-12.pdb, chain A (#12)
with 2c2p, chain A (#4), sequence alignment score = 12.2
RMSD between 5 pruned atom pairs is 1.329 angstroms; (across all 13 pairs:
4.552)
> show #4 models
> hide #!9 models
> matchmaker #4 to #12 & sel matrix BLOSUM-85
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-85
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 imodfit_fitted_real_space_refined_176-coot-12.pdb, chain A (#12)
with 2c2p, chain A (#4), sequence alignment score = 12.2
RMSD between 5 pruned atom pairs is 1.329 angstroms; (across all 13 pairs:
4.552)
> matchmaker #4 to #12 & sel matrix BLOSUM-70
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-70
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 imodfit_fitted_real_space_refined_176-coot-12.pdb, chain A (#12)
with 2c2p, chain A (#4), sequence alignment score = 15
RMSD between 6 pruned atom pairs is 0.903 angstroms; (across all 13 pairs:
3.638)
> matchmaker #4 to #12 & sel matrix BLOSUM-70
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-70
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 imodfit_fitted_real_space_refined_176-coot-12.pdb, chain A (#12)
with 2c2p, chain A (#4), sequence alignment score = 15
RMSD between 6 pruned atom pairs is 0.903 angstroms; (across all 13 pairs:
3.638)
> matchmaker #!9 to #12 & sel matrix BLOSUM-70
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-70
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 imodfit_fitted_real_space_refined_176-coot-12.pdb, chain A (#12)
with 1ssp, chain E (#9), sequence alignment score = 37.2
RMSD between 7 pruned atom pairs is 1.274 angstroms; (across all 104 pairs:
15.115)
> show #!9 models
> select clear
> select #9
2498 atoms, 2344 bonds, 21 pseudobonds, 510 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.1075,0.82113,-0.56053,172.09,0.82531,-0.24065,-0.51083,126.82,-0.55435,-0.51753,-0.65182,154.74
> view matrix models
> #9,0.15564,-0.76497,-0.62498,167.6,-0.82323,0.24924,-0.51008,190.18,0.54596,0.59389,-0.59095,102.7
> view matrix models
> #9,0.15564,-0.76497,-0.62498,168.26,-0.82323,0.24924,-0.51008,178.13,0.54596,0.59389,-0.59095,110.47
> matchmaker #!9 to #12 & sel matrix BLOSUM-70
No 'to' model specified
> select clear
> select #12 /A :1-200
2552 atoms, 2580 bonds, 1 pseudobond, 157 residues, 2 models selected
> matchmaker #!9 to #12 & sel matrix BLOSUM-70
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-70
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 imodfit_fitted_real_space_refined_176-coot-12.pdb, chain A (#12)
with 1ssp, chain E (#9), sequence alignment score = 37.2
RMSD between 7 pruned atom pairs is 1.274 angstroms; (across all 104 pairs:
15.115)
> hide #!9 models
> select #4
1582 atoms, 1473 bonds, 336 residues, 1 model selected
> view matrix models
> #4,0.911,-0.089154,0.40265,-33.935,-0.38975,-0.50526,0.76994,189.02,0.1348,-0.85835,-0.49504,289.12
> view matrix models
> #4,-0.92301,0.2187,0.31657,252.18,0.13592,-0.58438,0.80002,107.45,0.35996,0.78145,0.50966,-94.971
> view matrix models
> #4,-0.91755,0.23243,0.32261,248.75,0.13102,-0.5893,0.79722,109.62,0.37541,0.77376,0.51026,-96.594
> view matrix models
> #4,-0.68552,-0.61836,0.3843,317.62,0.5577,-0.10669,0.82316,-31.438,-0.46801,0.77862,0.418,56.589
> select clear
> select #12 /A :1-200
2552 atoms, 2580 bonds, 1 pseudobond, 157 residues, 2 models selected
> matchmaker #!9 to #12 & sel matrix BLOSUM-90
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-90
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 imodfit_fitted_real_space_refined_176-coot-12.pdb, chain A (#12)
with 1ssp, chain E (#9), sequence alignment score = 14.4
RMSD between 5 pruned atom pairs is 1.082 angstroms; (across all 104 pairs:
15.209)
> color #4 #ce5c00 transparency 0
> select clear
> select #4
1582 atoms, 1473 bonds, 336 residues, 1 model selected
> ~select #4
Nothing selected
> hide #4 models
> show #!6 models
> select #6
2023 atoms, 1839 bonds, 4 pseudobonds, 467 residues, 2 models selected
> view matrix models
> #6,0.73475,-0.5013,0.45699,5.6194,-0.131,-0.76587,-0.62951,307.62,0.66557,0.40267,-0.62839,269.33
> select clear
> select #12 /A :1-200
2552 atoms, 2580 bonds, 1 pseudobond, 157 residues, 2 models selected
> matchmaker #!9 to #12 & sel matrix BLOSUM-90
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-90
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 imodfit_fitted_real_space_refined_176-coot-12.pdb, chain A (#12)
with 1ssp, chain E (#9), sequence alignment score = 14.4
RMSD between 5 pruned atom pairs is 1.082 angstroms; (across all 104 pairs:
15.209)
> close #1
> close #3,5
> ui tool show "Model Loops"
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> sequence chain #12/A
Alignment identifier is 12/A
> ui tool show "Model Loops"
> modeller refine 12/A:1:internal-missing 6/A:1:internal-missing numModels 5
