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Opened 2 years ago
Last modified 2 years ago
#9962 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-4.18.0-477.27.1.el8_8.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231004_Xt_14-3_deepemhancer_alphadone_01.cxs
Opened Xt_14-3_refine10_deepemhancer.mrc as #5.1.1.2, grid size 416,416,416,
pixel 1.07, shown at level 0.13, step 1, values float32
Restoring stepper: 230822_Xt_14-3_6dimers-
rotamercorrect_real_space_refined_037.pdb
Log from Wed Oct 4 16:55:46 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231004_Xt_14-3_deepemhancer.cxs
> format session
Opened 230822_Xt_14-3_6dimers-rotamercorrect_real_space_refined_037.pdb map 4
as #4, grid size 69,66,154, pixel 1.33, shown at level 0.121, step 1, values
float32
Opened Xt_14-3_refine05_deepemhancer.mrc as #5.1.1.1, grid size 416,416,416,
pixel 1.07, shown at level 0.28, step 1, values float32
Opened Xt_14-3_refine10_deepemhancer.mrc as #5.1.1.2, grid size 416,416,416,
pixel 1.07, shown at level 0.276, step 1, values float32
Opened Xt_14-3_refine13_deepemhancer.mrc as #5.1.1.3, grid size 416,416,416,
pixel 1.07, shown at level 0.281, step 1, values float32
Log from Wed Oct 4 12:21:47 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /d/emr214/u/tl002/Xtropicalis_2209/deepemhancer/refine13/Xt_14-3_refine13_deepemhancer.mrc
Opened Xt_14-3_refine13_deepemhancer.mrc as #1, grid size 416,416,416, pixel
1.07, shown at level 0.0767, step 2, values float32
> open
> /d/emr214/u/tl002/Xtropicalis_2209/deepemhancer/refine10/Xt_14-3_refine10_deepemhancer.mrc
Opened Xt_14-3_refine10_deepemhancer.mrc as #2, grid size 416,416,416, pixel
1.07, shown at level 0.0722, step 2, values float32
> open
> /d/emr214/u/tl002/Xtropicalis_2209/deepemhancer/refine05/Xt_14-3_refine05_deepemhancer.mrc
Opened Xt_14-3_refine05_deepemhancer.mrc as #3, grid size 416,416,416, pixel
1.07, shown at level 0.264, step 2, values float32
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Phenix/RealSpaceRefine_37/230822_Xt_14-3_6dimers-
> rotamercorrect_real_space_refined_037.pdb
Chain information for 230822_Xt_14-3_6dimers-
rotamercorrect_real_space_refined_037.pdb #4
---
Chain | Description
Z a b d f h | No description available
k l m n o p | No description available
> molmap #4 4
Opened 230822_Xt_14-3_6dimers-rotamercorrect_real_space_refined_037.pdb map 4
as #5, grid size 115,129,166, pixel 1.33, shown at level 0.121, step 1, values
float32
> ui tool show "Fit in Map"
> fitmap #1 inMap #5
Fit map Xt_14-3_refine13_deepemhancer.mrc in map 230822_Xt_14-3_6dimers-
rotamercorrect_real_space_refined_037.pdb map 4 using 89866 points
correlation = 0.5945, correlation about mean = 0.3541, overlap = 5109
steps = 48, shift = 0.089, angle = 0.034 degrees
Position of Xt_14-3_refine13_deepemhancer.mrc (#1) relative to
230822_Xt_14-3_6dimers-rotamercorrect_real_space_refined_037.pdb map 4 (#5)
coordinates:
Matrix rotation and translation
0.99999985 -0.00045666 -0.00029901 0.14145839
0.00045673 0.99999987 0.00023152 -0.04924389
0.00029890 -0.00023165 0.99999993 0.05794404
Axis -0.39057384 -0.50418884 0.77022444
Axis point 92.22618626 321.88871506 0.00000000
Rotation angle (degrees) 0.03397286
Shift along axis 0.01420819
> fitmap #2 inMap #5
Fit map Xt_14-3_refine10_deepemhancer.mrc in map 230822_Xt_14-3_6dimers-
rotamercorrect_real_space_refined_037.pdb map 4 using 89919 points
correlation = 0.5937, correlation about mean = 0.3439, overlap = 4996
steps = 52, shift = 0.122, angle = 0.477 degrees
Position of Xt_14-3_refine10_deepemhancer.mrc (#2) relative to
230822_Xt_14-3_6dimers-rotamercorrect_real_space_refined_037.pdb map 4 (#5)
coordinates:
Matrix rotation and translation
0.99998879 -0.00420014 0.00218407 0.33219809
0.00418510 0.99996781 0.00684578 -1.89040540
-0.00221276 -0.00683656 0.99997418 1.41612342
Axis -0.82231390 0.26425110 0.50395556
Axis point 0.00000000 210.45456567 274.85199562
Rotation angle (degrees) 0.47667287
Shift along axis -0.05904954
> fitmap #3 inMap #5
Fit map Xt_14-3_refine05_deepemhancer.mrc in map 230822_Xt_14-3_6dimers-
rotamercorrect_real_space_refined_037.pdb map 4 using 89974 points
correlation = 0.3554, correlation about mean = 0.1021, overlap = 3918
steps = 476, shift = 1.34, angle = 1.25 degrees
Position of Xt_14-3_refine05_deepemhancer.mrc (#3) relative to
230822_Xt_14-3_6dimers-rotamercorrect_real_space_refined_037.pdb map 4 (#5)
coordinates:
Matrix rotation and translation
0.99993597 -0.01121250 -0.00152713 2.35503119
0.01123906 0.99976267 0.01866222 -5.26313998
0.00131752 -0.01867819 0.99982468 3.02065185
Axis -0.85519280 -0.06514999 0.51419914
Axis point 0.00000000 162.29597037 284.49651382
Rotation angle (degrees) 1.25095672
Shift along axis -0.11789559
> ui tool show "Side View"
> volume #1 step 1
> volume #2 step 1
> volume #3 step 1
> hide #!4 models
> hide #!3 models
> close #5
> show #!4 models
> hide #!4 models
> hide #!2 models
> volume #1 level 0.2106
> volume #2 level 0.1461
> volume #3 level 0.08397
> volume #3 level 0.101
> ui tool show ISOLDE
> set selectionWidth 4
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> show #!2 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 276 residues in model #4 to IUPAC-IUB
standards.
Chain information for 230822_Xt_14-3_6dimers-
rotamercorrect_real_space_refined_037.pdb
---
Chain | Description
4.2/Z 4.2/a 4.2/b 4.2/d 4.2/f 4.2/h | No description available
4.2/k 4.2/l 4.2/m 4.2/n 4.2/o 4.2/p | No description available
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Phenix/RealSpaceRefine_37/230822_Xt_14-3_6dimers-
> rotamercorrect_real_space_refined_037.pdb
Chain information for 230822_Xt_14-3_6dimers-
rotamercorrect_real_space_refined_037.pdb #5
---
Chain | Description
Z a b d f h | No description available
k l m n o p | No description available
> hide #4.1 models
> hide #4.3 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> hide #!4 models
> close #4.1,3#4#4.2
> select up
18692 atoms, 18805 bonds, 10 pseudobonds, 1203 residues, 2 models selected
> select up
24236 atoms, 24507 bonds, 10 pseudobonds, 1563 residues, 2 models selected
> select up
33597 atoms, 33982 bonds, 10 pseudobonds, 2172 residues, 2 models selected
> select down
24236 atoms, 24507 bonds, 10 pseudobonds, 1563 residues, 2 models selected
> select down
18692 atoms, 18805 bonds, 10 pseudobonds, 1203 residues, 2 models selected
> select down
15546 atoms, 176 bonds, 10 pseudobonds, 1203 residues, 2 models selected
> select down
15546 atoms, 176 bonds, 10 pseudobonds, 1203 residues, 2 models selected
> select clear
> select up
9483 atoms, 9209 bonds, 10 pseudobonds, 809 residues, 2 models selected
> select up
12625 atoms, 12683 bonds, 10 pseudobonds, 809 residues, 2 models selected
> select up
18193 atoms, 18393 bonds, 10 pseudobonds, 1177 residues, 2 models selected
> select up
26926 atoms, 27234 bonds, 10 pseudobonds, 1741 residues, 2 models selected
> molmap sel 4
Opened 230822_Xt_14-3_6dimers-rotamercorrect_real_space_refined_037.pdb map 4
as #4, grid size 69,66,154, pixel 1.33, shown at level 0.121, step 1, values
float32
> fitmap #3 inMap #4
Fit map Xt_14-3_refine05_deepemhancer.mrc in map 230822_Xt_14-3_6dimers-
rotamercorrect_real_space_refined_037.pdb map 4 using 1646808 points
correlation = 0.2053, correlation about mean = 0.08908, overlap = 1.473e+04
steps = 228, shift = 0.888, angle = 0.587 degrees
Position of Xt_14-3_refine05_deepemhancer.mrc (#3) relative to
230822_Xt_14-3_6dimers-rotamercorrect_real_space_refined_037.pdb map 4 (#4)
coordinates:
Matrix rotation and translation
0.99999828 -0.00096388 -0.00158542 0.57489698
0.00099341 0.99982401 0.01873404 -3.76383978
0.00156708 -0.01873558 0.99982325 2.98499357
Axis -0.99513210 -0.08372524 0.05198253
Axis point 0.00000000 157.69094251 202.84548690
Rotation angle (degrees) 1.07874023
Shift along axis -0.10180256
> fitmap #2 inMap #4
Fit map Xt_14-3_refine10_deepemhancer.mrc in map 230822_Xt_14-3_6dimers-
rotamercorrect_real_space_refined_037.pdb map 4 using 406180 points
correlation = 0.3978, correlation about mean = 0.2077, overlap = 1.403e+04
steps = 48, shift = 0.0949, angle = 0.123 degrees
Position of Xt_14-3_refine10_deepemhancer.mrc (#2) relative to
230822_Xt_14-3_6dimers-rotamercorrect_real_space_refined_037.pdb map 4 (#4)
coordinates:
Matrix rotation and translation
0.99997705 -0.00632502 0.00242590 0.58592294
0.00630889 0.99995832 0.00660028 -2.06711858
-0.00246754 -0.00658482 0.99997528 1.44055636
Axis -0.69743080 0.25884033 0.66827536
Axis point 0.00000000 215.65774389 315.29348418
Rotation angle (degrees) 0.54160336
Shift along axis 0.01899396
> fitmap #1 inMap #4
Fit map Xt_14-3_refine13_deepemhancer.mrc in map 230822_Xt_14-3_6dimers-
rotamercorrect_real_space_refined_037.pdb map 4 using 277411 points
correlation = 0.4387, correlation about mean = 0.2371, overlap = 1.445e+04
steps = 44, shift = 0.0172, angle = 0.0213 degrees
Position of Xt_14-3_refine13_deepemhancer.mrc (#1) relative to
230822_Xt_14-3_6dimers-rotamercorrect_real_space_refined_037.pdb map 4 (#4)
coordinates:
Matrix rotation and translation
0.99999996 -0.00021604 -0.00018679 0.09607822
0.00021613 0.99999986 0.00049205 -0.06500447
0.00018668 -0.00049209 0.99999986 0.12190808
Axis -0.86488649 -0.32821202 0.37980025
Axis point 0.00000000 259.63002292 142.49967420
Rotation angle (degrees) 0.03259770
Shift along axis -0.01546079
> hide #!5 models
> show #!5 models
> hide #!4 models
> select clear
> ui tool show ISOLDE
> set selectionWidth 4
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 276 residues in model #5 to IUPAC-IUB
standards.
Chain information for 230822_Xt_14-3_6dimers-
rotamercorrect_real_space_refined_037.pdb
---
Chain | Description
5.2/Z 5.2/a 5.2/b 5.2/d 5.2/f 5.2/h | No description available
5.2/k 5.2/l 5.2/m 5.2/n 5.2/o 5.2/p | No description available
> clipper associate #3 toModel #5
Opened Xt_14-3_refine05_deepemhancer.mrc as #5.1.1.1, grid size 416,416,416,
pixel 1.07, shown at step 1, values float32
> clipper associate #2 toModel #5
Opened Xt_14-3_refine10_deepemhancer.mrc as #5.1.1.2, grid size 416,416,416,
pixel 1.07, shown at step 1, values float32
> clipper associate #1 toModel #5
Opened Xt_14-3_refine13_deepemhancer.mrc as #5.1.1.3, grid size 416,416,416,
pixel 1.07, shown at step 1, values float32
> select clear
> select up
1171 atoms, 1173 bonds, 77 residues, 2 models selected
> select up
1243 atoms, 1245 bonds, 77 residues, 2 models selected
> select up
2821 atoms, 2848 bonds, 182 residues, 2 models selected
> select up
6631 atoms, 6706 bonds, 430 residues, 2 models selected
> ui tool show "Ramachandran Plot"
> isolde sim start /l
ISOLDE: started sim
> select clear
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231004_Xt_14-3_deepemhancer.cxs
——— End of log from Wed Oct 4 12:21:47 2023 ———
opened ChimeraX session
> ui tool show ISOLDE
> set selectionWidth 4
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> select clear
> open
> /d/emr214/u/tl002/Xlaevis_2303/Isolde/230931_Xl_14-3_1dimer_complete.pdb
Chain information for 230931_Xl_14-3_1dimer_complete.pdb #1
---
Chain | Description
b | No description available
j | No description available
> select add #1
13478 atoms, 13633 bonds, 2 pseudobonds, 871 residues, 2 models selected
> view matrix models
> #1,0.99912,0.036086,-0.021576,0.58143,-0.036334,0.99928,-0.01121,8.6522,0.021156,0.011984,0.9997,-4.9192
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.99912,0.036086,-0.021576,-31.877,-0.036334,0.99928,-0.01121,52.81,0.021156,0.011984,0.9997,3.6679
> view matrix models
> #1,0.99912,0.036086,-0.021576,-39.21,-0.036334,0.99928,-0.01121,46.126,0.021156,0.011984,0.9997,3.8496
> ui tool show Matchmaker
> matchmaker #1/b to #5.2/a pairing ss
Parameters
---
Chain pairing | ss
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 230822_Xt_14-3_6dimers-rotamercorrect_real_space_refined_037.pdb,
chain a (#5.2) with 230931_Xl_14-3_1dimer_complete.pdb, chain b (#1), sequence
alignment score = 2197.1
RMSD between 427 pruned atom pairs is 0.624 angstroms; (across all 438 pairs:
0.757)
> matchmaker #1/b to #5.2/a pairing ss
Parameters
---
Chain pairing | ss
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 230822_Xt_14-3_6dimers-rotamercorrect_real_space_refined_037.pdb,
chain a (#5.2) with 230931_Xl_14-3_1dimer_complete.pdb, chain b (#1), sequence
alignment score = 2197.1
RMSD between 427 pruned atom pairs is 0.624 angstroms; (across all 438 pairs:
0.757)
> matchmaker #1/b to #5.2/a pairing ss
Parameters
---
Chain pairing | ss
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 230822_Xt_14-3_6dimers-rotamercorrect_real_space_refined_037.pdb,
chain a (#5.2) with 230931_Xl_14-3_1dimer_complete.pdb, chain b (#1), sequence
alignment score = 2197.1
RMSD between 427 pruned atom pairs is 0.624 angstroms; (across all 438 pairs:
0.757)
> select clear
> show #!4 models
> hide #!4 models
> select add #1
13478 atoms, 13633 bonds, 2 pseudobonds, 871 residues, 2 models selected
> style sel stick
Changed 13478 atom styles
> style sel stick
Changed 13478 atom styles
> show sel atoms
> hide sel cartoons
> hide HC
> select clear
> hide #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5.2/a
Alignment identifier is 5.2/a
> sequence chain #5.2/l
Alignment identifier is 5.2/l
> select #5.2/l:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #5.2/l:1-10
163 atoms, 163 bonds, 10 residues, 1 model selected
> select #5.2/a:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #5.2/a:1-16
245 atoms, 245 bonds, 16 residues, 1 model selected
> select clear
> select #5.2/a:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #5.2/a:1-18
266 atoms, 266 bonds, 18 residues, 1 model selected
> clipper isolate #5.2/a:1-18 maskRadius 4.0 focus false
> show #!1 models
> hide #!1 models
> close #4
> volume #5.1.1.1 level 0.2952
> volume #5.1.1.1 level 0.239
> isolde sim start #5.2/a:1-18
ISOLDE: started sim
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/a:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #5.2/a:1-8
135 atoms, 135 bonds, 8 residues, 1 model selected
> clipper isolate #5.2/a:1-8 maskRadius 4.0 focus false
> isolde sim start #5.2/a:1-8
ISOLDE: started sim
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #5.2/a:14
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #5.2/a:14-24
171 atoms, 173 bonds, 11 residues, 1 model selected
> show #!1 models
> select clear
> hide #!1 models
> volume #5.1.1.1 level 0.1698
> volume #5.1.1.1 level 0.2703
> select #5.2/a:37
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #5.2/a:37-48
165 atoms, 166 bonds, 12 residues, 1 model selected
> volume #5.1.1.1 level 0.003953
> show #!1 models
> select add #1
13643 atoms, 13799 bonds, 2 pseudobonds, 883 residues, 4 models selected
> select subtract #1
165 atoms, 166 bonds, 12 residues, 2 models selected
> hide #!1 models
> volume #5.1.1.1 level 0.04259
> clipper spotlight
> volume #5.1.1.1 level 0.1965
> show #!1 models
> hide #!1 models
> select #5.2/a:48
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #5.2/a:48-56
128 atoms, 130 bonds, 9 residues, 1 model selected
> select #5.2/a:28
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #5.2/a:28-39
175 atoms, 176 bonds, 12 residues, 1 model selected
> show #!1 models
> hide #!1 models
> isolde sim start #5.2/a:26
ISOLDE: started sim
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/a:36
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #5.2/a:36-50
205 atoms, 206 bonds, 15 residues, 1 model selected
> select #5.2/a:13
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5.2/a:13-41
434 atoms, 438 bonds, 29 residues, 1 model selected
> select #5.2/a:41
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #5.2/a:41-53
174 atoms, 176 bonds, 13 residues, 1 model selected
> show #!1 models
> hide #!1 models
> isolde sim start #5.2/a:55-60
ISOLDE: started sim
> isolde sim pause
> show #!1 models
> hide #!1 models
> show #!1 models
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231004_Xt_14-3_deepemhancer_01.cxs
> hide #!1 models
> isolde sim start #5.2/a:57
ISOLDE: started sim
> show #!1 models
> hide #!1 models
> isolde sim pause
> show #!1 models
> volume #5.1.1.1 level 0.1882
> volume #5.1.1.2 level 0.2265
> isolde sim resume
> hide #!1 models
> show #!1 models
> hide #!1 models
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:54-58
ISOLDE: started sim
> select clear
> isolde pepflip #5.2/a:57
[Repeated 1 time(s)]
> show #!1 models
> volume #5.1.1.1 level 0.2113
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> hide #!1 models
> select #5.2/a:56
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5.2/a:56-67
180 atoms, 182 bonds, 12 residues, 1 model selected
> show #!1 models
> hide #!1 models
> show #!1 models
> select #5.2/a:67
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #5.2/a:67-75
135 atoms, 134 bonds, 9 residues, 1 model selected
> hide #!1 models
> volume #5.1.1.1 level 0.1832
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #5.1.1.2 level 0.1428
> volume #5.1.1.3 level 0.2247
> hide #!1 models
> select #5.2/a:82-83
45 atoms, 45 bonds, 2 residues, 1 model selected
> select #5.2/a:82-95
239 atoms, 242 bonds, 14 residues, 1 model selected
> isolde sim start #5.2/a:85
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #!1 models
> hide #!1 models
> volume #5.1.1.2 level 0.2713
> volume #5.1.1.3 level 0.468
> volume #5.1.1.1 level 0.2749
> isolde sim start #5.2/a:87
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> volume #5.1.1.1 level 0.3003
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #5.1.1.1 level 0.2362
> volume #5.1.1.1 level 0.2238
> isolde sim start #5.2/a:96-97
ISOLDE: started sim
> volume #5.1.1.2 level 0.1906
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #!1 models
> hide #!1 models
> isolde sim start #5.2/a:117
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:131
ISOLDE: started sim
> isolde sim pause
> show #!1 models
> hide #!1 models
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
34 atoms, 34 bonds, 3 residues, 2 models selected
> select up
6767 atoms, 6844 bonds, 438 residues, 2 models selected
> select down
34 atoms, 34 bonds, 3 residues, 2 models selected
> select #5.2/a:131
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #5.2/a:131-159
427 atoms, 431 bonds, 29 residues, 1 model selected
> show #!1 models
> hide #!1 models
> select #5.2/a:140
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #5.2/a:140-145
62 atoms, 62 bonds, 6 residues, 1 model selected
> isolde sim start #5.2/a:140-145
ISOLDE: started sim
> isolde sim pause
> volume #5.1.1.1 level 0.1188
> volume #5.1.1.2 level 0.2405
> volume #5.1.1.3 level 0.2246
> isolde sim resume
> isolde sim pause
> show #!1 models
> isolde sim resume
> isolde sim pause
> hide #!1 models
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #5.2/a:149
ISOLDE: started sim
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #!1 models
> hide #!1 models
> select #5.2/a:149
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #5.2/a:149-160
198 atoms, 198 bonds, 12 residues, 1 model selected
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> isolde sim start #5.2/a:161,163
ISOLDE: started sim
> isolde sim pause
> show #!1 models
> hide #!1 models
> show #!1 models
> isolde sim resume
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.3387
> volume #5.1.1.1 level 0.3502
> isolde sim start #5.2/a:158
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:160
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/a:163
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #5.2/a:163-173
181 atoms, 183 bonds, 11 residues, 1 model selected
> isolde sim start #5.2/a:170
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:174
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:174
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:172-176
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> volume #5.1.1.3 level 0.03212
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/a:177-178
25 atoms, 24 bonds, 2 residues, 1 model selected
> select #5.2/a:177-180
51 atoms, 50 bonds, 4 residues, 1 model selected
> volume #5.1.1.3 level 0.3174
> hide #!1 models
> isolde sim start #5.2/a:181-184
ISOLDE: started sim
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/a:185
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #5.2/a:185-195
170 atoms, 170 bonds, 11 residues, 1 model selected
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> isolde sim start #5.2/a:194
ISOLDE: started sim
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:195-196,198
ISOLDE: started sim
> volume #5.1.1.3 level 0.1913
> volume #5.1.1.1 level 0.2846
> isolde sim pause
> isolde sim resume
> isolde sim pause
> volume #5.1.1.3 level 0.2135
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> show #!1 models
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #5.2/a:195
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #5.2/a:195-206
170 atoms, 171 bonds, 12 residues, 1 model selected
> hide #!1 models
> isolde sim start #5.2/a:201
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> isolde sim start #5.2/a:211
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:210-212
ISOLDE: started sim
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:211
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:211
ISOLDE: started sim
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:209-213,215,217
ISOLDE: started sim
> isolde sim pause
> show #!1 models
> hide #!1 models
> isolde sim resume
> volume #5.1.1.2 level 0.2981
> volume #5.1.1.3 level 0.2422
> show #!1 models
> hide #!1 models
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/a:211
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #5.2/a:211-220
171 atoms, 170 bonds, 10 residues, 1 model selected
> isolde sim start #5.2/a:211-220
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #!1 models
> isolde sim start #5.2/a:209-221,274-276
ISOLDE: started sim
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #5.1.1.1 level 0.4641
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.2 level 0.293
> isolde sim start #5.2/a:215
ISOLDE: started sim
> show #!1 models
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> hide #!1 models
> volume #5.1.1.1 level 0.2332
> volume #5.1.1.2 level 0.2098
> show #!1 models
> hide #!1 models
> isolde sim start #5.2/a:217
ISOLDE: started sim
> isolde sim pause
> show #!1 models
> isolde sim resume
> hide #!1 models
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select up
131 atoms, 131 bonds, 8 residues, 2 models selected
> isolde sim start #5.2/a:215-222
ISOLDE: started sim
> select clear
> isolde sim pause
> isolde sim resume
> isolde sim pause
> volume #5.1.1.1 level 0.1473
> volume #5.1.1.2 level 0.2597
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> isolde sim start #5.2/a:225
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.2 level 0.2731
> volume #5.1.1.3 level 0.1537
> isolde sim start #5.2/a:225
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/a:225
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #5.2/a:225-238
223 atoms, 222 bonds, 14 residues, 1 model selected
> isolde sim start #5.2/a:240
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> select clear
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:241-243
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.3 level 0.2114
> volume #5.1.1.1 level 0.2365
> show #!1 models
> isolde sim start #5.2/a:242
ISOLDE: started sim
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:249
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:255
ISOLDE: started sim
> volume #5.1.1.3 level 0.2666
> volume #5.1.1.1 level 0.2857
> isolde sim pause
> hide #!1 models
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:249-251
ISOLDE: started sim
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/a:251-252
33 atoms, 32 bonds, 2 residues, 1 model selected
> select #5.2/a:251-266
277 atoms, 282 bonds, 16 residues, 1 model selected
> select #5.2/a:249
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #5.2/a:249-263
249 atoms, 252 bonds, 15 residues, 1 model selected
> select #5.2/a:262-263
38 atoms, 38 bonds, 2 residues, 1 model selected
> select #5.2/a:262-268
127 atoms, 130 bonds, 7 residues, 1 model selected
> show #!1 models
> isolde sim start #5.2/a:262-268
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:264-266
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> hide #!1 models
> show #!1 models
> isolde sim start #5.2/a:273
ISOLDE: started sim
> hide #!1 models
> isolde cisflip #5.2/a:273
> show #!1 models
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:271-274
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> hide #!1 models
> show #!1 models
> hide #!1 models
> isolde sim start #5.2/a:271-278
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select up
19 atoms, 18 bonds, 1 residue, 2 models selected
> isolde sim start #5.2/a:274-278
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:274-278
ISOLDE: started sim
> volume #5.1.1.1 level 0.1904
> isolde sim pause
> select clear
> isolde sim resume
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/a:272
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5.2/a:272-276
74 atoms, 74 bonds, 5 residues, 1 model selected
> show #!1 models
> hide #!1 models
> volume #5.1.1.1 level 0.4297
> volume #5.1.1.2 level 0.4246
> volume #5.1.1.3 level 0.412
> isolde sim start #5.2/a:282
ISOLDE: started sim
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #5.1.1.3 level 0.5879
> volume #5.1.1.1 level 0.3166
> isolde sim start #5.2/a:282
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #5.2/a:284-286,290
ISOLDE: started sim
> isolde sim pause
> show #!1 models
> isolde sim resume
> isolde sim pause
> hide #!1 models
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #5.2/a:282-292
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.2406
> volume #5.1.1.2 level 0.4102
> volume #5.1.1.3 level 0.4928
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #5.2/a:291
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #5.2/a:291-299
130 atoms, 131 bonds, 9 residues, 1 model selected
> isolde sim start #5.2/a:291-299
ISOLDE: started sim
> isolde sim pause
> volume #5.1.1.2 level 0.6251
> volume #5.1.1.3 level 0.849
> volume #5.1.1.1 level 0.3285
> volume #5.1.1.2 level 0.2739
> volume #5.1.1.1 level 0.3416
> show #!1 models
> hide #!1 models
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 5 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #5.2/a:294
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.3 level 0.2271
> volume #5.1.1.3 level 0.2925
> volume #5.1.1.2 level 0.2578
> volume #5.1.1.1 level 0.2156
> isolde sim start #5.2/a:294-295
ISOLDE: started sim
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #!1 models
> isolde sim start #5.2/a:294-297
ISOLDE: started sim
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> select #5.2/a:278
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #5.2/a:278-298
327 atoms, 331 bonds, 21 residues, 1 model selected
> isolde sim start #5.2/a:321,323
ISOLDE: started sim
> isolde sim pause
> select clear
> isolde sim resume
> isolde sim pause
> hide #!1 models
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #5.1.1.2 level 0.5311
> volume #5.1.1.1 level 0.6949
> select up
137 atoms, 137 bonds, 10 residues, 2 models selected
> isolde sim start #5.2/a:324-333
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:322-337
ISOLDE: started sim
> show #!1 models
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #5.2/a:323
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:334
ISOLDE: started sim
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/a:335
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #5.2/a:335-343
167 atoms, 167 bonds, 9 residues, 1 model selected
> volume #5.1.1.1 level 0.3831
> hide #!1 models
> volume #5.1.1.2 level 0.2815
> isolde sim start #5.2/a:340
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:338-342
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #!1 models
> hide #!1 models
> select clear
> isolde sim start #5.2/a:341
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231004_Xt_14-3_deepemhancer_02.cxs
> select #5.2/a:341
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #5.2/a:341-348
128 atoms, 131 bonds, 8 residues, 1 model selected
> show #!1 models
> hide #!1 models
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Phenix/RealSpaceRefine_37/230822_Xt_14-3_6dimers-
> rotamercorrect_real_space_refined_037.pdb
Chain information for 230822_Xt_14-3_6dimers-
rotamercorrect_real_space_refined_037.pdb #2
---
Chain | Description
Z a b d f h | No description available
k l m n o p | No description available
> select add #2
80903 atoms, 81829 bonds, 30 pseudobonds, 5230 residues, 4 models selected
> select add #5
161796 atoms, 163656 bonds, 60 pseudobonds, 10452 residues, 33 models selected
> select add #5
161796 atoms, 163656 bonds, 60 pseudobonds, 10452 residues, 33 models selected
> select clear
> select add #2
80898 atoms, 81828 bonds, 30 pseudobonds, 5226 residues, 2 models selected
> style sel stick
Changed 80898 atom styles
> hide HC
> select subtract #2
Nothing selected
> isolde sim start #5.2/a:356
ISOLDE: started sim
> hide #!2 models
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.2 level 0.2204
> volume #5.1.1.3 level 0.3007
> isolde sim start #5.2/a:355-357
ISOLDE: started sim
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start #5.2/a:358
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:358
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:356-357
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:355
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #5.1.1.2 level 0.1251
> volume #5.1.1.3 level 0.1197
> volume #5.1.1.1 level 0.06903
> volume #5.1.1.2 level 0.1077
> volume #5.1.1.3 level 0.2051
> isolde sim start #5.2/a:356
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.2952
> select #5.2/a:341
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #5.2/a:341-351
177 atoms, 181 bonds, 11 residues, 1 model selected
> isolde sim start #5.2/a:341-351
ISOLDE: started sim
> isolde sim pause
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #5.2/a:345
ISOLDE: started sim
> volume #5.1.1.2 level 0.1337
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> hide #!1 models
> select #5.2/a:344
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #5.2/a:344-358
232 atoms, 237 bonds, 15 residues, 1 model selected
> volume #5.1.1.1 level 0.4666
> volume #5.1.1.2 level 0.37
> volume #5.1.1.3 level 0.3401
> volume #5.1.1.1 level 0.1627
> volume #5.1.1.2 level 0.209
> volume #5.1.1.3 level 0.269
> volume #5.1.1.1 level 0.06337
> isolde sim start #5.2/a:369
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #!1 models
> select #5.2/a:369
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #5.2/a:369-374
105 atoms, 104 bonds, 6 residues, 1 model selected
> clipper isolate #5.2/a:369-374 maskRadius 4.0 focus false
> hide #!1 models
> isolde sim start #5.2/a:369-374
ISOLDE: started sim
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/a:374
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #5.2/a:374-384
155 atoms, 154 bonds, 11 residues, 1 model selected
> clipper isolate #5.2/a:374-384 maskRadius 4.0 focus false
> volume #5.1.1.1 level 0.206
> volume #5.1.1.2 level 0.3262
> volume #5.1.1.3 level 0.3816
> isolde sim start #5.2/a:377
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:380
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select up
705 atoms, 704 bonds, 49 residues, 2 models selected
> select up
748 atoms, 748 bonds, 49 residues, 2 models selected
> select up
2033 atoms, 2047 bonds, 130 residues, 2 models selected
> select up
6767 atoms, 6844 bonds, 438 residues, 2 models selected
> isolde sim start #5.2/a:369
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:272-274
ISOLDE: started sim
> show #!1 models
> hide #!1 models
> show #!2 models
> isolde cisflip #5.2/a:273
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> hide #!2 models
> isolde sim start #5.2/a:273
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde sim start #5.2/a:233
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:233
ISOLDE: started sim
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/a:248
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #5.2/a:248-249
30 atoms, 29 bonds, 2 residues, 1 model selected
> select #5.2/a:255
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #5.2/a:255
17 atoms, 16 bonds, 1 residue, 1 model selected
> volume #5.1.1.1 level 0.4832
> volume #5.1.1.2 level 0.4221
> close #5.1.1.1
> close #5.1.1.3
> volume #5.1.1.2 level 0.3603
> select up
1510 atoms, 1509 bonds, 99 residues, 2 models selected
> select up
1585 atoms, 1586 bonds, 99 residues, 2 models selected
> select up
2558 atoms, 2582 bonds, 161 residues, 2 models selected
> select up
6767 atoms, 6844 bonds, 438 residues, 2 models selected
> isolde sim start #5.2/a:264-266
ISOLDE: started sim
> show #!1 models
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> hide #!1 models
> save
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231004_Xt_14-3_deepemhancer_alphadone_01.cxs
Taking snapshot of stepper: 230822_Xt_14-3_6dimers-
rotamercorrect_real_space_refined_037.pdb
> select #5.2/a:226-227
33 atoms, 32 bonds, 2 residues, 1 model selected
> select #5.2/a:226-239
219 atoms, 218 bonds, 14 residues, 1 model selected
> select #5.2/a:213
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #5.2/a:213-225
218 atoms, 219 bonds, 13 residues, 1 model selected
> select #5.2/a:208
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #5.2/a:208-221
237 atoms, 238 bonds, 14 residues, 1 model selected
> volume #5.1.1.2 level 0.1679
> show #!1 models
> isolde sim start #5.2/a:281-282
ISOLDE: started sim
> isolde sim pause
> volume #5.1.1.2 level 0.171
> volume #5.1.1.2 level 0.1742
> volume #5.1.1.2 level 0.1789
> volume #5.1.1.2 level 0.1899
> volume #5.1.1.2 level 0.1978
> volume #5.1.1.2 level 0.2057
> volume #5.1.1.2 level 0.2167
> volume #5.1.1.2 level 0.2277
> volume #5.1.1.2 level 0.2419
> volume #5.1.1.2 level 0.2529
> volume #5.1.1.2 level 0.2703
> volume #5.1.1.2 level 0.2797
> volume #5.1.1.2 level 0.2939
> volume #5.1.1.2 level 0.2955
> volume #5.1.1.2 level 0.3333
> volume #5.1.1.2 level 0.3459
> volume #5.1.1.2 level 0.3506
> volume #5.1.1.2 level 0.3538
> volume #5.1.1.2 level 0.3569
> volume #5.1.1.2 level 0.3632
> volume #5.1.1.2 level 0.3679
> volume #5.1.1.2 level 0.3664
> volume #5.1.1.2 level 0.3553
> volume #5.1.1.2 level 0.3412
> volume #5.1.1.2 level 0.3238
> volume #5.1.1.2 level 0.3112
> volume #5.1.1.2 level 0.2955
> volume #5.1.1.2 level 0.2829
> volume #5.1.1.2 level 0.2766
> volume #5.1.1.2 level 0.275
> volume #5.1.1.2 level 0.2687
> volume #5.1.1.2 level 0.2498
> volume #5.1.1.2 level 0.2482
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231004_Xt_14-3_deepemhancer_alphadone_01.cxs
Taking snapshot of stepper: 230822_Xt_14-3_6dimers-
rotamercorrect_real_space_refined_037.pdb
> isolde sim start #5.2/a:369
ISOLDE: started sim
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> open
> /d/emr214/u/tl002/Xtropicalis_2209/deepemhancer/deepemhancer_withmask/Xt_14-3_refine13_deepemhancer_wmask.mrc
Opened Xt_14-3_refine13_deepemhancer_wmask.mrc as #3, grid size 416,416,416,
pixel 1.07, shown at level 0.000126, step 2, values float32
> volume #3 step 1
> volume #3 level 0.422
> volume #3 level 0.3074
> close #3
> hide #!1 models
> volume #5.1.1.2 level 0.1694
> volume #5.1.1.2 level 0.1301
> save
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231004_Xt_14-3_deepemhancer_alphadone_01.cxs
Taking snapshot of stepper: 230822_Xt_14-3_6dimers-
rotamercorrect_real_space_refined_037.pdb
——— End of log from Wed Oct 4 16:55:46 2023 ———
opened ChimeraX session
> open
> /d/emr214/u/tl002/Xtropicalis_2209/deepemhancer/refine10-repeat/Xt_14-3_refine10repeated_deepemhancer.mrc
Opened Xt_14-3_refine10repeated_deepemhancer.mrc as #3, grid size 416,416,416,
pixel 1.07, shown at level 0.085, step 2, values float32
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> open
> /d/emr214/u/tl002/Xtropicalis_2209/deepemhancer/refine10-repeat/Xt_14-3_refine10repeated_deepemhancer.mrc
Opened Xt_14-3_refine10repeated_deepemhancer.mrc as #4, grid size 416,416,416,
pixel 1.07, shown at level 0.085, step 2, values float32
> molmap #2 4
Opened 230822_Xt_14-3_6dimers-rotamercorrect_real_space_refined_037.pdb map 4
as #6, grid size 115,129,166, pixel 1.33, shown at level 0.121, step 1, values
float32
> ui tool show "Fit in Map"
> hide #!3 models
> hide #!4 models
> show #!4 models
> show #!3 models
> ui tool show "Fit in Map"
> fitmap #3 inMap #6
Fit map Xt_14-3_refine10repeated_deepemhancer.mrc in map
230822_Xt_14-3_6dimers-rotamercorrect_real_space_refined_037.pdb map 4 using
89984 points
correlation = 0.5917, correlation about mean = 0.3404, overlap = 5955
steps = 56, shift = 0.177, angle = 0.456 degrees
Position of Xt_14-3_refine10repeated_deepemhancer.mrc (#3) relative to
230822_Xt_14-3_6dimers-rotamercorrect_real_space_refined_037.pdb map 4 (#6)
coordinates:
Matrix rotation and translation
0.99999240 -0.00246245 0.00302262 -0.16118518
0.00244144 0.99997297 0.00693489 -1.63728380
-0.00303961 -0.00692746 0.99997139 1.49451060
Axis -0.87158139 0.38115635 0.30832727
Axis point 0.00000000 215.77734120 235.68264366
Rotation angle (degrees) 0.45564467
Shift along axis -0.02277674
> hide #!2 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> select add #3
1 atom, 1 residue, 5 models selected
> select subtract #3
1 atom, 1 residue, 1 model selected
> select clear
> select #3
4 models selected
> transparency #3.1 40
> volume #4 step 1
> volume #3 step 1
> select clear
> ui tool show ISOLDE
> set selectionWidth 4
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> clipper associate #3 toModel #5
Opened Xt_14-3_refine10repeated_deepemhancer.mrc as #5.1.1.1, grid size
416,416,416, pixel 1.07, shown at step 1, values float32
> select clear
> hide #!5 models
> show #!4 models
> open
> /d/emr214/u/tl002/Xtropicalis_2209/deepemhancer/refine10/Xt_14-3_refine10_deepemhancer.mrc
Opened Xt_14-3_refine10_deepemhancer.mrc as #3, grid size 416,416,416, pixel
1.07, shown at level 0.0722, step 2, values float32
> ui tool show "Fit in Map"
> fitmap #4 inMap #6
Fit map Xt_14-3_refine10repeated_deepemhancer.mrc in map
230822_Xt_14-3_6dimers-rotamercorrect_real_space_refined_037.pdb map 4 using
719343 points
correlation = 0.5913, correlation about mean = 0.3402, overlap = 4.756e+04
steps = 56, shift = 0.165, angle = 0.459 degrees
Position of Xt_14-3_refine10repeated_deepemhancer.mrc (#4) relative to
230822_Xt_14-3_6dimers-rotamercorrect_real_space_refined_037.pdb map 4 (#6)
coordinates:
Matrix rotation and translation
0.99999268 -0.00238734 0.00299075 -0.17286791
0.00236625 0.99997246 0.00703433 -1.64709116
-0.00300746 -0.00702720 0.99997079 1.52006051
Axis -0.87832825 0.37466710 0.29692430
Axis point 0.00000000 215.92588960 234.25375500
Rotation angle (degrees) 0.45864102
Shift along axis -0.01393320
> volume #3 step 1
> show #!6 models
> hide #!6 models
> fitmap #3 inMap #6
Fit map Xt_14-3_refine10_deepemhancer.mrc in map 230822_Xt_14-3_6dimers-
rotamercorrect_real_space_refined_037.pdb map 4 using 717846 points
correlation = 0.5928, correlation about mean = 0.3429, overlap = 3.994e+04
steps = 52, shift = 0.115, angle = 0.485 degrees
Position of Xt_14-3_refine10_deepemhancer.mrc (#3) relative to
230822_Xt_14-3_6dimers-rotamercorrect_real_space_refined_037.pdb map 4 (#6)
coordinates:
Matrix rotation and translation
0.99998791 -0.00439662 0.00220409 0.35274140
0.00438131 0.99996659 0.00690145 -1.92231492
-0.00223436 -0.00689171 0.99997376 1.44016762
Axis -0.81418005 0.26199218 0.51814182
Axis point 0.00000000 211.26713826 277.86690401
Rotation angle (degrees) 0.48533464
Shift along axis -0.04461543
> volume #3 level 0.1073
> volume #4 level 0.1273
> lighting soft
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.1302
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> show #!5 models
> hide #!3 models
> hide #!4 models
> close #3-4
> close #6
> volume #5.1.1.2 level 0.183
> volume #5.1.1.1 level 0.1436
> select #5.2/l:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #5.2/l:1-11
180 atoms, 180 bonds, 11 residues, 1 model selected
> clipper isolate #5.2/l:1-11 maskRadius 4.0 focus false
> lighting full
[Repeated 1 time(s)]
> lighting flat
> lighting full
> select #5.2/a:279
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #5.2/a:279-287
148 atoms, 149 bonds, 9 residues, 1 model selected
> clipper isolate #5.2/a:279-287 maskRadius 4.0 focus false
> show #!1 models
> volume #5.1.1.1 level 0.1701
> graphics silhouettes false
> isolde sim start #5.2/a:279-287
ISOLDE: started sim
> hide #!1 models
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:281-282
ISOLDE: started sim
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/a:285
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #5.2/a:285-295
163 atoms, 164 bonds, 11 residues, 1 model selected
> select #5.2/a:283
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #5.2/a:283-291
140 atoms, 140 bonds, 9 residues, 1 model selected
> isolde sim start #5.2/a:283-291
ISOLDE: started sim
> volume #5.1.1.1 level 0.3249
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #5.2/l:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #5.2/l:1-12
191 atoms, 191 bonds, 12 residues, 1 model selected
> clipper isolate #5.2/l:1-12 maskRadius 4.0 focus false
> isolde sim start #5.2/l:7
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> lighting shadows false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> isolde sim start #5.2/l:17-20
ISOLDE: started sim
> volume #5.1.1.1 level 0.2347
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/l:20
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #5.2/l:20-29
156 atoms, 159 bonds, 10 residues, 1 model selected
> isolde sim start #5.2/l:24
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.3242
> isolde sim start #5.2/l:28-31
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.2491
> isolde sim start #5.2/l:31
ISOLDE: started sim
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #!1 models
> hide #!1 models
> volume #5.1.1.1 level 0.2563
> show #!1 models
> hide #!1 models
> isolde sim start #5.2/l:31-35
ISOLDE: started sim
> isolde cisflip #5.2/l:32
[Repeated 1 time(s)]
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde cisflip #5.2/l:32
[Repeated 1 time(s)]
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:31-35
ISOLDE: started sim
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #!1 models
> hide #!1 models
> volume #5.1.1.1 level 0.06023
> volume #5.1.1.1 level 0.01654
> isolde sim start #5.2/l:38-40
ISOLDE: started sim
> isolde sim pause
> volume #5.1.1.1 level 0.06996
> volume #5.1.1.2 level 0.01354
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> isolde sim resume
> isolde sim pause
> volume #5.1.1.1 level 0.01221
> volume #5.1.1.1 level 0.02953
> isolde sim resume
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #5.2/l:37
ISOLDE: started sim
> isolde sim pause
> show #!1 models
> hide #!1 models
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:41
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/l:40
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5.2/l:40-47
136 atoms, 135 bonds, 8 residues, 1 model selected
> select #5.2/l:39
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #5.2/l:39-43
71 atoms, 70 bonds, 5 residues, 1 model selected
> isolde sim start #5.2/l:39-43
ISOLDE: started sim
> volume #5.1.1.1 level 0.06419
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:46
ISOLDE: started sim
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/l:46
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #5.2/l:46-52
129 atoms, 130 bonds, 7 residues, 1 model selected
> volume #5.1.1.1 level 0.192
> isolde sim start #5.2/l:55-57
ISOLDE: started sim
> show #!1 models
> hide #!1 models
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #!1 models
> hide #!1 models
> isolde sim start #5.2/l:54-58
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> volume #5.1.1.2 level 0.1252
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/l:58
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #5.2/l:58-63
107 atoms, 108 bonds, 6 residues, 1 model selected
> isolde sim start #5.2/l:62
ISOLDE: started sim
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start #5.2/l:69,71-72
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.2442
> volume #5.1.1.1 level 0.2055
> volume #5.1.1.2 level 0.1494
> volume #5.1.1.1 level 0.1122
> isolde sim start #5.2/l:77
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:79-81
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:84
ISOLDE: started sim
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.336
> isolde sim start #5.2/l:86
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:86/n:281
ISOLDE: started sim
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/l:88
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #5.2/l:88-93
89 atoms, 90 bonds, 6 residues, 1 model selected
> isolde sim start #5.2/l:95
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #5.2/l:105
ISOLDE: started sim
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:107-108
ISOLDE: started sim
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/l:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5.2/l:109-121
193 atoms, 192 bonds, 13 residues, 1 model selected
> isolde sim start #5.2/l:125-129
ISOLDE: started sim
> volume #5.1.1.1 level 0.1988
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> show #!1 models
> hide #!1 models
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #5.2/l:129
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5.2/l:129-134
91 atoms, 91 bonds, 6 residues, 1 model selected
> isolde sim start #5.2/l:129-134
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #5.2/l:129-134,144-146
ISOLDE: started sim
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #5.2/l:129-134,142-146
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:129-134,139-146
ISOLDE: started sim
> show #!1 models
> hide #!1 models
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:172-174
ISOLDE: started sim
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.3729
> isolde sim start #5.2/l:172-176
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> volume #5.1.1.1 level 0.152
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.3985
> isolde sim start #5.2/l:191,193
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #5.2/l:194
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #5.2/l:194-204
161 atoms, 161 bonds, 11 residues, 1 model selected
> isolde sim start #5.2/l:199
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:199
ISOLDE: started sim
> isolde sim pause
> select #5.2/l:199
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #5.2/l:199-206
116 atoms, 116 bonds, 8 residues, 1 model selected
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.2804
> select #5.2/l:205
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #5.2/l:205-214
165 atoms, 166 bonds, 10 residues, 1 model selected
> isolde sim start #5.2/l:205-214
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> volume #5.1.1.1 level 0.2234
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde sim start #5.2/l:211-219
ISOLDE: started sim
> select #5.2/l:211
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5.2/l:211-215
88 atoms, 88 bonds, 5 residues, 1 model selected
> isolde sim resume
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:211-215
ISOLDE: started sim
> volume #5.1.1.1 level 0.03169
> select clear
> volume #5.1.1.1 level 0.1722
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:216-220
ISOLDE: started sim
> isolde sim pause
> volume #5.1.1.1 level 0.1283
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> select #5.2/l:219
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #5.2/l:219-227
132 atoms, 134 bonds, 9 residues, 1 model selected
> select clear
[Repeated 2 time(s)]
> select #5.2/l:221
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #5.2/l:221-224
54 atoms, 54 bonds, 4 residues, 1 model selected
> isolde sim start #5.2/l:221-224
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:221-224
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.1524
> isolde sim start #5.2/l:221-224
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:221
ISOLDE: started sim
> isolde pepflip #5.2/l:221
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #5.1.1.1 level 0.1043
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.1754
> isolde sim start #5.2/l:219
ISOLDE: started sim
> volume #5.1.1.1 level 0.289
> isolde sim pause
> volume #5.1.1.1 level 0.1274
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:220-222
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.3242
> select clear
> isolde sim start #5.2/l:233
ISOLDE: started sim
> isolde sim pause
> volume #5.1.1.1 level 0.1553
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.3261
> save
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_deepemhancer_beta_01.cxs
Taking snapshot of stepper: 230822_Xt_14-3_6dimers-
rotamercorrect_real_space_refined_037.pdb
> isolde sim start #5.2/l:238
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.2721
> isolde sim start #5.2/l:242
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/l:242-243
34 atoms, 35 bonds, 2 residues, 1 model selected
> select #5.2/l:242-248
101 atoms, 102 bonds, 7 residues, 1 model selected
> isolde sim start #5.2/l:249
ISOLDE: started sim
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/l:250
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #5.2/l:250-255
110 atoms, 109 bonds, 6 residues, 1 model selected
> select #5.2/l:256
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #5.2/l:256-339
1334 atoms, 1349 bonds, 84 residues, 1 model selected
> isolde sim start #5.2/l:258-259
ISOLDE: started sim
> isolde sim pause
> show #!1 models
> isolde sim resume
> hide #!1 models
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:259
ISOLDE: started sim
> isolde pepflip #5.2/l:258
[Repeated 1 time(s)]
> isolde pepflip #5.2/l:259
[Repeated 1 time(s)]Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip #5.2/l:259
[Repeated 1 time(s)]
> isolde pepflip #5.2/l:260
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip #5.2/l:260
[Repeated 1 time(s)]
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:258-261
ISOLDE: started sim
> isolde pepflip #5.2/l:260
> isolde pepflip #5.2/l:261
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #5.2/l:263
ISOLDE: started sim
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/l:264
18 atoms, 18 bonds, 1 residue, 1 model selected
> select #5.2/l:264-269
96 atoms, 99 bonds, 6 residues, 1 model selected
> isolde sim start #5.2/l:271-273
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde pepflip #5.2/l:271
[Repeated 1 time(s)]
> isolde pepflip #5.2/l:272
[Repeated 1 time(s)]
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #!1 models
> hide #!1 models
> isolde sim start #5.2/l:271
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:270-277
ISOLDE: started sim
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:269-273
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde pepflip #5.2/l:271
> isolde sim resume
> isolde pepflip #5.2/l:271
> isolde sim pause
> isolde pepflip #5.2/l:270
> isolde pepflip #5.2/l:268
Peptide bond must be mobile in the simulation!