> fast true adjacentFlexible 1 protocol standard tempPath
> /home/smissour/Desktop/DNAP01-YERA41/titan-DNAP-WT-T20-P15
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 229, in launch_modeller
run(self.session, ("modeller %s %s numModels %d fast %s " % (sub_cmd, "
".join(aln_seq_args),
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2877, in run
result = ci.function(session, *args, optional=optional,
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 3417, in __call__
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 121, in model_loops
loops.model(session, targets, adjacent_flexible=adjacent_flexible,
block=block, chains=chains,
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model
mmap = seq.match_maps[chain]
KeyError: <chimerax.atomic.molobject.Chain object at 0x7f53af9d2700>
KeyError:
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model
mmap = seq.match_maps[chain]
See log for complete Python traceback.
> ui tool show "Modeller Comparative"
> modeller comparative 12/A:1 6/A:1 numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false
Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v10.1) for
protein structure modeling
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service
Opal job id: appModeller9v8Service1678376304657-1128050227
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service1678376304657-1128050227
stdout.txt = standard output
stderr.txt = standard error
Modeller job ID appModeller9v8Service1678376304657-1128050227 finished
Modeller error output
Traceback (most recent call last):
File "/usr/local/opal-local/bin/modeller9v8.py", line 332, in <module>
main()
File "/usr/local/opal-local/bin/modeller9v8.py", line 24, in main
VersionMap[cf["version"]](cf)
File "/usr/local/opal-local/bin/modeller9v8.py", line 34, in v2_run
execfile(fn)
File "ModellerModelling.py", line 67, in <module>
a.make()
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 625, in homcsr
self.check_alignment(aln)
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 578, in check_alignment
aln.check()
File "/usr/lib64/python2.7/site-packages/modeller/alignment.py", line 213, in
check
self.check_structure_structure(io=io)
File "/usr/lib64/python2.7/site-packages/modeller/alignment.py", line 222, in
check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.SequenceMismatchError: read_te_291E> Sequence difference between
alignment and pdb :
Modeller run output
**** IGNORE FOLLOWING LICENSE KEY MESSAGE ****
**** END IGNORED MESSAGE ****
MODELLER 10.4, 2022/10/28, r12463
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2022 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux franklin.cgl.ucsf.edu
3.10.0-1160.83.1.el7.x86_64 x86_64
Date and time of compilation : 2022/10/28 21:02:55
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2023/03/09 07:38:24
environ____W> The class 'environ' is deprecated; use 'Environ' instead
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL10v4}/modlib/sstruc.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076
0.183
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592
0.183
openf___224_> Open ${MODINSTALL10v4}/modlib/resdih.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053
0.230
rdrdih__263_> Number of dihedral angle types : 9
Maximal number of dihedral angle optima: 3
Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5
openf___224_> Open ${MODINSTALL10v4}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL10v4}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead
openf___224_> Open alignment.ali
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 282425 275.806
0.269
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 297517 290.544
0.284
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 312917 305.583
0.298
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 343717 335.661
0.328
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 405317 395.817
0.387
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 405345 395.845 0.387
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 405373 395.872 0.387
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 406261 396.739 0.387
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 407105 397.563 0.388
read_al_374_> Non-standard residue type,position,sequence: X 215 1
Read the alignment from file : alignment.ali
Total number of alignment positions: 223
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 6iod_6 223 2 6iod_6
2 target 212 1 target
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./6iod_6.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 475730 464.580
0.454
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 475730 464.580 0.454
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 475901 464.747
0.454
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 476751 465.577
0.455