> isolde sim resume
> isolde pepflip #5.2/l:269
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:271-272
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/l:273
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #5.2/l:273-278
86 atoms, 85 bonds, 6 residues, 1 model selected
> volume #5.1.1.1 level 0.2324
> select clear
> isolde sim start #5.2/l:272
ISOLDE: started sim
> isolde cisflip #5.2/l:272
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:271-273
ISOLDE: started sim
> isolde cisflip #5.2/l:272
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:271
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.1617
> isolde sim start #5.2/l:275-278
ISOLDE: started sim
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #!1 models
> isolde sim start #5.2/l:273-279
ISOLDE: started sim
> hide #!1 models
> select clear
> isolde sim pause
> isolde sim resume
> isolde pepflip #5.2/l:277
> isolde sim pause
> show #!1 models
> hide #!1 models
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #5.2/l:271-273
ISOLDE: started sim
> isolde cisflip #5.2/l:272
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:281-285
ISOLDE: started sim
> isolde sim pause
> show #!1 models
> isolde sim resume
> select clear
> hide #!1 models
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.3552
> isolde sim start #5.2/l:297-299
ISOLDE: started sim
> isolde sim pause
> volume #5.1.1.1 level 0.03994
> isolde sim resume
> isolde sim pause
> volume #5.1.1.1 level 0.2372
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/l:307
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #5.2/l:307-314
128 atoms, 129 bonds, 8 residues, 1 model selected
> volume #5.1.1.1 level 0.4308
> show #!1 models
> isolde sim start #5.2/l:322-323
ISOLDE: started sim
> hide #!1 models
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/l:323-324
39 atoms, 38 bonds, 2 residues, 1 model selected
> select #5.2/l:323-328
97 atoms, 96 bonds, 6 residues, 1 model selected
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #5.1.1.1 level 0.3088
> select #5.2/l:324
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #5.2/l:324-339
252 atoms, 251 bonds, 16 residues, 1 model selected
> select #5.2/l:323
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #5.2/l:323-339
269 atoms, 268 bonds, 17 residues, 1 model selected
> isolde sim start #5.2/l:323-339
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #5.2/l:339
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5.2/l:339-349
184 atoms, 188 bonds, 11 residues, 1 model selected
> select #5.2/l:348
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #5.2/l:348-356
134 atoms, 133 bonds, 9 residues, 1 model selected
> isolde sim start #5.2/l:356
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.2591
> show #!1 models
> select clear
> isolde sim start #5.2/l:360-361
ISOLDE: started sim
> hide #!1 models
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.3744
> isolde sim start #5.2/l:364
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> volume #5.1.1.1 level 0.08362
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.2073
> isolde sim start #5.2/l:284,363
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde sim start #5.2/l:292
ISOLDE: started sim
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:321
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde sim start #5.2/l:321
ISOLDE: started sim
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/l:348
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #5.2/l:348-356
134 atoms, 133 bonds, 9 residues, 1 model selected
> isolde sim start #5.2/l:353
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:351-353
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #5.2/l:355
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #5.2/l:355-357
45 atoms, 45 bonds, 3 residues, 1 model selected
> select #5.2/l:352
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #5.2/l:352-360
127 atoms, 128 bonds, 9 residues, 1 model selected
> isolde sim start #5.2/l:352-360
ISOLDE: started sim
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.2188
> volume #5.1.1.1 level 0.1459
> isolde sim start #5.2/l:376
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:380
ISOLDE: started sim
> volume #5.1.1.1 level 0.08303
> isolde sim pause
> volume #5.1.1.1 level 0.1276
> isolde sim resume
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:391
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.257
> volume #5.1.1.1 level 0.05166
> isolde sim start #5.2/l:426-429
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:425
ISOLDE: started sim
> isolde sim pause
> volume #5.1.1.1 level 0.2179
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select up
3232 atoms, 3240 bonds, 215 residues, 2 models selected
> select up
3314 atoms, 3326 bonds, 215 residues, 2 models selected
> select up
5791 atoms, 5850 bonds, 374 residues, 2 models selected
> select up
13398 atoms, 13550 bonds, 868 residues, 2 models selected
> ui tool show "Ramachandran Plot"
> isolde sim start #5.2/a:402
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:401-404
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #!1 models
> hide #!1 models
> isolde sim start #5.2/a:401-404
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:402
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.1237
> isolde sim start #5.2/a:402-404/l:260
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/a:402
ISOLDE: started sim
> isolde pepflip #5.2/a:401
[Repeated 1 time(s)]
> isolde pepflip #5.2/a:402
[Repeated 1 time(s)]
> isolde sim pause
> volume #5.1.1.1 level 0.2988
> show #!1 models
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #5.2/l:259
ISOLDE: started sim
> isolde pepflip #5.2/l:260
> isolde sim pause
> isolde sim resume
> isolde pepflip #5.2/a:402
[Repeated 1 time(s)]
> isolde pepflip #5.2/a:403
> isolde sim pause
> hide #!1 models
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #5.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select up
1834 atoms, 1831 bonds, 122 residues, 1 model selected
> select up
1849 atoms, 1847 bonds, 122 residues, 1 model selected
> select up
4301 atoms, 4334 bonds, 277 residues, 2 models selected
> select up
13398 atoms, 13550 bonds, 868 residues, 2 models selected
> isolde sim start #5.2/a:369
ISOLDE: started sim
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select up
3327 atoms, 3348 bonds, 218 residues, 2 models selected
> select up
13398 atoms, 13550 bonds, 868 residues, 2 models selected
> isolde sim start #5.2/l:221
ISOLDE: started sim
> volume #5.1.1.1 level 0.1148
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #5.2/l:221
ISOLDE: started sim
> isolde pepflip #5.2/l:222
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #5.1.1.1 level 0.2524
> select up
2102 atoms, 2109 bonds, 136 residues, 2 models selected
> select up
3975 atoms, 4014 bonds, 257 residues, 2 models selected
> select up
13398 atoms, 13550 bonds, 868 residues, 2 models selected
> select up
80898 atoms, 81828 bonds, 5226 residues, 2 models selected
> select down
13398 atoms, 13550 bonds, 868 residues, 2 models selected
> save
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_deepemhancer_complete_01.cxs
Taking snapshot of stepper: 230822_Xt_14-3_6dimers-
rotamercorrect_real_space_refined_037.pdb
> isolde sim start #5.2/l,a
ISOLDE: started sim
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select up
4482 atoms, 4521 bonds, 296 residues, 1 model selected
> select up
13398 atoms, 13550 bonds, 868 residues, 2 models selected
> select up
80898 atoms, 81828 bonds, 5226 residues, 2 models selected
> select down
13398 atoms, 13550 bonds, 868 residues, 2 models selected
> save
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_deepemhancer_complete_01.pdb
> models #5 relModel #5.1.1.1
> select up
2000 atoms, 2020 bonds, 129 residues, 1 model selected
> select up
6767 atoms, 6844 bonds, 438 residues, 1 model selected
> select up
80898 atoms, 81828 bonds, 5226 residues, 2 models selected
> select down
6767 atoms, 6844 bonds, 438 residues, 2 models selected
> isolde sim start #5.2/a
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_deepemhancer_complete_01.cxs
Taking snapshot of stepper: 230822_Xt_14-3_6dimers-
rotamercorrect_real_space_refined_037.pdb
> close session
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_deepemhancer_complete_01.pdb
Chain information for 231009_Xt_14-3_deepemhancer_complete_01.pdb #1
---
Chain | Description
Z a b d f h | No description available
k l m n o p | No description available
> open
> /d/emr214/u/tl002/Xtropicalis_2209/deepemhancer/refine10-repeat/Xt_14-3_refine10repeated_deepemhancer.mrc
Opened Xt_14-3_refine10repeated_deepemhancer.mrc as #2, grid size 416,416,416,
pixel 1.07, shown at level 0.085, step 2, values float32
> ui tool show "Model Panel"
> hide #!2 models
> select add #1
80898 atoms, 81828 bonds, 30 pseudobonds, 5226 residues, 2 models selected
> style sel stick
Changed 80898 atom styles
> hide sel atoms
> show sel cartoons
> select clear
> select up
51831 atoms, 52389 bonds, 3350 residues, 1 model selected
> select up
66990 atoms, 67750 bonds, 4340 residues, 1 model selected
> select up
80898 atoms, 81828 bonds, 5226 residues, 1 model selected
> select down
66990 atoms, 67750 bonds, 4340 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> style stick
Changed 13908 atom styles
> select add #1
13908 atoms, 14078 bonds, 5 pseudobonds, 886 residues, 2 models selected
> style sel stick
Changed 13908 atom styles
> show sel atoms
> select clear
> select up
421 atoms, 436 bonds, 15 residues, 1 model selected
> select up
425 atoms, 440 bonds, 15 residues, 1 model selected
> select up
13908 atoms, 14078 bonds, 886 residues, 1 model selected
> select down
425 atoms, 440 bonds, 15 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer.pdb
> relModel #2
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer.pdb #3
---
Chain | Description
a | No description available
l | No description available
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer.pdb #4
---
Chain | Description
a | No description available
l | No description available
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer.pdb #5
---
Chain | Description
a | No description available
l | No description available
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer.pdb #6
---
Chain | Description
a | No description available
l | No description available
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer.pdb #7
---
Chain | Description
a | No description available
l | No description available
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer.pdb #8
---
Chain | Description
a | No description available
l | No description available
> show #!2 models
> select add #3
13483 atoms, 13638 bonds, 5 pseudobonds, 871 residues, 2 models selected
> ui mousemode right "translate selected models"
> select subtract #3
Nothing selected
> close #4-8
> hide #!1 models
> hide #!2 models
> close #1
> rename #3/l #3/B
No name or id option specified for renaming
> rename #3/l B
> select up
263 atoms, 265 bonds, 18 residues, 1 model selected
> select up
6631 atoms, 6706 bonds, 430 residues, 1 model selected
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain /a
Alignment identifier is 3/a
> alter #3/l "B"
Unknown command: alter #3/l "B"
> changechains #3/l #3/B
Missing or invalid "fromIds" argument: Expected a text string
> changechains #3/l B
Chain IDs of 430 residues changed
> changechains #3/F u
Chain IDs of 1 residues changed
> changechains #3/u n
Chain IDs of 1 residues changed
> changechains #3/n nt
Chain IDs of 1 residues changed
> changechains #3/X Nt
Chain IDs of 1 residues changed
> save
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb
> relModel #2
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #1
---
Chain | Description
B | No description available
a | No description available
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #4
---
Chain | Description
B | No description available
a | No description available
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #5
---
Chain | Description
B | No description available
a | No description available
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #6
---
Chain | Description
B | No description available
a | No description available
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #7
---
Chain | Description
B | No description available
a | No description available
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #8
---
Chain | Description
B | No description available
a | No description available
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #9
---
Chain | Description
B | No description available
a | No description available
> select add #4
13485 atoms, 13639 bonds, 5 pseudobonds, 872 residues, 3 models selected
> ui mousemode right "translate selected models"
> select add #2
13485 atoms, 13639 bonds, 5 pseudobonds, 872 residues, 5 models selected
> select subtract #2
13485 atoms, 13639 bonds, 5 pseudobonds, 872 residues, 3 models selected
> show #!2 models
> select add #3
26966 atoms, 27276 bonds, 10 pseudobonds, 1742 residues, 4 models selected
> select subtract #3
13483 atoms, 13638 bonds, 5 pseudobonds, 871 residues, 2 models selected
> view matrix models #4,1,0,0,-22.579,0,1,0,47.444,0,0,1,-71.264
> view matrix models #4,1,0,0,-21.42,0,1,0,49.646,0,0,1,-75.879
> view matrix models #4,1,0,0,-19.525,0,1,0,46.307,0,0,1,-69.977
> select add #5
26966 atoms, 27276 bonds, 10 pseudobonds, 1742 residues, 4 models selected
> view matrix models
> #4,1,0,0,-20.325,0,1,0,47.211,0,0,1,-73.546,#5,1,0,0,-0.80011,0,1,0,0.9043,0,0,1,-3.5689
> select subtract #4
13483 atoms, 13638 bonds, 5 pseudobonds, 871 residues, 2 models selected
> view matrix models #5,1,0,0,-0.31573,0,1,0,-4.9415,0,0,1,-79.536
> select add #6
26966 atoms, 27276 bonds, 10 pseudobonds, 1742 residues, 4 models selected
> select subtract #5
13483 atoms, 13638 bonds, 5 pseudobonds, 871 residues, 2 models selected
> select add #9
26966 atoms, 27276 bonds, 10 pseudobonds, 1742 residues, 4 models selected
> view matrix models
> #6,1,0,0,27.558,0,1,0,-40.023,0,0,1,-7.967,#9,1,0,0,27.558,0,1,0,-40.023,0,0,1,-7.967
> view matrix models
> #6,1,0,0,33.949,0,1,0,-32.175,0,0,1,-4.2184,#9,1,0,0,33.949,0,1,0,-32.175,0,0,1,-4.2184
> select subtract #9
13483 atoms, 13638 bonds, 5 pseudobonds, 871 residues, 2 models selected
> view matrix models #6,1,0,0,37.94,0,1,0,-32.997,0,0,1,-91.497
> select add #8
26966 atoms, 27276 bonds, 10 pseudobonds, 1742 residues, 4 models selected
> select subtract #6
13483 atoms, 13638 bonds, 5 pseudobonds, 871 residues, 2 models selected
> view matrix models #8,1,0,0,-10.621,0,1,0,51.961,0,0,1,8.8295
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.91279,0.40204,-0.071999,-45.995,-0.40497,0.91378,-0.031653,124.06,0.053066,0.05805,0.9969,-6.2759
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.91279,0.40204,-0.071999,-53.237,-0.40497,0.91378,-0.031653,120.3,0.053066,0.05805,0.9969,-4.4944
> ui tool show "Fit in Map"
> fitmap #4 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#4) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.1827, steps = 132
shifted from previous position = 1.17
rotated from previous position = 24.6 degrees
atoms outside contour = 5510, contour level = 0.085003
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#4) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90927753 0.41617495 -0.00357668 -71.42299439
-0.41618618 0.90927322 -0.00335753 113.23103296
0.00185486 0.00454149 0.99998797 -74.03085494
Axis 0.00948927 -0.00652502 -0.99993369
Axis point 224.75324293 222.26752299 0.00000000
Rotation angle (degrees) 24.59542336
Shift along axis 72.60935880
> fitmap #5 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#5) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.2277, steps = 56
shifted from previous position = 3.52
rotated from previous position = 0.507 degrees
atoms outside contour = 4746, contour level = 0.085003
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#5) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.99996277 -0.00802522 -0.00317206 2.96060465
0.00801892 0.99996586 -0.00199420 -2.61563942
0.00318795 0.00196869 0.99999298 -81.73309330
Axis 0.22379300 -0.35916296 0.90604562
Axis point 3581.36700243 2372.70633756 0.00000000
Rotation angle (degrees) 0.50729967
Shift along axis -72.45190761
> fitmap #6 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#6) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.1108, steps = 92
shifted from previous position = 1.14
rotated from previous position = 3.78 degrees
atoms outside contour = 8219, contour level = 0.085003
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#6) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.99791113 -0.06374892 0.01046185 45.16738554
0.06360179 0.99787938 0.01384046 -43.38054481
-0.01132198 -0.01314616 0.99984948 -89.04244874
Axis -0.20446162 0.16504314 0.96486072
Axis point 428.79513309 366.33696669 0.00000000
Rotation angle (degrees) 3.78394760
Shift along axis -102.30821912
> fitmap #7 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#7) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.2314, steps = 48
shifted from previous position = 0.167
rotated from previous position = 0.232 degrees
atoms outside contour = 4690, contour level = 0.085003
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#7) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.99999618 -0.00096541 -0.00258957 0.66695892
0.00095773 0.99999514 -0.00296639 0.39202863
0.00259242 0.00296390 0.99999225 -0.76327765
Axis 0.73152263 -0.63921682 0.23722668
Axis point 0.00000000 262.40231940 143.84493388
Rotation angle (degrees) 0.23224239
Shift along axis 0.05623443
> fitmap #8 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#8) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.1816, steps = 60
shifted from previous position = 3.11
rotated from previous position = 4.32 degrees
atoms outside contour = 5511, contour level = 0.085003
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#8) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90624613 0.42272074 -0.00501242 -72.38351885
-0.42274008 0.90624326 -0.00373880 116.59850087
0.00296200 0.00550722 0.99998045 6.67842804
Axis 0.01093493 -0.00943105 -0.99989574
Axis point 226.55366002 221.25742026 0.00000000
Rotation angle (degrees) 25.00987709
Shift along axis -8.56888720
> fitmap #9 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#9) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.1189, steps = 188
shifted from previous position = 8.22
rotated from previous position = 25.9 degrees
atoms outside contour = 7855, contour level = 0.085003
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#9) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.89984896 -0.43619330 0.00269247 120.11233580
0.43598998 0.89920299 -0.03669757 -65.11344719
0.01358615 0.03419616 0.99932279 -10.04069920
Axis 0.08100959 -0.01244811 0.99663559
Axis point 202.23491524 228.83214774 0.00000000
Rotation angle (degrees) 25.94854419
Shift along axis 0.53387244
> select subtract #8
Nothing selected
> select add #2
4 models selected
> select subtract #2
Nothing selected
> select add #2
4 models selected
> transparency #2.1 40
> volume #2 step 1
> select clear
> volume #2 level 0.228
> select add #6
13483 atoms, 13638 bonds, 5 pseudobonds, 871 residues, 2 models selected
> view matrix models
> #6,0.99791,-0.063749,0.010462,48.895,0.063602,0.99788,0.01384,-48.589,-0.011322,-0.013146,0.99985,-91.152
> view matrix models
> #6,0.99791,-0.063749,0.010462,52.705,0.063602,0.99788,0.01384,-45.701,-0.011322,-0.013146,0.99985,-90.668
> select add #9
26966 atoms, 27276 bonds, 10 pseudobonds, 1742 residues, 4 models selected
> view matrix models
> #6,0.99791,-0.063749,0.010462,55.14,0.063602,0.99788,0.01384,-43.771,-0.011322,-0.013146,0.99985,-89.551,#9,0.89985,-0.43619,0.0026925,122.55,0.43599,0.8992,-0.036698,-63.184,0.013586,0.034196,0.99932,-8.9237
> view matrix models
> #6,0.99791,-0.063749,0.010462,53.257,0.063602,0.99788,0.01384,-45.588,-0.011322,-0.013146,0.99985,-93.547,#9,0.89985,-0.43619,0.0026925,120.66,0.43599,0.8992,-0.036698,-65,0.013586,0.034196,0.99932,-12.92
> select subtract #6
13483 atoms, 13638 bonds, 5 pseudobonds, 871 residues, 2 models selected
> view matrix models
> #9,0.89985,-0.43619,0.0026925,118.48,0.43599,0.8992,-0.036698,-63.949,0.013586,0.034196,0.99932,-15.772
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.77859,-0.62291,0.076103,146.53,0.62607,0.77933,-0.02622,-71.819,-0.042976,0.06806,0.99676,-13.271
> select add #6
26966 atoms, 27276 bonds, 10 pseudobonds, 1742 residues, 4 models selected
> select subtract #9
13483 atoms, 13638 bonds, 5 pseudobonds, 871 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.90053,-0.43374,0.030229,118.87,0.43479,0.89867,-0.057958,-61.253,-0.0020271,0.065336,0.99786,-106.51
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.90053,-0.43374,0.030229,117.96,0.43479,0.89867,-0.057958,-58.063,-0.0020271,0.065336,0.99786,-99.02
> fitmap #9 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#9) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.2068, steps = 76
shifted from previous position = 2.83
rotated from previous position = 13.9 degrees
atoms outside contour = 8856, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#9) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90186856 -0.43199588 0.00355729 117.86366547
0.43199178 0.90187556 0.00188863 -74.73025663
-0.00402411 -0.00016658 0.99999189 -7.44055541
Axis -0.00237866 0.00877453 0.99995867
Axis point 223.26248207 222.07311904 0.00000000
Rotation angle (degrees) 25.59529472
Shift along axis -8.37632790
> fitmap #6 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#6) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.2107, steps = 76
shifted from previous position = 6.42
rotated from previous position = 3.77 degrees
atoms outside contour = 8792, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#6) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.89927581 -0.43736394 0.00397652 120.21648837
0.43735856 0.89928457 0.00218009 -76.65766086
-0.00452951 -0.00022134 0.99998972 -88.42217994
Axis -0.00274523 0.00972376 0.99994895
Axis point 224.54330296 222.59234931 0.00000000
Rotation angle (degrees) 25.93706162
Shift along axis -89.49308936
> fitmap #6 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#6) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.2107, steps = 28
shifted from previous position = 0.0192
rotated from previous position = 0.0148 degrees
atoms outside contour = 8796, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#6) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.89933439 -0.43724539 0.00375689 120.24269167
0.43724018 0.89934219 0.00215515 -76.65069961
-0.00432106 -0.00029554 0.99999062 -88.41900835
Axis -0.00280231 0.00923693 0.99995341
Axis point 224.68371772 222.69891567 0.00000000
Rotation angle (degrees) 25.92938976
Shift along axis -89.45986421
> hide #!1 models
> fitmap #4 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#4) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.1827, steps = 48
shifted from previous position = 0.00491
rotated from previous position = 0.0248 degrees
atoms outside contour = 9446, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#4) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90928978 0.41614780 -0.00361878 -71.41091068
-0.41615838 0.90928743 -0.00292816 113.12518140
0.00207197 0.00416853 0.99998917 -73.99873420
Axis 0.00852602 -0.00683692 -0.99994028
Axis point 224.62336106 222.05003957 0.00000000
Rotation angle (degrees) 24.59351935
Shift along axis 72.61203568
> fitmap #5 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#5) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.2277, steps = 40
shifted from previous position = 0.00381
rotated from previous position = 0.015 degrees
atoms outside contour = 8516, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#5) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.99996338 -0.00800961 -0.00301512 2.92297229
0.00800299 0.99996555 -0.00220346 -2.56635404
0.00303267 0.00217925 0.99999303 -81.74918750
Axis 0.24804734 -0.34228600 0.90626310
Axis point 3431.91464568 2593.93915056 0.00000000
Rotation angle (degrees) 0.50618108
Shift along axis -72.48280982
> fitmap #6 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#6) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.2107, steps = 40
shifted from previous position = 0.00122
rotated from previous position = 0.00961 degrees
atoms outside contour = 8796, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#6) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.89926721 -0.43738392 0.00371449 120.28172204
0.43737894 0.89927484 0.00210421 -76.64623236
-0.00426070 -0.00026761 0.99999089 -88.42975218
Axis -0.00271127 0.00911655 0.99995477
Axis point 224.66308739 222.70653660 0.00000000
Rotation angle (degrees) 25.93818546
Shift along axis -89.45061771
> fitmap #7 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#7) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.2313, steps = 44
shifted from previous position = 0.0157
rotated from previous position = 0.0186 degrees
atoms outside contour = 8391, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#7) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.99999562 -0.00102630 -0.00277473 0.72291447
0.00101879 0.99999582 -0.00270701 0.31246423
0.00277750 0.00270417 0.99999249 -0.74092397
Axis 0.67486817 -0.69245785 0.25505897
Axis point 274.98731741 0.00000000 240.02994251
Rotation angle (degrees) 0.22970342
Shift along axis 0.08252435
> fitmap #8 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#8) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.1816, steps = 44
shifted from previous position = 0.00457
rotated from previous position = 0.00164 degrees
atoms outside contour = 9523, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#8) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90625709 0.42269715 -0.00502122 -72.37947487
-0.42271656 0.90625420 -0.00374681 116.59274764
0.00296674 0.00551813 0.99998037 6.67969942
Axis 0.01095791 -0.00944759 -0.99989533
Axis point 226.55851759 221.25481916 0.00000000
Rotation angle (degrees) 25.00839837
Shift along axis -8.57364900
> fitmap #9 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#9) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.2068, steps = 36
shifted from previous position = 0.00541
rotated from previous position = 0.0098 degrees
atoms outside contour = 8862, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#9) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90186365 -0.43200678 0.00347788 117.88500322
0.43200329 0.90187035 0.00173774 -74.69689225
-0.00388731 -0.00006475 0.99999244 -7.46810848
Axis -0.00208611 0.00852410 0.99996149
Axis point 223.20119566 222.13408793 0.00000000
Rotation angle (degrees) 25.59592919
Shift along axis -8.35046606
> select clear
> combine #4-9
Remapping chain ID 'B' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #5 to 'C'
Remapping chain ID 'M' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #5 to 'N'
Remapping chain ID 'Nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #5 to 'Nu'
Remapping chain ID 'a' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #5 to 'b'
Remapping chain ID 'nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #5 to 'nu'
Remapping chain ID 'B' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #6 to 'D'
Remapping chain ID 'M' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #6 to 'O'
Remapping chain ID 'Nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #6 to 'Nv'
Remapping chain ID 'a' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #6 to 'c'
Remapping chain ID 'nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #6 to 'nv'
Remapping chain ID 'B' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #7 to 'E'
Remapping chain ID 'M' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #7 to 'P'
Remapping chain ID 'Nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #7 to 'Nw'
Remapping chain ID 'a' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #7 to 'd'
Remapping chain ID 'nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #7 to 'nw'
Remapping chain ID 'B' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #8 to 'F'
Remapping chain ID 'M' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #8 to 'Q'
Remapping chain ID 'Nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #8 to 'Nx'
Remapping chain ID 'a' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #8 to 'e'
Remapping chain ID 'nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #8 to 'nx'
Remapping chain ID 'B' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #9 to 'G'
Remapping chain ID 'M' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #9 to 'R'
Remapping chain ID 'Nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #9 to 'Ny'
Remapping chain ID 'a' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #9 to 'f'
Remapping chain ID 'nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #9 to 'ny'
> hide #!4-9 target m
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> split #10
Split combination (#10) into 30 models
Chain information for combination B #10.1
---
Chain | Description
B | No description available
Chain information for combination C #10.2
---
Chain | Description
C | No description available
Chain information for combination D #10.3
---
Chain | Description
D | No description available
Chain information for combination E #10.4
---
Chain | Description
E | No description available
Chain information for combination F #10.5
---
Chain | Description
F | No description available
Chain information for combination G #10.6
---
Chain | Description
G | No description available
Chain information for combination a #10.19
---
Chain | Description
a | No description available
Chain information for combination b #10.20
---
Chain | Description
b | No description available
Chain information for combination c #10.21
---
Chain | Description
c | No description available
Chain information for combination d #10.22
---
Chain | Description
d | No description available
Chain information for combination e #10.23
---
Chain | Description
e | No description available
Chain information for combination f #10.24
---
Chain | Description
f | No description available
> fitmap #10 #3 eachModel true
Missing required "in_map" argument
Must specify one map, got 0
Must specify one map, got 0
> fitmap #10 inMap #2 eachModel true
Fit molecule combination B (#10.1) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6631 atoms
average map value = 0.1856, steps = 48
shifted from previous position = 0.118
rotated from previous position = 0.303 degrees
atoms outside contour = 4617, contour level = 0.228
Position of combination B (#10.1) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90856223 0.41774747 0.00131220 -72.45859781
-0.41774068 0.90855895 -0.00365354 113.61423851
-0.00271846 0.00277131 0.99999246 -73.20969250
Axis 0.00768961 0.00482412 -0.99995880
Axis point 222.21854498 223.43792249 0.00000000
Rotation angle (degrees) 24.69332879
Shift along axis 73.19758639
Fit molecule combination C (#10.2) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6631 atoms
average map value = 0.2259, steps = 44
shifted from previous position = 0.0358
rotated from previous position = 0.124 degrees
atoms outside contour = 4197, contour level = 0.228
Position of combination C (#10.2) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90841180 0.41805997 -0.00372220 -71.48911868
-0.41806992 0.90841152 -0.00246033 113.48008830
0.00235273 0.00379113 0.99999005 -74.00456354
Axis 0.00747626 -0.00726513 -0.99994566
Axis point 224.19352647 221.41724436 0.00000000
Rotation angle (degrees) 24.71391262
Shift along axis 72.64162276
Fit molecule combination D (#10.3) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6631 atoms
average map value = 0.2103, steps = 36
shifted from previous position = 0.0972
rotated from previous position = 0.207 degrees
atoms outside contour = 4323, contour level = 0.228
Position of combination D (#10.3) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90846584 0.41791405 -0.00613712 -71.03049628
-0.41792839 0.90847916 -0.00121646 113.29141762
0.00506708 0.00366999 0.99998043 -74.60713379
Axis 0.00584551 -0.01340325 -0.99989309
Axis point 225.16655815 220.29815584 0.00000000
Rotation angle (degrees) 24.70623321
Shift along axis 72.66547535
Fit molecule combination E (#10.4) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6631 atoms
average map value = 0.2277, steps = 48
shifted from previous position = 0.0821
rotated from previous position = 0.245 degrees
atoms outside contour = 4147, contour level = 0.228
Position of combination E (#10.4) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90760803 0.41978943 -0.00494892 -71.23798631
-0.41980792 0.90760596 -0.00356842 114.13288484
0.00299369 0.00531632 0.99998139 -74.34404603
Axis 0.01058107 -0.00945907 -0.99989928
Axis point 224.86017439 221.01657486 0.00000000
Rotation angle (degrees) 24.82454721
Shift along axis 72.50319218
Fit molecule combination F (#10.5) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6631 atoms
average map value = 0.1861, steps = 48
shifted from previous position = 0.117
rotated from previous position = 0.321 degrees
atoms outside contour = 4633, contour level = 0.228
Position of combination F (#10.5) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90886080 0.41709533 0.00188102 -72.96251634
-0.41708981 0.90886114 -0.00274199 113.27406769
-0.00285325 0.00170754 0.99999447 -73.03957239
Axis 0.00533382 0.00567515 -0.99996967
Axis point 221.57616952 224.28377039 0.00000000
Rotation angle (degrees) 24.65196237
Shift along axis 73.29103580
Fit molecule combination G (#10.6) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6631 atoms
average map value = 0.2085, steps = 40
shifted from previous position = 0.104
rotated from previous position = 0.18 degrees
atoms outside contour = 4329, contour level = 0.228
Position of combination G (#10.6) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90834012 0.41820221 -0.00501391 -71.13412774
-0.41821275 0.90834828 -0.00122854 113.22854144
0.00404059 0.00321281 0.99998668 -74.36842227
Axis 0.00530960 -0.01082458 -0.99992732
Axis point 224.37104405 220.19557474 0.00000000
Rotation angle (degrees) 24.72338719
Shift along axis 72.75967100
Fit molecule combination M (#10.7) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 1 atoms
average map value = 1.074, steps = 60
shifted from previous position = 3.74
rotated from previous position = 0 degrees
atoms outside contour = 0, contour level = 0.228
Position of combination M (#10.7) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90928978 0.41614780 -0.00361878 -74.20933506
-0.41615838 0.90928743 -0.00292816 113.43152161
0.00207197 0.00416853 0.99998917 -71.53435666
Axis 0.00852602 -0.00683692 -0.99994028
Axis point 223.89833435 228.56557478 0.00000000
Rotation angle (degrees) 24.59351935
Shift along axis 70.12185146
Fit molecule combination N (#10.8) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 1 atoms
average map value = 1.121, steps = 60
shifted from previous position = 3.39
rotated from previous position = 0 degrees
atoms outside contour = 0, contour level = 0.228
Position of combination N (#10.8) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90928978 0.41614780 -0.00361878 -73.18594767
-0.41615838 0.90928743 -0.00292816 113.07289435
0.00207197 0.00416853 0.99998917 -71.11045068
Axis 0.00852602 -0.00683692 -0.99994028
Axis point 223.58268335 226.02912291 0.00000000
Rotation angle (degrees) 24.59351935
Shift along axis 69.70914813
Fit molecule combination Nt (#10.9) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 40 atoms
average map value = 0.4218, steps = 56
shifted from previous position = 0.377
rotated from previous position = 25.8 degrees
atoms outside contour = 12, contour level = 0.228
Position of combination Nt (#10.9) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.80616691 0.42674619 0.40985682 -138.74654998
-0.40861688 0.90251929 -0.13598227 138.25381467
-0.42793360 -0.05785001 0.90195688 8.93206795
Axis 0.06589677 0.70659271 -0.70454550
Axis point 68.30381417 0.00000000 384.05194148
Rotation angle (degrees) 36.35868068
Shift along axis 82.25314023
Fit molecule combination Nu (#10.10) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 40 atoms
average map value = 0.4531, steps = 48
shifted from previous position = 0.337
rotated from previous position = 6.89 degrees
atoms outside contour = 15, contour level = 0.228
Position of combination Nu (#10.10) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.89660600 0.42771262 0.11471525 -92.03697372
-0.43144064 0.90209981 0.00865446 114.22015120
-0.09978298 -0.05725246 0.99336072 -48.61268252
Axis -0.07422169 0.24155918 -0.96754344
Axis point 164.49055982 240.81224848 0.00000000
Rotation angle (degrees) 26.35854046
Shift along axis 81.45694823
Fit molecule combination Nv (#10.11) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 40 atoms
average map value = 0.436, steps = 52
shifted from previous position = 1.14
rotated from previous position = 5.11 degrees
atoms outside contour = 13, contour level = 0.228
Position of combination Nv (#10.11) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.92261392 0.37979103 0.06739682 -82.26997792
-0.37790961 0.92500986 -0.03925676 110.29876059
-0.07725209 0.01074893 0.99695365 -56.42770740
Axis 0.06469014 0.18712586 -0.98020360
Axis point 203.30124948 270.07383924 0.00000000
Rotation angle (degrees) 22.73699698
Shift along axis 70.62833656
Fit molecule combination Nw (#10.12) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 40 atoms
average map value = 0.4695, steps = 48
shifted from previous position = 0.111
rotated from previous position = 3.82 degrees
atoms outside contour = 11, contour level = 0.228
Position of combination Nw (#10.12) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90552068 0.42070578 0.05512666 -86.83096373
-0.42256964 0.90590837 0.02765718 106.40887665
-0.03830417 -0.04833900 0.99809625 -60.52961345
Axis -0.08921496 0.10968220 -0.98995480
Axis point 180.00879263 229.99402096 0.00000000
Rotation angle (degrees) 25.20866476
Shift along axis 79.33936171
Fit molecule combination Nx (#10.13) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 40 atoms
average map value = 0.448, steps = 52
shifted from previous position = 0.365
rotated from previous position = 24.6 degrees
atoms outside contour = 11, contour level = 0.228
Position of combination Nx (#10.13) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.80604779 0.44737797 0.38747892 -169.36782338
-0.42770804 0.89283321 -0.14111939 154.45884113
-0.40908776 -0.05197888 0.91101339 10.82197215
Axis 0.07511675 0.67124922 -0.73741573
Axis point 119.56929163 444.34813777 0.00000000
Rotation angle (degrees) 36.39484390
Shift along axis 82.97772220
Fit molecule combination Ny (#10.14) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 40 atoms
average map value = 0.4045, steps = 68
shifted from previous position = 0.552
rotated from previous position = 1.74 degrees
atoms outside contour = 16, contour level = 0.228
Position of combination Ny (#10.14) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.91967062 0.39269058 -0.00023709 -71.51290318
-0.39262523 0.91950622 -0.01880779 110.97235066
-0.00716763 0.01739006 0.99982309 -73.33260200
Axis 0.04604269 0.00881547 -0.99890057
Axis point 232.26798631 237.94052953 0.00000000
Rotation angle (degrees) 23.14691008
Shift along axis 70.93760504
Fit molecule combination O (#10.15) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 1 atoms
average map value = 1.017, steps = 60
shifted from previous position = 3.99
rotated from previous position = 0 degrees
atoms outside contour = 0, contour level = 0.228
Position of combination O (#10.15) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90928978 0.41614780 -0.00361878 -73.20523421
-0.41615838 0.90928743 -0.00292816 111.18782736
0.00207197 0.00416853 0.99998917 -71.00271048
Axis 0.00852602 -0.00683692 -0.99994028
Axis point 219.24772724 225.12860553 0.00000000
Rotation angle (degrees) 24.59351935
Shift along axis 69.61413799
Fit molecule combination P (#10.16) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 1 atoms
average map value = 1.02, steps = 56
shifted from previous position = 3.08
rotated from previous position = 0 degrees
atoms outside contour = 0, contour level = 0.228
Position of combination P (#10.16) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90928978 0.41614780 -0.00361878 -73.16527361
-0.41615838 0.90928743 -0.00292816 112.39091563
0.00207197 0.00416853 0.99998917 -71.57271029
Axis 0.00852602 -0.00683692 -0.99994028
Axis point 222.03393815 225.65142342 0.00000000
Rotation angle (degrees) 24.59351935
Shift along axis 70.17621904
Fit molecule combination Q (#10.17) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 1 atoms
average map value = 0.9125, steps = 52
shifted from previous position = 2.84
rotated from previous position = 0 degrees
atoms outside contour = 0, contour level = 0.228
Position of combination Q (#10.17) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90928978 0.41614780 -0.00361878 -72.76481018
-0.41615838 0.90928743 -0.00292816 113.62907102
0.00207197 0.00416853 0.99998917 -71.54917300
Axis 0.00852602 -0.00683692 -0.99994028
Axis point 225.07410986 225.35121152 0.00000000
Rotation angle (degrees) 24.59351935
Shift along axis 70.14763235
Fit molecule combination R (#10.18) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 1 atoms
average map value = 1.119, steps = 100
shifted from previous position = 4.45
rotated from previous position = 0 degrees
atoms outside contour = 0, contour level = 0.228
Position of combination R (#10.18) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90928978 0.41614780 -0.00361878 -73.77314814
-0.41615838 0.90928743 -0.00292816 112.32889120
0.00207197 0.00416853 0.99998917 -70.30660236
Axis 0.00852602 -0.00683692 -0.99994028
Axis point 221.57318595 226.98567245 0.00000000
Rotation angle (degrees) 24.59351935
Shift along axis 68.90542803
Fit molecule combination a (#10.19) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6767 atoms
average map value = 0.1785, steps = 48
shifted from previous position = 0.0904
rotated from previous position = 0.354 degrees
atoms outside contour = 4777, contour level = 0.228
Position of combination a (#10.19) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90952886 0.41563963 -0.00097397 -72.10041078
-0.41563608 0.90952723 0.00262122 111.65053740
0.00197533 -0.00197926 0.99999609 -73.05988315
Axis -0.00553413 -0.00354784 -0.99997839
Axis point 221.22019854 220.64817031 0.00000000
Rotation angle (degrees) 24.56005735
Shift along axis 73.06119923
Fit molecule combination b (#10.20) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6767 atoms
average map value = 0.2266, steps = 48
shifted from previous position = 0.0353
rotated from previous position = 0.262 degrees
atoms outside contour = 4310, contour level = 0.228
Position of combination b (#10.20) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90973018 0.41514705 -0.00662710 -70.64433653
-0.41515411 0.90975104 0.00033682 112.10146925
0.00616884 0.00244485 0.99997798 -74.45483545
Axis 0.00253857 -0.01540932 -0.99987805
Axis point 224.99261610 219.53311262 0.00000000
Rotation angle (degrees) 24.53198871
Shift along axis 72.53901263
Fit molecule combination c (#10.21) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6767 atoms
average map value = 0.2097, steps = 48
shifted from previous position = 0.0862
rotated from previous position = 0.505 degrees
atoms outside contour = 4429, contour level = 0.228
Position of combination c (#10.21) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90936721 0.41581517 -0.01220724 -69.34182733
-0.41585667 0.90942966 -0.00096416 112.58113962
0.01070071 0.00595324 0.99992502 -76.03681029
Axis 0.00831403 -0.02753306 -0.99958632
Axis point 228.04980749 217.91403935 0.00000000
Rotation angle (degrees) 24.58281204
Shift along axis 72.32914190
Fit molecule combination d (#10.22) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6767 atoms
average map value = 0.2324, steps = 40
shifted from previous position = 0.0447
rotated from previous position = 0.308 degrees
atoms outside contour = 4190, contour level = 0.228
Position of combination d (#10.22) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.91010358 0.41432092 -0.00704616 -70.20582340
-0.41432671 0.91012796 0.00068572 111.54853368
0.00669702 0.00229533 0.99997494 -74.51276825
Axis 0.00194218 -0.01658275 -0.99986061
Axis point 224.72548010 218.54720469 0.00000000
Rotation angle (degrees) 24.48037757
Shift along axis 72.51624789
Fit molecule combination e (#10.23) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6767 atoms
average map value = 0.1755, steps = 44
shifted from previous position = 0.126
rotated from previous position = 0.352 degrees
atoms outside contour = 4846, contour level = 0.228
Position of combination e (#10.23) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90959606 0.41549344 -0.00045561 -72.50176212
-0.41549146 0.90959422 0.00228300 111.27544500
0.00136299 -0.00188731 0.99999729 -72.96282638
Axis -0.00501844 -0.00218846 -0.99998501
Axis point 220.00943368 221.48297554 0.00000000
Rotation angle (degrees) 24.55072445
Shift along axis 73.08205675
Fit molecule combination f (#10.24) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6767 atoms
average map value = 0.2043, steps = 48
shifted from previous position = 0.0826
rotated from previous position = 0.539 degrees
atoms outside contour = 4483, contour level = 0.228
Position of combination f (#10.24) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90940990 0.41570493 -0.01276912 -68.47308569
-0.41574825 0.90947937 -0.00082333 112.35465745
0.01127099 0.00605748 0.99991813 -76.14029759
Axis 0.00827190 -0.02890030 -0.99954807
Axis point 228.26496082 215.89743424 0.00000000
Rotation angle (degrees) 24.57692330
Shift along axis 72.29240204
Fit molecule combination nt (#10.25) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 44 atoms
average map value = 0.448, steps = 80
shifted from previous position = 0.698
rotated from previous position = 29.8 degrees
atoms outside contour = 15, contour level = 0.228
Position of combination nt (#10.25) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.85560450 0.26168898 0.44660925 -144.83446021
-0.21815367 0.96472727 -0.14734409 112.69354848
-0.46941444 0.02863882 0.88251340 9.48242345
Axis 0.16776885 0.87326796 -0.45744582
Axis point 0.43498194 0.00000000 350.64966867
Rotation angle (degrees) 31.63326406
Shift along axis 69.77525988
Fit molecule combination nu (#10.26) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 44 atoms
average map value = 0.5339, steps = 48
shifted from previous position = 0.382
rotated from previous position = 3.95 degrees
atoms outside contour = 15, contour level = 0.228
Position of combination nu (#10.26) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.92463087 0.37738666 0.05135237 -81.31758102
-0.37784159 0.92586981 -0.00091358 104.41182953
-0.04789038 -0.01855834 0.99868018 -62.83622997
Axis -0.02315813 0.13025260 -0.99121035
Axis point 200.34055852 250.71404816 0.00000000
Rotation angle (degrees) 22.39332428
Shift along axis 77.76699657
Fit molecule combination nv (#10.27) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 44 atoms
average map value = 0.4159, steps = 68
shifted from previous position = 0.533
rotated from previous position = 9.42 degrees
atoms outside contour = 17, contour level = 0.228
Position of combination nv (#10.27) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.83831842 0.53820258 -0.08694942 -50.32844541
-0.54062255 0.84124926 -0.00519064 147.97494329
0.07035252 0.05135822 0.99619921 -92.69125234
Axis 0.05179898 -0.14408919 -0.98820806
Axis point 241.10704368 172.45594180 0.00000000
Rotation angle (degrees) 33.08271327
Shift along axis 67.66969117
Fit molecule combination nw (#10.28) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 44 atoms
average map value = 0.4921, steps = 60
shifted from previous position = 0.337
rotated from previous position = 1.79 degrees
atoms outside contour = 15, contour level = 0.228
Position of combination nw (#10.28) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.91644614 0.39971760 0.01876985 -77.13359508
-0.39993344 0.91649496 0.00949912 105.71683789
-0.01340551 -0.01621212 0.99977871 -69.03877846
Axis -0.03211052 0.04018349 -0.99867622
Axis point 208.60580025 230.49657860 0.00000000