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 478009 466.806
0.456
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 479913 468.665
0.458
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 479913 468.665 0.458
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 480003 468.753
0.458
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 482859 471.542
0.460
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 482859 471.542 0.460
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 482994 471.674
0.461
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 487278 475.857
0.465
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 487278 475.857 0.465
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 487476 476.051
0.465
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 493902 482.326
0.471
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 493902 482.326 0.471
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 494199 482.616
0.471
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 503821 492.013
0.480
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 503821 492.013 0.480
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 504271 492.452
0.481
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 518721 506.563
0.495
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 518721 506.563 0.495
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 519396 507.223
0.495
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 541054 528.373
0.516
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 541054 528.373 0.516
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 541054 528.373
0.516
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 541036 528.355
0.516
read_te_291E> Sequence difference between alignment and pdb :
x (mismatch at alignment position 213)
Alignment ADVRP/TG-XAGGCATG-C/
PDB ADVRP/tl/elljetlj/ -
Match ******
Alignment residue type 17 (T, THR) does not match pdb
residue type 51 (t, DTHY),
for align code 6iod_6 (atom file 6iod_6), pdb residue number " 6", chain "C"
Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.
Another possibility is that some residues in the atom file are missing,
perhaps because they could not be resolved experimentally. (Note that Modeller
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
In this case, simply replace the section of your alignment corresponding
to these missing residues with gaps.
read_te_288W> Protein not accepted: 1 6iod_6
No output models from Modeller; see log for Modeller text output.
> select clear
> select #12/A:201-202
33 atoms, 32 bonds, 2 residues, 1 model selected
> select #12/A:201-692
7904 atoms, 8004 bonds, 1 pseudobond, 473 residues, 2 models selected
> select #12/A:201-692
7904 atoms, 8004 bonds, 1 pseudobond, 473 residues, 2 models selected
> select #12/A:1282
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/A:753-1282
8582 atoms, 8686 bonds, 530 residues, 1 model selected
> select #12/A:554-1282
11595 atoms, 11733 bonds, 1 pseudobond, 710 residues, 2 models selected
> select #12/A:201-1282
17459 atoms, 17676 bonds, 1 pseudobond, 1063 residues, 2 models selected
> delete atoms (#!12 & sel)
> delete bonds (#!12 & sel)
> select add #12/C:15
22 atoms, 24 bonds, 1 residue, 1 model selected
> select clear
> ui tool show "Modeller Comparative"
> modeller comparative 12/A:1 6/A:1 numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false
Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v10.1) for
protein structure modeling
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service
Opal job id: appModeller9v8Service16783764165861672787093
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service16783764165861672787093
stdout.txt = standard output
stderr.txt = standard error
> ui tool show "Model Loops"
> modeller refine 12/A:1:internal-missing 6/A:1:internal-missing numModels 5
> fast true adjacentFlexible 1 protocol standard tempPath
> /home/smissour/Desktop/DNAP01-YERA41/titan-DNAP-WT-T20-P15
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 229, in launch_modeller
run(self.session, ("modeller %s %s numModels %d fast %s " % (sub_cmd, "
".join(aln_seq_args),
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2877, in run
result = ci.function(session, *args, optional=optional,
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 3417, in __call__
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/modeller/cmd.py", line 121, in model_loops
loops.model(session, targets, adjacent_flexible=adjacent_flexible,
block=block, chains=chains,
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model
mmap = seq.match_maps[chain]
KeyError: <chimerax.atomic.molobject.Chain object at 0x7f53af9d2700>
KeyError:
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/modeller/loops.py", line 135, in model
mmap = seq.match_maps[chain]
See log for complete Python traceback.