Rotation angle (degrees) 23.60040447
Shift along axis 75.67225796
Fit molecule combination nx (#10.29) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 44 atoms
average map value = 0.4107, steps = 72
shifted from previous position = 1.55
rotated from previous position = 25.7 degrees
atoms outside contour = 17, contour level = 0.228
Position of combination nx (#10.29) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.88318469 0.26749340 0.38526885 -165.36860977
-0.23788891 0.96340122 -0.12355951 119.91915233
-0.40421984 0.01747468 0.91449492 2.24660493
Axis 0.14877932 0.83284480 -0.53313624
Axis point 6.02218437 0.00000000 459.65980041
Rotation angle (degrees) 28.29237781
Shift along axis 74.07286677
Fit molecule combination ny (#10.30) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 44 atoms
average map value = 0.3749, steps = 60
shifted from previous position = 0.27
rotated from previous position = 6.07 degrees
atoms outside contour = 17, contour level = 0.228
Position of combination ny (#10.30) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.88098155 0.46735459 -0.07383225 -49.62521202
-0.47148310 0.88021208 -0.05413297 143.41431711
0.03968875 0.08250080 0.99580039 -89.03503240
Axis 0.14299778 -0.11880848 -0.98256612
Axis point 270.72174857 194.50899727 0.00000000
Rotation angle (degrees) 28.53841323
Shift along axis 63.34767344
> fitmap #10 inMap #2 eachModel true
Fit molecule combination B (#10.1) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6631 atoms
average map value = 0.1856, steps = 40
shifted from previous position = 0.0202
rotated from previous position = 0.0514 degrees
atoms outside contour = 4614, contour level = 0.228
Position of combination B (#10.1) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90849900 0.41788571 0.00104788 -72.41877733
-0.41788162 0.90849714 -0.00280979 113.48845139
-0.00212617 0.00211480 0.99999550 -73.18992727
Axis 0.00589216 0.00379768 -0.99997543
Axis point 222.09399755 222.96015086 0.00000000
Rotation angle (degrees) 24.70169393
Shift along axis 73.19241890
Fit molecule combination C (#10.2) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6631 atoms
average map value = 0.2259, steps = 44
shifted from previous position = 0.00159
rotated from previous position = 0.035 degrees
atoms outside contour = 4198, contour level = 0.228
Position of combination C (#10.2) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90830133 0.41830372 -0.00326849 -71.58804993
-0.41831258 0.90829891 -0.00276970 113.59482967
0.00181019 0.00388297 0.99999082 -73.92349900
Axis 0.00795147 -0.00607019 -0.99994996
Axis point 224.02436028 221.62974438 0.00000000
Rotation angle (degrees) 24.72914038
Shift along axis 72.66102751
Fit molecule combination D (#10.3) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6631 atoms
average map value = 0.2103, steps = 40
shifted from previous position = 0.0143
rotated from previous position = 0.0215 degrees
atoms outside contour = 4328, contour level = 0.228
Position of combination D (#10.3) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90844255 0.41796985 -0.00577346 -71.09897180
-0.41798256 0.90845433 -0.00114680 113.29558010
0.00476559 0.00345501 0.99998268 -74.53374721
Axis 0.00550436 -0.01260605 -0.99990539
Axis point 224.98624931 220.34686037 0.00000000
Rotation angle (degrees) 24.70937699
Shift along axis 72.70713190
Fit molecule combination E (#10.4) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6631 atoms
average map value = 0.2277, steps = 36
shifted from previous position = 0.0217
rotated from previous position = 0.0181 degrees
atoms outside contour = 4141, contour level = 0.228
Position of combination E (#10.4) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90772138 0.41954389 -0.00498150 -71.21600829
-0.41956304 0.90771854 -0.00372973 114.12370596
0.00295702 0.00547561 0.99998064 -74.33497807
Axis 0.01096924 -0.00945968 -0.99989509
Axis point 225.00309564 221.13034346 0.00000000
Rotation angle (degrees) 24.80917775
Shift along axis 72.46642020
Fit molecule combination F (#10.5) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6631 atoms
average map value = 0.1861, steps = 44
shifted from previous position = 0.00333
rotated from previous position = 0.00207 degrees
atoms outside contour = 4635, contour level = 0.228
Position of combination F (#10.5) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90886195 0.41709295 0.00185249 -72.95458499
-0.41708755 0.90886224 -0.00272002 113.27021525
-0.00281816 0.00169947 0.99999458 -73.04439246
Axis 0.00529785 0.00559893 -0.99997029
Axis point 221.58701471 224.26145623 0.00000000
Rotation angle (degrees) 24.65179987
Shift along axis 73.28991165
Fit molecule combination G (#10.6) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6631 atoms
average map value = 0.2085, steps = 40
shifted from previous position = 0.0189
rotated from previous position = 0.014 degrees
atoms outside contour = 4320, contour level = 0.228
Position of combination G (#10.6) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90830358 0.41827968 -0.00516843 -71.09467049
-0.41829142 0.90831181 -0.00139736 113.29610625
0.00411006 0.00343114 0.99998567 -74.38696201
Axis 0.00577132 -0.01109023 -0.99992185
Axis point 224.51701561 220.19174882 0.00000000
Rotation angle (degrees) 24.72845659
Shift along axis 72.71435896
Fit molecule combination M (#10.7) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 1 atoms
average map value = 1.071, steps = 40
shifted from previous position = 0.0116
rotated from previous position = 0 degrees
atoms outside contour = 0, contour level = 0.228
Position of combination M (#10.7) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90928978 0.41614780 -0.00361878 -74.21653397
-0.41615838 0.90928743 -0.00292816 113.43786770
0.00207197 0.00416853 0.99998917 -71.54086290
Axis 0.00852602 -0.00683692 -0.99994028
Axis point 223.90936528 228.58540933 0.00000000
Rotation angle (degrees) 24.59351935
Shift along axis 70.12825255
Fit molecule combination N (#10.8) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 1 atoms
average map value = 1.122, steps = 40
shifted from previous position = 0.0412
rotated from previous position = 0 degrees
atoms outside contour = 0, contour level = 0.228
Position of combination N (#10.8) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90928978 0.41614780 -0.00361878 -73.21073778
-0.41615838 0.90928743 -0.00292816 113.09661235
0.00207197 0.00416853 0.99998917 -71.08767031
Axis 0.00852602 -0.00683692 -0.99994028
Axis point 223.62443063 226.09731890 0.00000000
Rotation angle (degrees) 24.59351935
Shift along axis 69.68599560
Fit molecule combination Nt (#10.9) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 40 atoms
average map value = 0.4218, steps = 44
shifted from previous position = 0.00203
rotated from previous position = 0.0825 degrees
atoms outside contour = 12, contour level = 0.228
Position of combination Nt (#10.9) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.80601658 0.42597690 0.41095129 -138.82006206
-0.40776827 0.90288217 -0.13612065 138.11674463
-0.42902484 -0.05785740 0.90143786 9.16923965
Axis 0.06598409 0.70818755 -0.70293420
Axis point 68.04779047 0.00000000 383.12223920
Rotation angle (degrees) 36.37348804
Shift along axis 82.20727101
Fit molecule combination Nu (#10.10) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 40 atoms
average map value = 0.4536, steps = 40
shifted from previous position = 0.0138
rotated from previous position = 0.124 degrees
atoms outside contour = 15, contour level = 0.228
Position of combination Nu (#10.10) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.89753205 0.42603282 0.11372009 -91.80967522
-0.42973377 0.90291017 0.00906138 113.76639162
-0.09881858 -0.05700224 0.99347151 -48.83670945
Axis -0.07471265 0.24036415 -0.96780323
Axis point 164.75593069 240.83851104 0.00000000
Rotation angle (degrees) 26.23910061
Shift along axis 81.46903169
Fit molecule combination Nv (#10.11) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 40 atoms
average map value = 0.4358, steps = 40
shifted from previous position = 0.00719
rotated from previous position = 0.146 degrees
atoms outside contour = 13, contour level = 0.228
Position of combination Nv (#10.11) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.92221720 0.38049467 0.06884221 -82.51012941
-0.37844296 0.92470554 -0.04123812 110.79959952
-0.07934966 0.01197766 0.99677488 -56.06405904
Axis 0.06865672 0.19119080 -0.97914878
Axis point 203.26490903 271.10771811 0.00000000
Rotation angle (degrees) 22.80212008
Shift along axis 70.41404502
Fit molecule combination Nw (#10.12) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 40 atoms
average map value = 0.4692, steps = 40
shifted from previous position = 0.0166
rotated from previous position = 0.397 degrees
atoms outside contour = 12, contour level = 0.228
Position of combination Nw (#10.12) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90649657 0.41787460 0.06037199 -88.03580760
-0.42014801 0.90691857 0.03121478 104.93358841
-0.04170861 -0.05366126 0.99768776 -59.22215232
Axis -0.10003387 0.12031097 -0.98768340
Axis point 175.72122009 230.86169766 0.00000000
Rotation angle (degrees) 25.10234330
Shift along axis 79.92396148
Fit molecule combination Nx (#10.13) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 40 atoms
average map value = 0.4481, steps = 44
shifted from previous position = 0.0163
rotated from previous position = 0.531 degrees
atoms outside contour = 13, contour level = 0.228
Position of combination Nx (#10.13) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.80458788 0.44353568 0.39486003 -170.61117650
-0.42302324 0.89475172 -0.14307589 154.09387888
-0.41676095 -0.05191785 0.90753228 12.72570939
Axis 0.07655306 0.68158630 -0.72772230
Axis point 118.73781787 451.24990515 -0.00000000
Rotation angle (degrees) 36.54052570
Shift along axis 82.70668691
Fit molecule combination Ny (#10.14) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 40 atoms
average map value = 0.4048, steps = 28
shifted from previous position = 0.0292
rotated from previous position = 0.32 degrees
atoms outside contour = 16, contour level = 0.228
Position of combination Ny (#10.14) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.91900311 0.39424974 -0.00065066 -71.44430258
-0.39414965 0.91873001 -0.02410858 112.76156093
-0.00890702 0.02241231 0.99970913 -73.46264744
Axis 0.05890108 0.01045355 -0.99820909
Axis point 234.74881526 239.94707578 0.00000000
Rotation angle (degrees) 23.26016996
Shift along axis 70.30169420
Fit molecule combination O (#10.15) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 1 atoms
average map value = 1.011, steps = 28
shifted from previous position = 0.0284
rotated from previous position = 0 degrees
atoms outside contour = 0, contour level = 0.228
Position of combination O (#10.15) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90928978 0.41614780 -0.00361878 -73.18171501
-0.41615838 0.90928743 -0.00292816 111.17258748
0.00207197 0.00416853 0.99998917 -70.99835885
Axis 0.00852602 -0.00683692 -0.99994028
Axis point 219.22448213 225.06693929 0.00000000
Rotation angle (degrees) 24.59351935
Shift along axis 69.61009133
Fit molecule combination P (#10.16) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 1 atoms
average map value = 1.023, steps = 28
shifted from previous position = 0.0196
rotated from previous position = 0 degrees
atoms outside contour = 0, contour level = 0.228
Position of combination P (#10.16) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90928978 0.41614780 -0.00361878 -73.17464654
-0.41615838 0.90928743 -0.00292816 112.40577943
0.00207197 0.00416853 0.99998917 -71.58142004
Axis 0.00852602 -0.00683692 -0.99994028
Axis point 222.06344536 225.68055308 0.00000000
Rotation angle (degrees) 24.59351935
Shift along axis 70.18474673
Fit molecule combination Q (#10.17) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 1 atoms
average map value = 0.9099, steps = 28
shifted from previous position = 0.0282
rotated from previous position = 0 degrees
atoms outside contour = 0, contour level = 0.228
Position of combination Q (#10.17) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90928978 0.41614780 -0.00361878 -72.76235516
-0.41615838 0.90928743 -0.00292816 113.60740572
0.00207197 0.00416853 0.99998917 -71.53125873
Axis 0.00852602 -0.00683692 -0.99994028
Axis point 225.02543596 225.33433884 0.00000000
Rotation angle (degrees) 24.59351935
Shift along axis 70.12988820
Fit molecule combination R (#10.18) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 1 atoms
average map value = 1.116, steps = 44
shifted from previous position = 0.00777
rotated from previous position = 0 degrees
atoms outside contour = 0, contour level = 0.228
Position of combination R (#10.18) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90928978 0.41614780 -0.00361878 -73.76908638
-0.41615838 0.90928743 -0.00292816 112.32683857
0.00207197 0.00416853 0.99998917 -70.30030308
Axis 0.00852602 -0.00683692 -0.99994028
Axis point 221.57043698 226.97518480 0.00000000
Rotation angle (degrees) 24.59351935
Shift along axis 68.89917778
Fit molecule combination a (#10.19) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6767 atoms
average map value = 0.1785, steps = 44
shifted from previous position = 0.00347
rotated from previous position = 0.00879 degrees
atoms outside contour = 4774, contour level = 0.228
Position of combination a (#10.19) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90955812 0.41557525 -0.00111010 -72.06084847
-0.41557144 0.90955677 0.00261753 111.63600816
0.00209748 -0.00191947 0.99999596 -73.08229439
Axis -0.00545861 -0.00385913 -0.99997766
Axis point 221.29984642 220.60242361 0.00000000
Rotation angle (degrees) 24.55601303
Shift along axis 73.04319600
Fit molecule combination b (#10.20) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6767 atoms
average map value = 0.2266, steps = 28
shifted from previous position = 0.0288
rotated from previous position = 0.0327 degrees
atoms outside contour = 4308, contour level = 0.228
Position of combination b (#10.20) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90982425 0.41493302 -0.00710039 -70.52139594
-0.41494270 0.90984754 0.00012016 112.11414147
0.00651014 0.00283693 0.99997478 -74.52882994
Axis 0.00327324 -0.01639839 -0.99986018
Axis point 225.36377386 219.50744149 0.00000000
Rotation angle (degrees) 24.51905747
Shift along axis 72.44908389
Fit molecule combination c (#10.21) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6767 atoms
average map value = 0.2097, steps = 40
shifted from previous position = 0.0169
rotated from previous position = 0.0251 degrees
atoms outside contour = 4425, contour level = 0.228
Position of combination c (#10.21) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90937758 0.41580330 -0.01183342 -69.43046023
-0.41584023 0.90943739 -0.00073595 112.52807069
0.01045574 0.00559007 0.99992971 -75.96361649
Axis 0.00760370 -0.02679095 -0.99961214
Axis point 227.80207536 217.95131985 0.00000000
Rotation angle (degrees) 24.58124279
Shift along axis 72.39149106
Fit molecule combination d (#10.22) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6767 atoms
average map value = 0.2323, steps = 40
shifted from previous position = 0.000463
rotated from previous position = 0.0189 degrees
atoms outside contour = 4192, contour level = 0.228
Position of combination d (#10.22) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.91016900 0.41417258 -0.00731185 -70.11411517
-0.41417824 0.91019545 0.00079435 111.48195459
0.00698421 0.00230542 0.99997295 -74.56038364
Axis 0.00182392 -0.01725587 -0.99984944
Axis point 224.83602085 218.37174438 0.00000000
Rotation angle (degrees) 24.47132484
Shift along axis 72.49755708
Fit molecule combination e (#10.23) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6767 atoms
average map value = 0.1755, steps = 40
shifted from previous position = 0.0188
rotated from previous position = 0.0257 degrees
atoms outside contour = 4846, contour level = 0.228
Position of combination e (#10.23) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90958175 0.41552492 -0.00029825 -72.55646050
-0.41552268 0.90957880 0.00270213 111.15604736
0.00139408 -0.00233388 0.99999630 -72.91285893
Axis -0.00605971 -0.00203634 -0.99997957
Axis point 219.69884413 221.35407099 0.00000000
Rotation angle (degrees) 24.55284187
Shift along axis 73.12468895
Fit molecule combination f (#10.24) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6767 atoms
average map value = 0.2043, steps = 40
shifted from previous position = 0.0165
rotated from previous position = 0.0132 degrees
atoms outside contour = 4487, contour level = 0.228
Position of combination f (#10.24) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90940934 0.41570946 -0.01266095 -68.50828375
-0.41575438 0.90947635 -0.00102636 112.41990622
0.01108817 0.00619723 0.99991932 -76.13234657
Axis 0.00868394 -0.02855030 -0.99955464
Axis point 228.32000124 216.06373624 0.00000000
Rotation angle (degrees) 24.57708757
Shift along axis 72.29389583
Fit molecule combination nt (#10.25) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 44 atoms
average map value = 0.4478, steps = 60
shifted from previous position = 0.0122
rotated from previous position = 0.117 degrees
atoms outside contour = 15, contour level = 0.228
Position of combination nt (#10.25) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.85495221 0.26090184 0.44831568 -145.02313292
-0.21721172 0.96494221 -0.14732822 112.54802678
-0.47103692 0.02857917 0.88165041 9.89140913
Axis 0.16736052 0.87468373 -0.45488331
Axis point 0.43619013 0.00000000 349.63526083
Rotation angle (degrees) 31.70421873
Shift along axis 69.67334420
Fit molecule combination nu (#10.26) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 44 atoms
average map value = 0.5341, steps = 40
shifted from previous position = 0.0211
rotated from previous position = 0.51 degrees
atoms outside contour = 13, contour level = 0.228
Position of combination nu (#10.26) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.92596880 0.37298157 0.05887723 -82.72016884
-0.37352591 0.92761783 -0.00188565 103.70085792
-0.05531888 -0.02024612 0.99826345 -61.32433482
Axis -0.02430517 0.15117011 -0.98820891
Axis point 196.40046559 255.66175075 0.00000000
Rotation angle (degrees) 22.19174097
Shift along axis 78.28825148
Fit molecule combination nv (#10.27) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 44 atoms
average map value = 0.416, steps = 44
shifted from previous position = 0.00693
rotated from previous position = 0.516 degrees
atoms outside contour = 17, contour level = 0.228
Position of combination nv (#10.27) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.83582480 0.54082604 -0.09436152 -48.46544471
-0.54390244 0.83910597 -0.00844399 149.61353526
0.07461259 0.05838116 0.99550219 -94.19691743
Axis 0.06075882 -0.15363481 -0.98625793
Axis point 243.39997080 171.02508161 0.00000000
Rotation angle (degrees) 33.36161362
Shift along axis 66.97190589
Fit molecule combination nw (#10.28) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 44 atoms
average map value = 0.4926, steps = 44
shifted from previous position = 0.0204
rotated from previous position = 0.218 degrees
atoms outside contour = 15, contour level = 0.228
Position of combination nw (#10.28) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.91605241 0.40068524 0.01730078 -76.74108656
-0.40083499 0.91612969 0.00613973 106.94576502
-0.01338965 -0.01255907 0.99983148 -69.50949876
Axis -0.02330575 0.03825184 -0.99899632
Axis point 211.20330261 231.39291659 0.00000000
Rotation angle (degrees) 23.65088814
Shift along axis 75.31911448
Fit molecule combination nx (#10.29) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 44 atoms
average map value = 0.4119, steps = 40
shifted from previous position = 0.0531
rotated from previous position = 0.121 degrees
atoms outside contour = 16, contour level = 0.228
Position of combination nx (#10.29) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.88254549 0.26760375 0.38665449 -165.69732501
-0.23738019 0.96335227 -0.12491221 120.30834321
-0.40591145 0.01845659 0.91372602 2.57139747
Axis 0.15081228 0.83371470 -0.53120190
Axis point 5.53605084 0.00000000 459.06562261
Rotation angle (degrees) 28.38031978
Shift along axis 73.94771168
Fit molecule combination ny (#10.30) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 44 atoms
average map value = 0.3751, steps = 40
shifted from previous position = 0.00543
rotated from previous position = 0.254 degrees
atoms outside contour = 17, contour level = 0.228
Position of combination ny (#10.30) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.88229574 0.46538247 -0.07052226 -50.68493438
-0.46918237 0.88153628 -0.05255184 142.30623372
0.03771122 0.07945406 0.99612495 -88.38389840
Axis 0.13894961 -0.11392673 -0.98372441
Axis point 269.27617630 196.03150341 0.00000000
Rotation angle (degrees) 28.36023228
Shift along axis 63.69026229
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> hide #!2 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> select clear
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!10 models
> show #!9 models
> show #!8 models
> hide #!10 models
> show #!7 models
> show #!6 models
> show #!5 models
> show #!4 models
> changechains #4/B A
Chain IDs of 430 residues changed
> changechains #4-9/B A
Chain IDs of 2150 residues changed
> close #10
> select add #4
13483 atoms, 13638 bonds, 5 pseudobonds, 871 residues, 2 models selected
> select add #5
26966 atoms, 27276 bonds, 10 pseudobonds, 1742 residues, 4 models selected
> select add #6
40449 atoms, 40914 bonds, 15 pseudobonds, 2613 residues, 6 models selected
> select add #7
53932 atoms, 54552 bonds, 20 pseudobonds, 3484 residues, 8 models selected
> select add #8
67415 atoms, 68190 bonds, 25 pseudobonds, 4355 residues, 10 models selected
> select add #9
80898 atoms, 81828 bonds, 30 pseudobonds, 5226 residues, 12 models selected
> select subtract #9
67415 atoms, 68190 bonds, 25 pseudobonds, 4355 residues, 10 models selected
> select subtract #8
53932 atoms, 54552 bonds, 20 pseudobonds, 3484 residues, 8 models selected
> select subtract #7
40449 atoms, 40914 bonds, 15 pseudobonds, 2613 residues, 6 models selected
> select subtract #6
26966 atoms, 27276 bonds, 10 pseudobonds, 1742 residues, 4 models selected
> select subtract #5
13483 atoms, 13638 bonds, 5 pseudobonds, 871 residues, 2 models selected
> select subtract #4
Nothing selected
> combine #4-9
Remapping chain ID 'A' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #5 to 'B'
Remapping chain ID 'M' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #5 to 'N'
Remapping chain ID 'Nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #5 to 'Nu'
Remapping chain ID 'a' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #5 to 'b'
Remapping chain ID 'nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #5 to 'nu'
Remapping chain ID 'A' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #6 to 'C'
Remapping chain ID 'M' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #6 to 'O'
Remapping chain ID 'Nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #6 to 'Nv'
Remapping chain ID 'a' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #6 to 'c'
Remapping chain ID 'nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #6 to 'nv'
Remapping chain ID 'A' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #7 to 'D'
Remapping chain ID 'M' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #7 to 'P'
Remapping chain ID 'Nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #7 to 'Nw'
Remapping chain ID 'a' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #7 to 'd'
Remapping chain ID 'nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #7 to 'nw'
Remapping chain ID 'A' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #8 to 'E'
Remapping chain ID 'M' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #8 to 'Q'
Remapping chain ID 'Nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #8 to 'Nx'
Remapping chain ID 'a' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #8 to 'e'
Remapping chain ID 'nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #8 to 'nx'
Remapping chain ID 'A' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #9 to 'F'
Remapping chain ID 'M' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #9 to 'R'
Remapping chain ID 'Nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #9 to 'Ny'
Remapping chain ID 'a' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #9 to 'f'
Remapping chain ID 'nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #9 to 'ny'
> fitmap #10 inMap #2 eachModel true
Fit molecule combination (#10) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 80898 atoms
average map value = 0.2068, steps = 40
shifted from previous position = 0.0171
rotated from previous position = 0.00713 degrees
atoms outside contour = 53538, contour level = 0.228
Position of combination (#10) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90926574 0.41620027 -0.00362732 -71.41045964
-0.41621065 0.90926385 -0.00281805 113.11383137
0.00212532 0.00407209 0.99998945 -74.01213011
Axis 0.00827684 -0.00691042 -0.99994187
Axis point 224.58330054 221.98219535 0.00000000
Rotation angle (degrees) 24.59677765
Shift along axis 72.63511037
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> show #!9 models
> show #!8 models
> show #!7 models
> show #!6 models
> show #!5 models
> show #!4 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> split #10
Split combination (#10) into 30 models
Chain information for combination A #10.1
---
Chain | Description
A | No description available
Chain information for combination B #10.2
---
Chain | Description
B | No description available
Chain information for combination C #10.3
---
Chain | Description
C | No description available
Chain information for combination D #10.4
---
Chain | Description
D | No description available
Chain information for combination E #10.5
---
Chain | Description
E | No description available
Chain information for combination F #10.6
---
Chain | Description
F | No description available
Chain information for combination a #10.19
---
Chain | Description
a | No description available
Chain information for combination b #10.20
---
Chain | Description
b | No description available
Chain information for combination c #10.21
---
Chain | Description
c | No description available
Chain information for combination d #10.22
---
Chain | Description
d | No description available
Chain information for combination e #10.23
---
Chain | Description
e | No description available
Chain information for combination f #10.24
---
Chain | Description
f | No description available
> hide #!10 models
> show #!10 models
> fitmap #10 inMap #2 eachModel true
Fit molecule combination A (#10.1) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6631 atoms
average map value = 0.1856, steps = 48
shifted from previous position = 0.119
rotated from previous position = 0.288 degrees
atoms outside contour = 4615, contour level = 0.228
Position of combination A (#10.1) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90841347 0.41807182 0.00095782 -72.41773225
-0.41806730 0.90841075 -0.00310660 113.59053109
-0.00216887 0.00242164 0.99999472 -73.22992330
Axis 0.00661143 0.00373934 -0.99997115
Axis point 222.18431480 223.04924769 0.00000000
Rotation angle (degrees) 24.71353133
Shift along axis 73.17377914
Fit molecule combination B (#10.2) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6631 atoms
average map value = 0.2259, steps = 44
shifted from previous position = 0.0381
rotated from previous position = 0.14 degrees
atoms outside contour = 4205, contour level = 0.228
Position of combination B (#10.2) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90825798 0.41839674 -0.00340663 -71.56444011
-0.41840578 0.90825651 -0.00259241 113.57975058
0.00200944 0.00377993 0.99999084 -73.96911493
Axis 0.00761472 -0.00647202 -0.99995006
Axis point 224.01726618 221.48766029 0.00000000
Rotation angle (degrees) 24.73501163
Shift along axis 72.68538790
Fit molecule combination C (#10.3) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6631 atoms
average map value = 0.2103, steps = 40
shifted from previous position = 0.0979
rotated from previous position = 0.19 degrees
atoms outside contour = 4329, contour level = 0.228
Position of combination C (#10.3) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90837713 0.41811269 -0.00572345 -71.11014288
-0.41812605 0.90838806 -0.00132168 113.36494734
0.00464650 0.00359371 0.99998275 -74.50915888
Axis 0.00587742 -0.01239953 -0.99990585
Axis point 224.99179342 220.39918887 0.00000000
Rotation angle (degrees) 24.71839549
Shift along axis 72.67852684
Fit molecule combination D (#10.4) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6631 atoms
average map value = 0.2277, steps = 48
shifted from previous position = 0.0496
rotated from previous position = 0.234 degrees
atoms outside contour = 4140, contour level = 0.228
Position of combination D (#10.4) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90770277 0.41958459 -0.00494593 -71.22596174
-0.41960372 0.90769948 -0.00379086 114.14765389
0.00289883 0.00551631 0.99998058 -74.32372691
Axis 0.01108951 -0.00934705 -0.99989482
Axis point 225.00155061 221.16283998 0.00000000
Rotation angle (degrees) 24.81175334
Shift along axis 72.45910402
Fit molecule combination E (#10.5) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6631 atoms
average map value = 0.1861, steps = 60
shifted from previous position = 0.11
rotated from previous position = 0.314 degrees
atoms outside contour = 4633, contour level = 0.228
Position of combination E (#10.5) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90882687 0.41716985 0.00174537 -72.93199536
-0.41716516 0.90882720 -0.00251899 113.23933354
-0.00263709 0.00156122 0.99999530 -73.04711015
Axis 0.00489025 0.00525250 -0.99997425
Axis point 221.54818315 224.10443248 0.00000000
Rotation angle (degrees) 24.65656626
Shift along axis 73.28336304
Fit molecule combination F (#10.6) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6631 atoms
average map value = 0.2085, steps = 36
shifted from previous position = 0.0959
rotated from previous position = 0.177 degrees
atoms outside contour = 4324, contour level = 0.228
Position of combination F (#10.6) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90829132 0.41830757 -0.00506551 -71.12248198
-0.41831880 0.90829925 -0.00135929 113.29285442
0.00403240 0.00335363 0.99998625 -74.36319296
Axis 0.00563282 -0.01087370 -0.99992501
Axis point 224.44641850 220.21072927 0.00000000
Rotation angle (degrees) 24.73011624
Shift along axis 72.72508468
Fit molecule combination M (#10.7) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 1 atoms
average map value = 1.07, steps = 64
shifted from previous position = 3.76
rotated from previous position = 0 degrees
atoms outside contour = 0, contour level = 0.228
Position of combination M (#10.7) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90926574 0.41620027 -0.00362732 -74.21847588
-0.41621065 0.90926385 -0.00281805 113.42512820
0.00212532 0.00407209 0.99998945 -71.53530874
Axis 0.00827684 -0.00691042 -0.99994187
Axis point 223.86389116 228.52239274 0.00000000
Rotation angle (degrees) 24.59677765
Shift along axis 70.13304029
Fit molecule combination N (#10.8) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 1 atoms
average map value = 1.12, steps = 60
shifted from previous position = 3.4
rotated from previous position = 0 degrees
atoms outside contour = 0, contour level = 0.228
Position of combination N (#10.8) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90926574 0.41620027 -0.00362732 -73.18297287
-0.41621065 0.90926385 -0.00281805 113.05807713
0.00212532 0.00407209 0.99998945 -71.11574533
Axis 0.00827684 -0.00691042 -0.99994187
Axis point 223.53501864 225.95458197 0.00000000
Rotation angle (degrees) 24.59677765
Shift along axis 69.72460844
Fit molecule combination Nt (#10.9) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 40 atoms
average map value = 0.4218, steps = 52
shifted from previous position = 0.368
rotated from previous position = 25.8 degrees
atoms outside contour = 12, contour level = 0.228
Position of combination Nt (#10.9) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.80600240 0.42756479 0.40932688 -138.74623179
-0.40868192 0.90222981 -0.13769701 138.64326572
-0.42818130 -0.05630038 0.90193738 8.71302247
Axis 0.06861274 0.70597186 -0.70490852
Axis point 67.57983618 0.00000000 384.77235136
Rotation angle (degrees) 36.38155497
Shift along axis 82.21660191
Fit molecule combination Nu (#10.10) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 40 atoms
average map value = 0.4529, steps = 48
shifted from previous position = 0.336
rotated from previous position = 6.9 degrees
atoms outside contour = 15, contour level = 0.228
Position of combination Nu (#10.10) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.89722610 0.42631956 0.11505194 -92.03805400
-0.43012736 0.90271992 0.00933777 113.80053392
-0.09987880 -0.05786508 0.99331559 -48.51513188
Axis -0.07588759 0.24270659 -0.96712697
Axis point 164.08133370 240.93334357 0.00000000
Rotation angle (degrees) 26.28132363
Shift along axis 81.52497800
Fit molecule combination Nv (#10.11) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 40 atoms
average map value = 0.4354, steps = 60
shifted from previous position = 1.16
rotated from previous position = 5.06 degrees
atoms outside contour = 12, contour level = 0.228
Position of combination Nv (#10.11) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.92292073 0.37918780 0.06658784 -82.12258346
-0.37742645 0.92526849 -0.03778221 109.90538753
-0.07593818 0.00973797 0.99706497 -56.61115485
Axis 0.06160360 0.18476606 -0.98084989
Axis point 203.21142920 269.38090529 0.00000000
Rotation angle (degrees) 22.68678135
Shift along axis 70.77478425
Fit molecule combination Nw (#10.12) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 40 atoms
average map value = 0.4686, steps = 48
shifted from previous position = 0.148
rotated from previous position = 4.14 degrees
atoms outside contour = 13, contour level = 0.228
Position of combination Nw (#10.12) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90613154 0.41861718 0.06070658 -88.15348033
-0.42084668 0.90664399 0.02974481 105.46936694
-0.04258757 -0.05250087 0.99771236 -59.20878221
Axis -0.09678417 0.12155336 -0.98785505
Axis point 176.17009667 231.62662080 0.00000000
Rotation angle (degrees) 25.14384164
Shift along axis 79.84171208
Fit molecule combination Nx (#10.13) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 40 atoms
average map value = 0.4482, steps = 56
shifted from previous position = 0.38
rotated from previous position = 25 degrees
atoms outside contour = 13, contour level = 0.228
Position of combination Nx (#10.13) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.80473021 0.44588684 0.39191097 -170.17878207
-0.42469817 0.89369279 -0.14472268 154.92914476
-0.41477795 -0.04998116 0.90854892 11.90605594
Axis 0.07957144 0.67752126 -0.73118625
Axis point 120.40449330 449.15512845 0.00000000
Rotation angle (degrees) 36.53571131
Shift along axis 82.72087386
Fit molecule combination Ny (#10.14) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 40 atoms
average map value = 0.4047, steps = 80
shifted from previous position = 0.549
rotated from previous position = 1.74 degrees
atoms outside contour = 16, contour level = 0.228
Position of combination Ny (#10.14) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.91921546 0.39375493 -0.00001290 -71.58787000
-0.39367268 0.91902278 -0.02046818 111.68276132
-0.00804759 0.01881974 0.99979050 -73.28614380
Axis 0.04982943 0.01019052 -0.99870575
Axis point 232.79886039 238.52516716 0.00000000
Rotation angle (degrees) 23.21758768
Shift along axis 70.76221650
Fit molecule combination O (#10.15) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 1 atoms
average map value = 1.01, steps = 64
shifted from previous position = 4
rotated from previous position = 0 degrees
atoms outside contour = 0, contour level = 0.228
Position of combination O (#10.15) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90926574 0.41620027 -0.00362732 -73.17717378
-0.41621065 0.90926385 -0.00281805 111.16188668
0.00212532 0.00407209 0.99998945 -70.99808167
Axis 0.00827684 -0.00691042 -0.99994187
Axis point 219.18755103 224.99079513 0.00000000
Rotation angle (degrees) 24.59677765
Shift along axis 69.62010309
Fit molecule combination P (#10.16) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 1 atoms
average map value = 1.02, steps = 60
shifted from previous position = 3.1
rotated from previous position = 0 degrees
atoms outside contour = 0, contour level = 0.228
Position of combination P (#10.16) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90926574 0.41620027 -0.00362732 -73.16713364
-0.41621065 0.90926385 -0.00281805 112.37297695
0.00212532 0.00407209 0.99998945 -71.57278177
Axis 0.00827684 -0.00691042 -0.99994187
Axis point 221.97698731 225.58604979 0.00000000
Rotation angle (degrees) 24.59677765
Shift along axis 70.18648374
Fit molecule combination Q (#10.17) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 1 atoms
average map value = 0.912, steps = 52
shifted from previous position = 2.86
rotated from previous position = 0 degrees
atoms outside contour = 0, contour level = 0.228
Position of combination Q (#10.17) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90926574 0.41620027 -0.00362732 -72.76782688
-0.41621065 0.90926385 -0.00281805 113.60003733
0.00212532 0.00407209 0.99998945 -71.53799663
Axis 0.00827684 -0.00691042 -0.99994187
Axis point 224.99059867 225.28283117 0.00000000
Rotation angle (degrees) 24.59677765
Shift along axis 70.14652611
Fit molecule combination R (#10.18) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 1 atoms
average map value = 1.118, steps = 92
shifted from previous position = 4.47
rotated from previous position = 0 degrees
atoms outside contour = 0, contour level = 0.228
Position of combination R (#10.18) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90926574 0.41620027 -0.00362732 -73.76791172
-0.41621065 0.90926385 -0.00281805 112.30902850
0.00212532 0.00407209 0.99998945 -70.30536870
Axis 0.00827684 -0.00691042 -0.99994187
Axis point 221.51500901 226.90352553 0.00000000
Rotation angle (degrees) 24.59677765
Shift along axis 68.91461371
Fit molecule combination a (#10.19) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6767 atoms
average map value = 0.1785, steps = 48
shifted from previous position = 0.0944
rotated from previous position = 0.356 degrees
atoms outside contour = 4778, contour level = 0.228
Position of combination a (#10.19) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90956486 0.41556066 -0.00105117 -72.07318261
-0.41555660 0.90956304 0.00278917 111.59248085
0.00211517 -0.00210011 0.99999556 -73.06139702
Axis -0.00588264 -0.00380965 -0.99997544
Axis point 221.21088971 220.54215648 0.00000000
Rotation angle (degrees) 24.55514401
Shift along axis 73.05845538
Fit molecule combination b (#10.20) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6767 atoms
average map value = 0.2266, steps = 48
shifted from previous position = 0.063
rotated from previous position = 0.264 degrees
atoms outside contour = 4310, contour level = 0.228
Position of combination b (#10.20) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90979835 0.41498942 -0.00712316 -70.51995311
-0.41500087 0.90982100 -0.00014235 112.18732376
0.00642172 0.00308563 0.99997462 -74.54803990
Axis 0.00388863 -0.01631702 -0.99985931
Axis point 225.45615445 219.61555934 0.00000000
Rotation angle (degrees) 24.52268828
Shift along axis 72.43276220
Fit molecule combination c (#10.21) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6767 atoms
average map value = 0.2097, steps = 48
shifted from previous position = 0.0881
rotated from previous position = 0.508 degrees
atoms outside contour = 4429, contour level = 0.228
Position of combination c (#10.21) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90941117 0.41571602 -0.01230894 -69.31818401
-0.41575914 0.90947414 -0.00105916 112.57822706
0.01075435 0.00608077 0.99992368 -76.06280313
Axis 0.00858345 -0.02772612 -0.99957870
Axis point 228.14392723 217.95210470 0.00000000
Rotation angle (degrees) 24.57681328
Shift along axis 72.31441208
Fit molecule combination d (#10.22) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6767 atoms
average map value = 0.2323, steps = 40
shifted from previous position = 0.0579
rotated from previous position = 0.308 degrees
atoms outside contour = 4194, contour level = 0.228
Position of combination d (#10.22) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.91011970 0.41428463 -0.00709806 -70.18893488
-0.41429042 0.91014447 0.00070330 111.53281686
0.00675162 0.00230057 0.99997456 -74.52836348
Axis 0.00192745 -0.01671269 -0.99985848
Axis point 224.74499942 218.51850841 0.00000000
Rotation angle (degrees) 24.47814805
Shift along axis 72.51851656
Fit molecule combination e (#10.23) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6767 atoms
average map value = 0.1755, steps = 48
shifted from previous position = 0.136
rotated from previous position = 0.339 degrees
atoms outside contour = 4848, contour level = 0.228
Position of combination e (#10.23) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90961517 0.41545146 -0.00056649 -72.46151392
-0.41544943 0.90961368 0.00217546 111.30050932
0.00141909 -0.00174348 0.99999747 -72.99227955
Axis -0.00471644 -0.00238964 -0.99998602
Axis point 220.13841019 221.47971110 0.00000000
Rotation angle (degrees) 24.54805214
Shift along axis 73.06705184
Fit molecule combination f (#10.24) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6767 atoms
average map value = 0.2043, steps = 60
shifted from previous position = 0.0879
rotated from previous position = 0.546 degrees
atoms outside contour = 4481, contour level = 0.228
Position of combination f (#10.24) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90944618 0.41562008 -0.01294595 -68.41782090
-0.41566573 0.90951698 -0.00093359 112.36739479
0.01138654 0.00623024 0.99991576 -76.18317954
Axis 0.00861376 -0.02925728 -0.99953480
Axis point 228.42430861 215.88234744 0.00000000
Rotation angle (degrees) 24.57199649
Shift along axis 72.27083987
Fit molecule combination nt (#10.25) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 44 atoms
average map value = 0.4481, steps = 72
shifted from previous position = 0.702
rotated from previous position = 29.6 degrees
atoms outside contour = 16, contour level = 0.228
Position of combination nt (#10.25) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.85695171 0.26288182 0.44331357 -144.42953303
-0.22013775 0.96442652 -0.14635866 112.75888101
-0.46601839 0.02783225 0.88433717 8.74778797
Axis 0.16680371 0.87076838 -0.46253534
Axis point 0.82868470 0.00000000 352.41998725
Rotation angle (degrees) 31.47613793
Shift along axis 70.04932606
Fit molecule combination nu (#10.26) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 44 atoms
average map value = 0.5339, steps = 48
shifted from previous position = 0.376
rotated from previous position = 4.01 degrees
atoms outside contour = 15, contour level = 0.228
Position of combination nu (#10.26) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.92479905 0.37688146 0.05202958 -81.43836481
-0.37737409 0.92606082 -0.00038347 104.18982569
-0.04832708 -0.01927999 0.99864547 -62.67103901
Axis -0.02482669 0.13185093 -0.99095861
Axis point 199.74503907 250.81170412 0.00000000
Rotation angle (degrees) 22.36891034
Shift along axis 77.86377653
Fit molecule combination nv (#10.27) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 44 atoms
average map value = 0.4165, steps = 64
shifted from previous position = 0.523
rotated from previous position = 10.1 degrees
atoms outside contour = 17, contour level = 0.228
Position of combination nv (#10.27) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.83463365 0.54135967 -0.10156955 -46.71012017
-0.54478767 0.83854192 -0.00733821 149.60602551
0.08119771 0.06145855 0.99480138 -95.78897215
Axis 0.06234054 -0.16561550 -0.98421805
Axis point 244.84616147 168.74286399 0.00000000
Rotation angle (degrees) 33.48934247
Shift along axis 66.58822384
Fit molecule combination nw (#10.28) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 44 atoms
average map value = 0.4926, steps = 76
shifted from previous position = 0.336
rotated from previous position = 1.83 degrees
atoms outside contour = 15, contour level = 0.228
Position of combination nw (#10.28) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.91658738 0.39931817 0.02031196 -77.58190372
-0.39953403 0.91668500 0.00782156 106.14540731
-0.01549637 -0.01528447 0.99976310 -68.81624893
Axis -0.02888297 0.04476108 -0.99858010
Axis point 208.72634107 232.41008643 0.00000000
Rotation angle (degrees) 23.57780649
Shift along axis 75.71051587
Fit molecule combination nx (#10.29) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 44 atoms
average map value = 0.4105, steps = 72
shifted from previous position = 1.56
rotated from previous position = 25.5 degrees
atoms outside contour = 17, contour level = 0.228
Position of combination nx (#10.29) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.88396190 0.26924159 0.38225689 -164.79323304
-0.24003512 0.96292070 -0.12315383 120.13780112
-0.40124120 0.01710821 0.91581265 1.51413395
Axis 0.14843538 0.82915400 -0.53895323
Axis point 6.68640158 0.00000000 462.00118414
Rotation angle (degrees) 28.19464399
Shift along axis 74.33554549
Fit molecule combination ny (#10.30) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 44 atoms
average map value = 0.3755, steps = 48
shifted from previous position = 0.255
rotated from previous position = 5.14 degrees
atoms outside contour = 17, contour level = 0.228
Position of combination ny (#10.30) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.88579225 0.46007526 -0.06085096 -53.75948109
-0.46302480 0.88498961 -0.04900425 139.55622459
0.03130683 0.07158309 0.99694320 -86.41943645
Axis 0.12890238 -0.09851249 -0.98675198
Axis point 265.26879109 200.79739302 0.00000000
Rotation angle (degrees) 27.88813237
Shift along axis 64.59679407
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> hide #!10 models
> select ::name="MG"
14 atoms, 14 residues, 14 models selected
> select add #10
80906 atoms, 81828 bonds, 5234 residues, 39 models selected
> select subtract #10
8 atoms, 8 residues, 8 models selected
> select add #3
13490 atoms, 13638 bonds, 5 pseudobonds, 878 residues, 9 models selected
> select subtract #3
7 atoms, 7 residues, 7 models selected
> select add #1
13489 atoms, 13638 bonds, 5 pseudobonds, 877 residues, 8 models selected
> select subtract #1
6 atoms, 6 residues, 6 models selected
> combine #4-9
Remapping chain ID 'A' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #5 to 'B'
Remapping chain ID 'M' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #5 to 'N'
Remapping chain ID 'Nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #5 to 'Nu'
Remapping chain ID 'a' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #5 to 'b'
Remapping chain ID 'nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #5 to 'nu'
Remapping chain ID 'A' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #6 to 'C'
Remapping chain ID 'M' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #6 to 'O'
Remapping chain ID 'Nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #6 to 'Nv'
Remapping chain ID 'a' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #6 to 'c'
Remapping chain ID 'nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #6 to 'nv'
Remapping chain ID 'A' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #7 to 'D'
Remapping chain ID 'M' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #7 to 'P'
Remapping chain ID 'Nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #7 to 'Nw'
Remapping chain ID 'a' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #7 to 'd'
Remapping chain ID 'nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #7 to 'nw'
Remapping chain ID 'A' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #8 to 'E'
Remapping chain ID 'M' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #8 to 'Q'
Remapping chain ID 'Nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #8 to 'Nx'
Remapping chain ID 'a' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #8 to 'e'
Remapping chain ID 'nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #8 to 'nx'
Remapping chain ID 'A' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #9 to 'F'