Modeller job ID appModeller9v8Service16783764165861672787093 finished
Modeller error output
Traceback (most recent call last):
File "/usr/local/opal-local/bin/modeller9v8.py", line 332, in <module>
main()
File "/usr/local/opal-local/bin/modeller9v8.py", line 24, in main
VersionMap[cf["version"]](cf)
File "/usr/local/opal-local/bin/modeller9v8.py", line 34, in v2_run
execfile(fn)
File "ModellerModelling.py", line 67, in <module>
a.make()
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 625, in homcsr
self.check_alignment(aln)
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 578, in check_alignment
aln.check()
File "/usr/lib64/python2.7/site-packages/modeller/alignment.py", line 213, in
check
self.check_structure_structure(io=io)
File "/usr/lib64/python2.7/site-packages/modeller/alignment.py", line 222, in
check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.SequenceMismatchError: read_te_291E> Sequence difference between
alignment and pdb :
Modeller run output
**** IGNORE FOLLOWING LICENSE KEY MESSAGE ****
**** END IGNORED MESSAGE ****
MODELLER 10.4, 2022/10/28, r12463
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2022 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux franklin.cgl.ucsf.edu
3.10.0-1160.83.1.el7.x86_64 x86_64
Date and time of compilation : 2022/10/28 21:02:55
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2023/03/09 07:40:16
environ____W> The class 'environ' is deprecated; use 'Environ' instead
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL10v4}/modlib/sstruc.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076
0.183
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592
0.183
openf___224_> Open ${MODINSTALL10v4}/modlib/resdih.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053
0.230
rdrdih__263_> Number of dihedral angle types : 9
Maximal number of dihedral angle optima: 3
Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5
openf___224_> Open ${MODINSTALL10v4}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL10v4}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead
openf___224_> Open alignment.ali
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 282425 275.806
0.269
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 297517 290.544
0.284
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 312917 305.583
0.298
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 343717 335.661
0.328
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 405317 395.817
0.387
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 405345 395.845 0.387
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 405373 395.872 0.387
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 406261 396.739 0.387
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 407105 397.563 0.388
read_al_374_> Non-standard residue type,position,sequence: X 215 1
Read the alignment from file : alignment.ali
Total number of alignment positions: 223
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 6iod_6 223 2 6iod_6
2 target 212 1 target
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./6iod_6.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 475730 464.580
0.454
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 475730 464.580 0.454
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 475901 464.747
0.454
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 476751 465.577
0.455
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 478009 466.806
0.456
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 479913 468.665
0.458
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 479913 468.665 0.458
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 480003 468.753
0.458
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 482859 471.542
0.460
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 482859 471.542 0.460
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 482994 471.674
0.461
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 487278 475.857
0.465
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 487278 475.857 0.465
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 487476 476.051
0.465
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 493902 482.326
0.471
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 493902 482.326 0.471
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 494199 482.616
0.471
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 503821 492.013
0.480
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 503821 492.013 0.480
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 504271 492.452
0.481
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 518721 506.563
0.495
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 518721 506.563 0.495
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 519396 507.223
0.495
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 541054 528.373
0.516
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 541054 528.373 0.516
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 541054 528.373
0.516
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 541036 528.355
0.516
read_te_291E> Sequence difference between alignment and pdb :
x (mismatch at alignment position 213)
Alignment ADVRP/TG-XAGGCATG-C/
PDB ADVRP/tl/elljetlj/ -
Match ******
Alignment residue type 17 (T, THR) does not match pdb
residue type 51 (t, DTHY),
for align code 6iod_6 (atom file 6iod_6), pdb residue number " 6", chain "C"
Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.
Another possibility is that some residues in the atom file are missing,
perhaps because they could not be resolved experimentally. (Note that Modeller
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
In this case, simply replace the section of your alignment corresponding
to these missing residues with gaps.
read_te_288W> Protein not accepted: 1 6iod_6
No output models from Modeller; see log for Modeller text output.
OpenGL version: 3.3.0 NVIDIA 470.57.02
OpenGL renderer: Quadro K2000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T3610
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 12 Intel(R) Xeon(R) CPU E5-1650 v2 @ 3.50GHz
Cache Size: 12288 KB
Memory:
total used free shared buff/cache available
Mem: 31G 15G 2.9G 559M 13G 15G
Swap: 32G 1.0M 32G
Graphics:
02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK107GL [Quadro K2000] [10de:0ffe] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:094c]
Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
biopython: 1.79
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-Clipper: 0.17.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
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: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.3
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-Phenix: 0.3
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RIBFIND: 0.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 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: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
distro: 1.6.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
line-profiler: 3.3.0
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
ribfind: 2.0.2
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → modeller refine: KeyError for seq.match_maps[chain] |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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