Remapping chain ID 'M' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #9 to 'R'
Remapping chain ID 'Nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #9 to 'Ny'
Remapping chain ID 'a' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #9 to 'f'
Remapping chain ID 'nt' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #9 to 'ny'
> hide #!11 models
> show #!11 models
> hide #!11 models
> select ~sel
269654 atoms, 272760 bonds, 40 pseudobonds, 17414 residues, 45 models selected
> select subtract #10
188756 atoms, 190932 bonds, 40 pseudobonds, 12188 residues, 14 models selected
> select subtract #11
107858 atoms, 109104 bonds, 10 pseudobonds, 6962 residues, 12 models selected
> select subtract #3
94375 atoms, 95466 bonds, 5 pseudobonds, 6091 residues, 10 models selected
> select subtract #2
94375 atoms, 95466 bonds, 5 pseudobonds, 6091 residues, 8 models selected
> select subtract #1
80892 atoms, 81828 bonds, 5220 residues, 6 models selected
> select add #11
161790 atoms, 163656 bonds, 30 pseudobonds, 10446 residues, 8 models selected
> select subtract #11
80892 atoms, 81828 bonds, 5220 residues, 6 models selected
> delete atoms sel
> delete bonds sel
> show #!10 models
> select ::name="MG"
20 atoms, 20 residues, 15 models selected
> select subtract #4
19 atoms, 19 residues, 14 models selected
> select subtract #5
18 atoms, 18 residues, 13 models selected
> select subtract #6
17 atoms, 17 residues, 12 models selected
> select subtract #7
16 atoms, 16 residues, 11 models selected
> select subtract #8
15 atoms, 15 residues, 10 models selected
> select subtract #9
14 atoms, 14 residues, 9 models selected
> select add #11
80906 atoms, 81828 bonds, 30 pseudobonds, 5234 residues, 10 models selected
> select subtract #11
8 atoms, 8 residues, 8 models selected
> select add #3
13490 atoms, 13638 bonds, 5 pseudobonds, 878 residues, 9 models selected
> select subtract #3
7 atoms, 7 residues, 7 models selected
> select add #1
13489 atoms, 13638 bonds, 5 pseudobonds, 877 residues, 8 models selected
> select subtract #1
6 atoms, 6 residues, 6 models selected
> delete atoms sel
> delete bonds sel
> show #!11 models
> combine #4-10
Remapping chain ID 'M' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #5 to 'N'
Remapping chain ID 'M' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #6 to 'O'
Remapping chain ID 'M' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #7 to 'P'
Remapping chain ID 'M' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #8 to 'Q'
Remapping chain ID 'M' in 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #9 to 'R'
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!11 models
> show #!11 models
> show #!12 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> hide #!12 models
> show #!11 models
> save
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_6dimers.pdb
> models #11 relModel #2
> hide #!11 models
> show #!12 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> select add #12
80898 atoms, 81828 bonds, 5226 residues, 1 model selected
> hide #!11 models
> select subtract #12
Nothing selected
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> save
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_6dimers_individualchaindock.pdb
> models #12 relModel #2
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_6dimers_individualchaindock.pdb
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_6dimers.pdb
Chain information for 231009_Xt_14-3_dEMhcr_6dimers_individualchaindock.pdb
#13
---
Chain | Description
A B C D E F | No description available
a b c d e f | No description available
Chain information for 231009_Xt_14-3_dEMhcr_6dimers.pdb #14
---
Chain | Description
A B C D E F | No description available
a b c d e f | No description available
> hide #!12 models
> hide #13 models
> hide #!14 models
> show #!14 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #!2 models
> select add #13
80898 atoms, 81828 bonds, 5226 residues, 1 model selected
> select add #14
161796 atoms, 163656 bonds, 30 pseudobonds, 10452 residues, 3 models selected
> show sel & #!14 atoms
> style sel & #!14 stick
Changed 80898 atom styles
> hide sel & #!14 atoms
> show sel & #!14 cartoons
> show sel & #!14 atoms
> hide HC
> show #13 models
> style sel stick
Changed 161796 atom styles
> show sel atoms
> hide sel cartoons
> show sel cartoons
> hide HC
> color (#13#!14 & sel) byhetero
> select clear
> hide #13 models
> show #13 models
> hide #!14 models
> show #!14 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> hide #!14 models
> hide #14.1 models
> show #13 models
> hide #13 models
> close #11,13-14#4-10,12
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #4
---
Chain | Description
B | No description available
a | No description available
> split #4
Split 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#4) into 5 models
Chain information for 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb B #4.1
---
Chain | Description
B | No description available
Chain information for 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb a #4.4
---
Chain | Description
a | No description available
> fitmap #4.4 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb a (#4.4) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6767 atoms
average map value = 0.2323, steps = 64
shifted from previous position = 0.263
rotated from previous position = 0.421 degrees
atoms outside contour = 4189, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb a (#4.4) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.99997376 -0.00322836 -0.00648587 1.99967891
0.00323636 0.99999401 0.00122409 -0.95465235
0.00648188 -0.00124505 0.99997822 -0.58958943
Axis -0.16798414 -0.88223771 0.43981582
Axis point 108.77586303 0.00000000 314.27047849
Rotation angle (degrees) 0.42109051
Shift along axis 0.24700520
> fitmap #4.5 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb nt (#4.5) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 44 atoms
average map value = 0.4923, steps = 48
shifted from previous position = 0.376
rotated from previous position = 1.82 degrees
atoms outside contour = 15, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb nt (#4.5) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.99953081 -0.02063670 0.02263365 -1.79098418
0.02043912 0.99975125 0.00892623 -4.90196754
-0.02281223 -0.00845943 0.99970398 4.19361690
Axis -0.27302719 0.71368923 0.64506111
Axis point 191.31228682 0.00000000 86.76650600
Rotation angle (degrees) 1.82453160
Shift along axis -0.30435491
> show #!1 models
> hide #!1 models
> show #!1 models
> combine #4.4,4.5,4.2
No structures specified
> combine #4.4-4.5
No structures specified
> select add #4.3
40 atoms, 42 bonds, 1 residue, 1 model selected
> select add #4.4
6807 atoms, 6886 bonds, 439 residues, 2 models selected
> select add #4.5
6851 atoms, 6932 bonds, 440 residues, 3 models selected
> select subtract #4.4
84 atoms, 88 bonds, 2 residues, 2 models selected
> select add #4.4
6851 atoms, 6932 bonds, 440 residues, 3 models selected
> select subtract #4.5
6807 atoms, 6886 bonds, 439 residues, 2 models selected
> select add #4.2
6808 atoms, 6886 bonds, 440 residues, 3 models selected
> select subtract #4.3
6768 atoms, 6844 bonds, 439 residues, 2 models selected
> select add #4.5
6812 atoms, 6890 bonds, 440 residues, 3 models selected
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #5
---
Chain | Description
B | No description available
a | No description available
> close #4#5
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #4
---
Chain | Description
B | No description available
a | No description available
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_6dimers_individualchaindock.pdb
Chain information for 231009_Xt_14-3_dEMhcr_6dimers_individualchaindock.pdb #5
---
Chain | Description
A B C D E F | No description available
a b c d e f | No description available
> close #5
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #5
---
Chain | Description
B | No description available
a | No description available
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> hide #!1 models
> hide #!5 models
> select up
3726 atoms, 3760 bonds, 244 residues, 1 model selected
> select up
4571 atoms, 4620 bonds, 299 residues, 1 model selected
> select up
6671 atoms, 6748 bonds, 431 residues, 1 model selected
> select up
13483 atoms, 13638 bonds, 871 residues, 1 model selected
> select down
6671 atoms, 6748 bonds, 431 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> select up
7502 atoms, 7544 bonds, 490 residues, 2 models selected
> select up
7580 atoms, 7630 bonds, 490 residues, 2 models selected
> select up
9604 atoms, 9702 bonds, 622 residues, 2 models selected
> select up
13622 atoms, 13780 bonds, 878 residues, 2 models selected
> select up
20295 atoms, 20528 bonds, 4 pseudobonds, 1311 residues, 3 models selected
> select down
13623 atoms, 13780 bonds, 1 pseudobond, 879 residues, 3 models selected
> delete atoms (#!4-5 & sel)
> delete bonds (#!4-5 & sel)
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> close #5
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #4
---
Chain | Description
B | No description available
a | No description available
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb #5
---
Chain | Description
B | No description available
a | No description available
> hide #!5 models
> hide #!4 models
> show #!5 models
> select up
4515 atoms, 4564 bonds, 295 residues, 1 model selected
> select up
4976 atoms, 5032 bonds, 324 residues, 1 model selected
> select up
6671 atoms, 6748 bonds, 431 residues, 1 model selected
> select up
13483 atoms, 13638 bonds, 871 residues, 1 model selected
> select down
6671 atoms, 6748 bonds, 431 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!4 models
> hide #!5 models
> select up
3716 atoms, 3751 bonds, 242 residues, 1 model selected
> select up
4458 atoms, 4503 bonds, 292 residues, 1 model selected
> select up
6671 atoms, 6748 bonds, 431 residues, 1 model selected
> select ~sel
40590 atoms, 41056 bonds, 18 pseudobonds, 2622 residues, 10 models selected
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> show #!5 models
> select clear
> select add #1
13483 atoms, 13638 bonds, 5 pseudobonds, 871 residues, 2 models selected
> select add #2
13483 atoms, 13638 bonds, 5 pseudobonds, 871 residues, 4 models selected
> select add #3
26966 atoms, 27276 bonds, 10 pseudobonds, 1742 residues, 6 models selected
> select subtract #2
26966 atoms, 27276 bonds, 10 pseudobonds, 1742 residues, 4 models selected
> select subtract #1
13483 atoms, 13638 bonds, 5 pseudobonds, 871 residues, 2 models selected
> select subtract #3
Nothing selected
> show #!1 models
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> fitmap #4 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#4) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6671 atoms
average map value = 0.2292, steps = 44
shifted from previous position = 0.102
rotated from previous position = 0.348 degrees
atoms outside contour = 4160, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#4) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.99998612 0.00263436 -0.00456278 0.49266974
-0.00264814 0.99999194 -0.00301861 0.87319663
0.00455479 0.00303065 0.99998503 -1.07160056
Axis 0.49787195 -0.75040185 -0.43476498
Axis point 230.26259946 0.00000000 101.17230727
Rotation angle (degrees) 0.34808092
Shift along axis 0.05593247
> fitmap #5 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#5) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6812 atoms
average map value = 0.234, steps = 64
shifted from previous position = 0.263
rotated from previous position = 0.434 degrees
atoms outside contour = 4198, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#5) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.99997183 -0.00311749 -0.00682726 2.07298412
0.00312458 0.99999459 0.00102802 -0.89152478
0.00682401 -0.00104933 0.99997617 -0.64621433
Axis -0.13708477 -0.90085122 0.41191606
Axis point 111.03165532 0.00000000 308.25091629
Rotation angle (degrees) 0.43412697
Shift along axis 0.25277058
> fitmap #5 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#5) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6812 atoms
average map value = 0.234, steps = 44
shifted from previous position = 0.017
rotated from previous position = 0.0187 degrees
atoms outside contour = 4211, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#5) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.99997304 -0.00328422 -0.00656684 2.03265762
0.00329173 0.99999394 0.00113349 -0.94082457
0.00656308 -0.00115507 0.99997780 -0.61428470
Axis -0.15398842 -0.88346278 0.44247156
Axis point 111.27243527 0.00000000 314.85426886
Rotation angle (degrees) 0.42576529
Shift along axis 0.24637424
> fitmap #4 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#4) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6671 atoms
average map value = 0.2292, steps = 44
shifted from previous position = 0.00114
rotated from previous position = 0.00759 degrees
atoms outside contour = 4161, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#4) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.99998599 0.00263726 -0.00458994 0.49882226
-0.00265172 0.99999153 -0.00314818 0.89984348
0.00458160 0.00316030 0.99998451 -1.09406683
Axis 0.51187481 -0.74418624 -0.42915152
Axis point 233.96902158 0.00000000 101.80660444
Rotation angle (degrees) 0.35306631
Shift along axis 0.05520386
> fitmap #5 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#5) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 6812 atoms
average map value = 0.234, steps = 40
shifted from previous position = 0.00632
rotated from previous position = 0.00576 degrees
atoms outside contour = 4206, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed.pdb (#5) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.99997240 -0.00328036 -0.00666654 2.05784322
0.00328807 0.99999394 0.00114610 -0.94314135
0.00666274 -0.00116799 0.99997712 -0.63091106
Axis -0.15387304 -0.88631898 0.43676282
Axis point 111.74669893 0.00000000 313.84524523
Rotation angle (degrees) 0.43083710
Shift along axis 0.24371899
> select up
6321 atoms, 2823 bonds, 4 pseudobonds, 414 residues, 3 models selected
> select up
6366 atoms, 6417 bonds, 4 pseudobonds, 414 residues, 3 models selected
> select up
8672 atoms, 8759 bonds, 4 pseudobonds, 562 residues, 3 models selected
> select up
13483 atoms, 13638 bonds, 4 pseudobonds, 871 residues, 3 models selected
> select down
8672 atoms, 8759 bonds, 4 pseudobonds, 562 residues, 3 models selected
> select clear
> combine #4-5
> save
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb
> models #6 relModel #2
> hide #!4 models
> hide #!5 models
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb
#7
---
Chain | Description
B | No description available
a | No description available
> hide #!6 models
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb
#8
---
Chain | Description
B | No description available
a | No description available
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb
#9
---
Chain | Description
B | No description available
a | No description available
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb
#10
---
Chain | Description
B | No description available
a | No description available
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb
#11
---
Chain | Description
B | No description available
a | No description available
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb
Chain information for 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb
#12
---
Chain | Description
B | No description available
a | No description available
> ui tool show Matchmaker
> select add #3
13483 atoms, 13638 bonds, 5 pseudobonds, 871 residues, 2 models selected
> select subtract #3
Nothing selected
> select add #2
2 models selected
> select subtract #2
Nothing selected
> select add #2
2 models selected
> show #!2 models
> select add #7
13483 atoms, 13638 bonds, 4 pseudobonds, 871 residues, 4 models selected
> select add #10
26966 atoms, 27276 bonds, 8 pseudobonds, 1742 residues, 6 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,1,0,0,0.24818,0,1,0,-0.5083,0,0,1,-0.13664,#7,1,0,0,0.24818,0,1,0,-0.5083,0,0,1,-0.13664,#10,1,0,0,0.24818,0,1,0,-0.5083,0,0,1,-0.13664
> select subtract #10
13483 atoms, 13638 bonds, 4 pseudobonds, 871 residues, 4 models selected
> select add #10
26966 atoms, 27276 bonds, 8 pseudobonds, 1742 residues, 6 models selected
> select subtract #2
26966 atoms, 27276 bonds, 8 pseudobonds, 1742 residues, 4 models selected
> view matrix models
> #7,1,0,0,-22.483,0,1,0,46.277,0,0,1,9.4719,#10,1,0,0,-22.483,0,1,0,46.277,0,0,1,9.4719
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.95114,0.30512,0.047191,-74.374,-0.30831,0.94679,0.092419,73.027,-0.016481,-0.10245,0.9946,28.733,#10,0.95114,0.30512,0.047191,-74.374,-0.30831,0.94679,0.092419,73.027,-0.016481,-0.10245,0.9946,28.733
> view matrix models
> #7,0.91052,0.4134,-0.0074958,-73.787,-0.41339,0.90988,-0.034907,120.73,-0.0076101,0.034882,0.99936,5.1517,#10,0.91052,0.4134,-0.0074958,-73.787,-0.41339,0.90988,-0.034907,120.73,-0.0076101,0.034882,0.99936,5.1517
> view matrix models
> #7,0.91547,0.40122,-0.030577,-67.338,-0.40236,0.91189,-0.080998,129.36,-0.0046154,0.086454,0.99625,-2.5593,#10,0.91547,0.40122,-0.030577,-67.338,-0.40236,0.91189,-0.080998,129.36,-0.0046154,0.086454,0.99625,-2.5593
> view matrix models
> #7,0.90867,0.39374,-0.1389,-40.985,-0.40077,0.91582,-0.025711,116.13,0.11708,0.079029,0.98997,-15.474,#10,0.90867,0.39374,-0.1389,-40.985,-0.40077,0.91582,-0.025711,116.13,0.11708,0.079029,0.98997,-15.474
> view matrix models
> #7,0.9128,0.40387,-0.060684,-60.651,-0.40597,0.91348,-0.027176,117.49,0.044458,0.049442,0.99779,-3.3846,#10,0.9128,0.40387,-0.060684,-60.651,-0.40597,0.91348,-0.027176,117.49,0.044458,0.049442,0.99779,-3.3846
> view matrix models
> #7,0.89078,0.44003,0.11353,-102.6,-0.43851,0.89786,-0.039346,126.79,-0.11924,-0.014733,0.99276,28.56,#10,0.89078,0.44003,0.11353,-102.6,-0.43851,0.89786,-0.039346,126.79,-0.11924,-0.014733,0.99276,28.56
> view matrix models
> #7,0.91332,0.40261,0.061224,-87.894,-0.40116,0.91534,-0.035047,118.35,-0.070151,0.0074492,0.99751,17.794,#10,0.91332,0.40261,0.061224,-87.894,-0.40116,0.91534,-0.035047,118.35,-0.070151,0.0074492,0.99751,17.794
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.91332,0.40261,0.061224,-85.143,-0.40116,0.91534,-0.035047,119.23,-0.070151,0.0074492,0.99751,17.623,#10,0.91332,0.40261,0.061224,-85.143,-0.40116,0.91534,-0.035047,119.23,-0.070151,0.0074492,0.99751,17.623
> select subtract #10
13483 atoms, 13638 bonds, 4 pseudobonds, 871 residues, 2 models selected
> view matrix models
> #7,0.91332,0.40261,0.061224,-90.176,-0.40116,0.91534,-0.035047,131.39,-0.070151,0.0074492,0.99751,-61.862
> view matrix models
> #7,0.91332,0.40261,0.061224,-97.127,-0.40116,0.91534,-0.035047,119.77,-0.070151,0.0074492,0.99751,-62.039
> view matrix models
> #7,0.91332,0.40261,0.061224,-89.905,-0.40116,0.91534,-0.035047,116.9,-0.070151,0.0074492,0.99751,-68.105
> select add #8
26966 atoms, 27276 bonds, 8 pseudobonds, 1742 residues, 4 models selected
> select subtract #7
13483 atoms, 13638 bonds, 4 pseudobonds, 871 residues, 2 models selected
> view matrix models #8,1,0,0,12.046,0,1,0,1.5826,0,0,1,-82.489
> view matrix models #8,1,0,0,4.9572,0,1,0,-7.3867,0,0,1,-82.426
> view matrix models #8,1,0,0,-1.8307,0,1,0,-5.2244,0,0,1,-82.633
> select subtract #8
Nothing selected
> select add #9
13483 atoms, 13638 bonds, 4 pseudobonds, 871 residues, 2 models selected
> select add #12
26966 atoms, 27276 bonds, 8 pseudobonds, 1742 residues, 4 models selected
> view matrix models
> #9,1,0,0,43.979,0,1,0,-29.31,0,0,1,-9.3433,#12,1,0,0,43.979,0,1,0,-29.31,0,0,1,-9.3433
> view matrix models
> #9,1,0,0,42.682,0,1,0,-37.885,0,0,1,-9.098,#12,1,0,0,42.682,0,1,0,-37.885,0,0,1,-9.098
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.71815,-0.69222,0.071349,170.29,0.69238,0.72105,0.026386,-88.445,-0.069711,0.030452,0.9971,-4.3218,#12,0.71815,-0.69222,0.071349,170.29,0.69238,0.72105,0.026386,-88.445,-0.069711,0.030452,0.9971,-4.3218
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.71815,-0.69222,0.071349,167.41,0.69238,0.72105,0.026386,-86.381,-0.069711,0.030452,0.9971,-1.4692,#12,0.71815,-0.69222,0.071349,167.41,0.69238,0.72105,0.026386,-86.381,-0.069711,0.030452,0.9971,-1.4692
> select subtract #9
13483 atoms, 13638 bonds, 4 pseudobonds, 871 residues, 2 models selected
> select add #9
26966 atoms, 27276 bonds, 8 pseudobonds, 1742 residues, 4 models selected
> select subtract #12
13483 atoms, 13638 bonds, 4 pseudobonds, 871 residues, 2 models selected
> view matrix models
> #9,0.71815,-0.69222,0.071349,170.2,0.69238,0.72105,0.026386,-82.458,-0.069711,0.030452,0.9971,-82.501
> view matrix models
> #9,0.71815,-0.69222,0.071349,169.51,0.69238,0.72105,0.026386,-87.115,-0.069711,0.030452,0.9971,-83.555
> fitmap #7 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#7) to
map Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.1219, steps = 128
shifted from previous position = 5.23
rotated from previous position = 4.71 degrees
atoms outside contour = 10872, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#7)
relative to Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90075949 0.43427603 -0.00605621 -73.43295203
-0.43429984 0.90076213 -0.00335180 117.60370511
0.00399960 0.00564937 0.99997604 -79.48437836
Axis 0.01036189 -0.01157595 -0.99987931
Axis point 222.18936358 221.71303518 0.00000000
Rotation angle (degrees) 25.74332707
Shift along axis 77.35250658
> fitmap #8 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#8) to
map Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.2277, steps = 76
shifted from previous position = 4.49
rotated from previous position = 0.393 degrees
atoms outside contour = 8545, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#8)
relative to Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.99997680 -0.00680364 -0.00031929 2.18640833
0.00680391 0.99997650 0.00084292 -2.93211955
0.00031355 -0.00084507 0.99999959 -80.94671445
Axis -0.12297410 -0.04610330 0.99133842
Axis point 971.67675973 -1134.78946751 0.00000000
Rotation angle (degrees) 0.39323669
Shift along axis -80.37927895
> fitmap #9 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#9) to
map Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.2111, steps = 88
shifted from previous position = 2.94
rotated from previous position = 18.5 degrees
atoms outside contour = 8767, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#9)
relative to Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.89973488 -0.43640947 0.00489001 119.79396393
0.43637917 0.89974165 0.00617912 -77.33185391
-0.00709638 -0.00342567 0.99996895 -87.57958274
Axis -0.01100302 0.01373131 0.99984518
Axis point 225.04829139 220.52636381 0.00000000
Rotation angle (degrees) 25.87835297
Shift along axis -89.94598635
> fitmap #10 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#10) to
map Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.1816, steps = 80
shifted from previous position = 1.65
rotated from previous position = 4.25 degrees
atoms outside contour = 9529, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#10)
relative to Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90595451 0.42337398 -0.00095043 -73.22855240
-0.42337502 0.90595286 -0.00173118 116.41030731
0.00012811 0.00197076 0.99999805 7.55607402
Axis 0.00437189 -0.00127373 -0.99998963
Axis point 225.40793631 222.95198991 0.00000000
Rotation angle (degrees) 25.04809547
Shift along axis -8.02441791
> fitmap #11 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#11) to
map Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.2316, steps = 68
shifted from previous position = 0.581
rotated from previous position = 0.0133 degrees
atoms outside contour = 8372, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#11)
relative to Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.99999999 0.00014449 -0.00002166 -0.01781924
-0.00014449 0.99999997 0.00018086 -0.02357251
0.00002169 -0.00018085 0.99999998 0.02924277
Axis -0.77787743 -0.09321991 -0.62146340
Axis point 0.00000000 154.41507641 131.45157093
Rotation angle (degrees) 0.01332110
Shift along axis -0.00211470
> fitmap #12 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#12) to
map Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.2073, steps = 92
shifted from previous position = 2.7
rotated from previous position = 18.8 degrees
atoms outside contour = 8874, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#12)
relative to Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90231729 -0.43104597 0.00478333 117.37109490
0.43101834 0.90232426 0.00584071 -75.38717878
-0.00683372 -0.00320847 0.99997150 -6.62191933
Axis -0.01049557 0.01347388 0.99985414
Axis point 224.74304937 221.14695452 0.00000000
Rotation angle (degrees) 25.53707397
Shift along axis -8.86858759
> select clear
> select add #7
13483 atoms, 13638 bonds, 4 pseudobonds, 871 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.95917,0.25606,0.12012,-81.196,-0.26336,0.96344,0.049209,73.791,-0.10313,-0.078835,0.99154,-50.946
> fitmap #7 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#7) to
map Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.1828, steps = 104
shifted from previous position = 4.56
rotated from previous position = 12.1 degrees
atoms outside contour = 9452, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#7)
relative to Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90885158 0.41711921 0.00061083 -72.32333142
-0.41711821 0.90885131 -0.00129839 113.09421604
-0.00109673 0.00092525 0.99999897 -73.11764911
Axis 0.00266546 0.00204684 -0.99999435
Axis point 222.17351896 222.40426650 0.00000000
Rotation angle (degrees) 24.65296119
Shift along axis 73.15594708
> fitmap #7 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#7) to
map Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.1828, steps = 40
shifted from previous position = 0.00421
rotated from previous position = 0.0176 degrees
atoms outside contour = 9453, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#7)
relative to Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90880194 0.41722721 0.00070112 -72.35238855
-0.41722580 0.90880151 -0.00156694 113.17889223
-0.00129095 0.00113151 0.99999853 -73.12668364
Axis 0.00323377 0.00238725 -0.99999192
Axis point 222.20136531 222.54855497 0.00000000
Rotation angle (degrees) 24.65982095
Shift along axis 73.16230864
> fitmap #8 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#8) to
map Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.2277, steps = 28
shifted from previous position = 0.0057
rotated from previous position = 0.00786 degrees
atoms outside contour = 8540, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#8)
relative to Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.99997699 -0.00678066 -0.00018707 2.15344972
0.00678081 0.99997668 0.00081462 -2.92228347
0.00018154 -0.00081587 0.99999965 -80.94013957
Axis -0.11932653 -0.02697605 0.99248852
Axis point 747.46801199 -1101.77514021 0.00000000
Rotation angle (degrees) 0.39145080
Shift along axis -80.51029176
> fitmap #9 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#9) to
map Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.2111, steps = 40
shifted from previous position = 0.00203
rotated from previous position = 0.00793 degrees
atoms outside contour = 8767, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#9)
relative to Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.89972352 -0.43643139 0.00502209 119.76848196
0.43640040 0.89973112 0.00621257 -77.33998778
-0.00722989 -0.00339795 0.99996809 -87.56862867
Axis -0.01100898 0.01403482 0.99984090
Axis point 224.98406781 220.46425210 0.00000000
Rotation angle (degrees) 25.87984594
Shift along axis -89.95867777
> fitmap #10 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#10) to
map Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.1816, steps = 44
shifted from previous position = 0.0262
rotated from previous position = 0.00649 degrees
atoms outside contour = 9526, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#10)
relative to Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90598424 0.42331023 -0.00100545 -73.21067778
-0.42331138 0.90598274 -0.00166153 116.36762892
0.00020758 0.00193094 0.99999811 7.57388619
Axis 0.00424325 -0.00143277 -0.99998997
Axis point 225.36090958 222.91923330 0.00000000
Rotation angle (degrees) 25.04405813
Shift along axis -8.05119011
> fitmap #11 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#11) to
map Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.2316, steps = 36
shifted from previous position = 0.00174
rotated from previous position = 0.00149 degrees
atoms outside contour = 8372, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#11)
relative to Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.99999999 0.00014599 -0.00001410 -0.02054051
-0.00014599 0.99999997 0.00020570 -0.02769911
0.00001413 -0.00020570 0.99999998 0.03306371
Axis -0.81420974 -0.05588161 -0.57787520
Axis point 0.00000000 158.37989838 134.90836990
Rotation angle (degrees) 0.01447507
Shift along axis -0.00083454
> fitmap #12 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#12) to
map Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 13483 atoms
average map value = 0.2073, steps = 40
shifted from previous position = 0.0154
rotated from previous position = 0.00615 degrees
atoms outside contour = 8861, contour level = 0.228
Position of 231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb (#12)
relative to Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90231448 -0.43105261 0.00471434 117.38935835
0.43102464 0.90232072 0.00592256 -75.40614567
-0.00680678 -0.00331201 0.99997135 -6.59426597
Axis -0.01071043 0.01336242 0.99985336
Axis point 224.79318101 221.16893092 0.00000000
Rotation angle (degrees) 25.53750638
Shift along axis -8.85819807
> select clear
> combine #7-12
Remapping chain ID 'B' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #8 to 'C'
Remapping chain ID 'M' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #8 to 'N'
Remapping chain ID 'Nt' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #8 to 'Nu'
Remapping chain ID 'a' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #8 to 'b'
Remapping chain ID 'nt' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #8 to 'nu'
Remapping chain ID 'B' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #9 to 'D'
Remapping chain ID 'M' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #9 to 'O'
Remapping chain ID 'Nt' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #9 to 'Nv'
Remapping chain ID 'a' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #9 to 'c'
Remapping chain ID 'nt' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #9 to 'nv'
Remapping chain ID 'B' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #10 to 'E'
Remapping chain ID 'M' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #10 to 'P'
Remapping chain ID 'Nt' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #10 to 'Nw'
Remapping chain ID 'a' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #10 to 'd'
Remapping chain ID 'nt' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #10 to 'nw'
Remapping chain ID 'B' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #11 to 'F'
Remapping chain ID 'M' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #11 to 'Q'
Remapping chain ID 'Nt' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #11 to 'Nx'
Remapping chain ID 'a' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #11 to 'e'
Remapping chain ID 'nt' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #11 to 'nx'
Remapping chain ID 'B' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #12 to 'G'
Remapping chain ID 'M' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #12 to 'R'
Remapping chain ID 'Nt' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #12 to 'Ny'
Remapping chain ID 'a' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #12 to 'f'
Remapping chain ID 'nt' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #12 to 'ny'
> save
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_6dimers_hybrid_dock.pdb
> models #13 relModel #2
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_6dimers_hybrid_dock.pdb
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_6dimers_individualchaindock.pdb
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_6dimers.pdb
Chain information for 231009_Xt_14-3_dEMhcr_6dimers_hybrid_dock.pdb #14
---
Chain | Description
B C D E F G | No description available
a b c d e f | No description available
Chain information for 231009_Xt_14-3_dEMhcr_6dimers_individualchaindock.pdb
#15
---
Chain | Description
A B C D E F | No description available
a b c d e f | No description available
Chain information for 231009_Xt_14-3_dEMhcr_6dimers.pdb #16
---
Chain | Description
A B C D E F | No description available
a b c d e f | No description available
> select add #14
80898 atoms, 81828 bonds, 24 pseudobonds, 5226 residues, 2 models selected
> select add #15
161796 atoms, 163656 bonds, 24 pseudobonds, 10452 residues, 3 models selected
> select add #16
242694 atoms, 245484 bonds, 54 pseudobonds, 15678 residues, 5 models selected
> style sel stick
Changed 242694 atom styles
> hide sel atoms
> show sel cartoons
> show #15#!14,16 target m
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!2 models
> select clear
> hide #15 models
> hide #!16 models
> hide #!14 models
> show #15 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!14 models
> hide #15 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!16 models
> hide #!14 models
> show #!14 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #14.1 models
> hide #16.1 models
> hide #!14 models
> show #16.1 models
> hide #16.1 models
> show #14.1 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> hide #14.1 models
> hide #!16 models
> show #!16 models
> show #16.1 models
> hide #16.1 models
> hide #!16 models
> show #!7 models
> hide #!7 models
> changechains #7/B A
Chain IDs of 430 residues changed
> show #!7 models
> changechains #8/B A
Chain IDs of 430 residues changed
> changechains #9/B A
Chain IDs of 430 residues changed
> changechains #10/B A
Chain IDs of 430 residues changed
> changechains #11/B A
Chain IDs of 430 residues changed
> changechains #12/B A
Chain IDs of 430 residues changed
> show #!8 models
> show #!9 models
> show #!10 models
> show #!11 models
> show #!12 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> show #14.1 models
> hide #14.1 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> combine #7-12
Remapping chain ID 'A' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #8 to 'B'
Remapping chain ID 'M' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #8 to 'N'
Remapping chain ID 'Nt' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #8 to 'Nu'
Remapping chain ID 'a' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #8 to 'b'
Remapping chain ID 'nt' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #8 to 'nu'
Remapping chain ID 'A' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #9 to 'C'
Remapping chain ID 'M' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #9 to 'O'
Remapping chain ID 'Nt' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #9 to 'Nv'
Remapping chain ID 'a' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #9 to 'c'
Remapping chain ID 'nt' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #9 to 'nv'
Remapping chain ID 'A' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #10 to 'D'
Remapping chain ID 'M' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #10 to 'P'
Remapping chain ID 'Nt' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #10 to 'Nw'
Remapping chain ID 'a' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #10 to 'd'
Remapping chain ID 'nt' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #10 to 'nw'
Remapping chain ID 'A' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #11 to 'E'
Remapping chain ID 'M' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #11 to 'Q'
Remapping chain ID 'Nt' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #11 to 'Nx'
Remapping chain ID 'a' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #11 to 'e'
Remapping chain ID 'nt' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #11 to 'nx'
Remapping chain ID 'A' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #12 to 'F'
Remapping chain ID 'M' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #12 to 'R'
Remapping chain ID 'Nt' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #12 to 'Ny'
Remapping chain ID 'a' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #12 to 'f'
Remapping chain ID 'nt' in
231009_Xt_14-3_dEMhcr_1dimer_renamed_fit_individual.pdb #12 to 'ny'
> save
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_6dimers_hybrid_dock.pdb
> models #17 relModel #2
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_6dimers_hybrid_dock.pdb
Chain information for 231009_Xt_14-3_dEMhcr_6dimers_hybrid_dock.pdb #18
---
Chain | Description
A B C D E F | No description available
a b c d e f | No description available
> hide #!17 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> select add #18
80898 atoms, 81828 bonds, 24 pseudobonds, 5226 residues, 2 models selected
> style sel stick
Changed 80898 atom styles
> show sel atoms
> hide sel atoms
> show sel cartoons
> select clear
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!18 models
> show #!18 models
> hide #!14 models
> show #!18 atoms
> hide #!18 atoms
> select add #18
80898 atoms, 81828 bonds, 24 pseudobonds, 5226 residues, 2 models selected
> select subtract #18.1
80898 atoms, 81828 bonds, 5226 residues, 1 model selected
> select add #18.1
80898 atoms, 81828 bonds, 24 pseudobonds, 5226 residues, 2 models selected
> show sel atoms
> select clear
> close #14-16,18#1-13,17
> close #
Expected a models specifier or a keyword
> close #
Expected a models specifier or a keyword
> open /d/emr214/u/tl002/Xlaevis_2303/Isolde/231004_Xl_14-3_complete.pdb
Chain information for 231004_Xl_14-3_complete.pdb #1
---
Chain | Description
b | No description available
c d f i q | No description available
j k l m n r | No description available
> select add #1
80847 atoms, 81772 bonds, 12 pseudobonds, 5226 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> style sel stick
Changed 80847 atom styles
> show sel atoms
> select clear
[Repeated 1 time(s)]
> select ::name="MG"
6 atoms, 6 residues, 1 model selected
> select clear
> select up
43513 atoms, 43897 bonds, 8 pseudobonds, 2867 residues, 2 models selected
> select up
44370 atoms, 44816 bonds, 8 pseudobonds, 2867 residues, 2 models selected
> select up
50024 atoms, 50583 bonds, 8 pseudobonds, 3235 residues, 2 models selected
> select up
53894 atoms, 54510 bonds, 8 pseudobonds, 3484 residues, 2 models selected
> select up
63873 atoms, 64558 bonds, 10 pseudobonds, 4142 residues, 2 models selected
> select up
64121 atoms, 64823 bonds, 10 pseudobonds, 4142 residues, 2 models selected
> select up
65655 atoms, 66401 bonds, 10 pseudobonds, 4244 residues, 2 models selected
> select up
67367 atoms, 68137 bonds, 10 pseudobonds, 4355 residues, 2 models selected
> select up
80847 atoms, 81772 bonds, 12 pseudobonds, 5226 residues, 2 models selected
> select down
67367 atoms, 68137 bonds, 10 pseudobonds, 4355 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select clear
> changechains #1/b a
Chain IDs of 438 residues changed
> changechains #1/j A
Chain IDs of 430 residues changed
> changechains #1/J nt
Chain IDs of 1 residues changed
> changechains #1/U Nt
Chain IDs of 1 residues changed
> changechains #1/Y M
Chain IDs of 1 residues changed
> select clear
> hide atoms
> open
> /d/emr214/u/tl002/Xlaevis_2303/deepEMhancer/14-3_refine07/Xl_14-3_refine07_deepemhancer.mrc
Opened Xl_14-3_refine07_deepemhancer.mrc as #2, grid size 416,416,416, pixel
1.07, shown at level 0.134, step 2, values float32
> fitmap #1 inMap #2
Fit molecule 231004_Xl_14-3_complete.pdb (#1) to map
Xl_14-3_refine07_deepemhancer.mrc (#2) using 13480 atoms
average map value = 0.2601, steps = 44
shifted from previous position = 0.0217
rotated from previous position = 0.0732 degrees
atoms outside contour = 6008, contour level = 0.13449
Position of 231004_Xl_14-3_complete.pdb (#1) relative to
Xl_14-3_refine07_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.99999927 -0.00115625 -0.00034656 0.20188430
0.00115611 0.99999924 -0.00041963 -0.12143539
0.00034704 0.00041923 0.99999985 -0.10255369
Axis 0.32822945 -0.27138842 0.90477276
Axis point 103.64106996 172.71076116 0.00000000
Rotation angle (degrees) 0.07321648
Shift along axis 0.00643274
> fitmap #1 inMap #2
Fit molecule 231004_Xl_14-3_complete.pdb (#1) to map
Xl_14-3_refine07_deepemhancer.mrc (#2) using 13480 atoms
average map value = 0.2601, steps = 40
shifted from previous position = 0.00279
rotated from previous position = 0.0096 degrees
atoms outside contour = 6012, contour level = 0.13449
Position of 231004_Xl_14-3_complete.pdb (#1) relative to
Xl_14-3_refine07_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.99999923 -0.00116412 -0.00043641 0.22153327
0.00116400 0.99999928 -0.00027841 -0.15419810
0.00043673 0.00027791 0.99999987 -0.10366123
Axis 0.21834093 -0.34268227 0.91372649
Axis point 130.67734328 188.99618806 0.00000000
Rotation angle (degrees) 0.07299320
Shift along axis 0.00649272
> fitmap #1 inMap #2
Fit molecule 231004_Xl_14-3_complete.pdb (#1) to map
Xl_14-3_refine07_deepemhancer.mrc (#2) using 13480 atoms
average map value = 0.2601, steps = 44
shifted from previous position = 0.0217
rotated from previous position = 0.0732 degrees
atoms outside contour = 6008, contour level = 0.13449
Position of 231004_Xl_14-3_complete.pdb (#1) relative to
Xl_14-3_refine07_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.99999927 -0.00115625 -0.00034656 0.20188430
0.00115611 0.99999924 -0.00041963 -0.12143539
0.00034704 0.00041923 0.99999985 -0.10255369
Axis 0.32822945 -0.27138842 0.90477276
Axis point 103.64106996 172.71076116 0.00000000
Rotation angle (degrees) 0.07321648
Shift along axis 0.00643274
> volume #2 step 1
> save /d/emr214/u/tl002/Xlaevis_2303/Isolde/231009_Xl_14-3_dEMhcr_1dimer.pdb
> relModel #2
> open /d/emr214/u/tl002/Xlaevis_2303/Isolde/231009_Xl_14-3_dEMhcr_1dimer.pdb
Chain information for 231009_Xl_14-3_dEMhcr_1dimer.pdb #3
---
Chain | Description
A | No description available
a | No description available
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> open /d/emr214/u/tl002/Xlaevis_2303/Isolde/231009_Xl_14-3_dEMhcr_1dimer.pdb
Chain information for 231009_Xl_14-3_dEMhcr_1dimer.pdb #4
---
Chain | Description
A | No description available
a | No description available
> open /d/emr214/u/tl002/Xlaevis_2303/Isolde/231009_Xl_14-3_dEMhcr_1dimer.pdb
Chain information for 231009_Xl_14-3_dEMhcr_1dimer.pdb #5
---
Chain | Description
A | No description available
a | No description available
> open /d/emr214/u/tl002/Xlaevis_2303/Isolde/231009_Xl_14-3_dEMhcr_1dimer.pdb
Chain information for 231009_Xl_14-3_dEMhcr_1dimer.pdb #6
---
Chain | Description
A | No description available
a | No description available
> open /d/emr214/u/tl002/Xlaevis_2303/Isolde/231009_Xl_14-3_dEMhcr_1dimer.pdb
Chain information for 231009_Xl_14-3_dEMhcr_1dimer.pdb #7
---
Chain | Description
A | No description available
a | No description available
> open /d/emr214/u/tl002/Xlaevis_2303/Isolde/231009_Xl_14-3_dEMhcr_1dimer.pdb
Chain information for 231009_Xl_14-3_dEMhcr_1dimer.pdb #8
---
Chain | Description
A | No description available
a | No description available
> show #!2 models
> select add #4
13480 atoms, 13635 bonds, 2 pseudobonds, 871 residues, 2 models selected
> select add #5
26960 atoms, 27270 bonds, 4 pseudobonds, 1742 residues, 4 models selected
> select add #6
40440 atoms, 40905 bonds, 6 pseudobonds, 2613 residues, 6 models selected
> ui tool show "Side View"
> ui mousemode right "translate selected models"
> view matrix models
> #4,1,0,0,2.6752,0,1,0,-0.10508,0,0,1,-81.011,#5,1,0,0,2.6752,0,1,0,-0.10508,0,0,1,-81.011,#6,1,0,0,2.6752,0,1,0,-0.10508,0,0,1,-81.011
> select subtract #5
26960 atoms, 27270 bonds, 4 pseudobonds, 1742 residues, 4 models selected
> select subtract #6
13480 atoms, 13635 bonds, 2 pseudobonds, 871 residues, 2 models selected
> select subtract #4
Nothing selected
> select add #4
13480 atoms, 13635 bonds, 2 pseudobonds, 871 residues, 2 models selected
> select add #6
26960 atoms, 27270 bonds, 4 pseudobonds, 1742 residues, 4 models selected
> select subtract #6
13480 atoms, 13635 bonds, 2 pseudobonds, 871 residues, 2 models selected
> select add #6
26960 atoms, 27270 bonds, 4 pseudobonds, 1742 residues, 4 models selected
> view matrix models
> #4,1,0,0,-11.268,0,1,0,10.536,0,0,1,-84.079,#6,1,0,0,-11.268,0,1,0,10.536,0,0,1,-84.079
> undo move
Expected fewer arguments
> undo
[Repeated 8 time(s)]
> select add #3
53920 atoms, 54540 bonds, 8 pseudobonds, 3484 residues, 8 models selected
> select subtract #6
40440 atoms, 40905 bonds, 6 pseudobonds, 2613 residues, 6 models selected
> view matrix models
> #3,1,0,0,2.9832,0,1,0,0.53969,0,0,1,-80.55,#4,1,0,0,2.9832,0,1,0,0.53969,0,0,1,-80.55,#5,1,0,0,2.9832,0,1,0,0.53969,0,0,1,-80.55
> select subtract #4
26960 atoms, 27270 bonds, 4 pseudobonds, 1742 residues, 4 models selected
> select subtract #5
13480 atoms, 13635 bonds, 2 pseudobonds, 871 residues, 2 models selected
> select add #6
26960 atoms, 27270 bonds, 4 pseudobonds, 1742 residues, 4 models selected
> view matrix models
> #3,1,0,0,-14.761,0,1,0,51.305,0,0,1,-75.969,#6,1,0,0,-17.744,0,1,0,50.765,0,0,1,4.5818
> view matrix models
> #3,1,0,0,-31.336,0,1,0,46.272,0,0,1,-77.765,#6,1,0,0,-34.32,0,1,0,45.732,0,0,1,2.7856
> view matrix models
> #3,1,0,0,-29.386,0,1,0,37.6,0,0,1,-78.408,#6,1,0,0,-32.37,0,1,0,37.061,0,0,1,2.142
> view matrix models
> #3,1,0,0,-28.133,0,1,0,36.559,0,0,1,-71.38,#6,1,0,0,-31.116,0,1,0,36.02,0,0,1,9.1704
> select add #5
40440 atoms, 40905 bonds, 6 pseudobonds, 2613 residues, 6 models selected
> select add #8
53920 atoms, 54540 bonds, 8 pseudobonds, 3484 residues, 8 models selected
> select subtract #6
40440 atoms, 40905 bonds, 6 pseudobonds, 2613 residues, 6 models selected
> select subtract #3
26960 atoms, 27270 bonds, 4 pseudobonds, 1742 residues, 4 models selected
> view matrix models
> #5,1,0,0,53.267,0,1,0,-12.434,0,0,1,-89.291,#8,1,0,0,50.283,0,1,0,-12.974,0,0,1,-8.7405
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.87062,-0.48968,-0.047251,144.41,0.48835,0.87185,-0.037389,-69.605,0.059504,0.0094768,0.99818,-99.899,#8,0.87062,-0.48968,-0.047251,138.27,0.48835,0.87185,-0.037389,-74.544,0.059504,0.0094768,0.99818,-19.677
> fitmap #3 inMap #2
Fit molecule 231009_Xl_14-3_dEMhcr_1dimer.pdb (#3) to map
Xl_14-3_refine07_deepemhancer.mrc (#2) using 13480 atoms
average map value = 0.2056, steps = 144
shifted from previous position = 11.2
rotated from previous position = 25.2 degrees
atoms outside contour = 6994, contour level = 0.13449
Position of 231009_Xl_14-3_dEMhcr_1dimer.pdb (#3) relative to
Xl_14-3_refine07_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90471549 0.42600361 -0.00328788 -71.70233346
-0.42601164 0.90471475 -0.00230435 116.23012089
0.00199293 0.00348546 0.99999194 -73.58116998
Axis 0.00679514 -0.00619775 -0.99995771
Axis point 224.73820235 219.73562740 0.00000000
Rotation angle (degrees) 25.21560069
Shift along axis 72.37046496
> fitmap #4 inMap #2
Fit molecule 231009_Xl_14-3_dEMhcr_1dimer.pdb (#4) to map
Xl_14-3_refine07_deepemhancer.mrc (#2) using 13480 atoms
average map value = 0.2522, steps = 68
shifted from previous position = 2.26
rotated from previous position = 0.289 degrees
atoms outside contour = 6199, contour level = 0.13449
Position of 231009_Xl_14-3_dEMhcr_1dimer.pdb (#4) relative to
Xl_14-3_refine07_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.99998759 -0.00490908 -0.00084781 2.09083283
0.00490972 0.99998766 0.00075634 -1.88941157
0.00084409 -0.00076050 0.99999935 -81.16540061
Axis -0.15050521 -0.16787510 0.97425158
Axis point 3083.48307329 -2006.14520878 0.00000000
Rotation angle (degrees) 0.28872341
Shift along axis -79.07301551
> fitmap #5 inMap #2
Fit molecule 231009_Xl_14-3_dEMhcr_1dimer.pdb (#5) to map
Xl_14-3_refine07_deepemhancer.mrc (#2) using 13480 atoms
average map value = 0.2086, steps = 72
shifted from previous position = 4.6
rotated from previous position = 4.93 degrees
atoms outside contour = 6976, contour level = 0.13449
Position of 231009_Xl_14-3_dEMhcr_1dimer.pdb (#5) relative to
Xl_14-3_refine07_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.89931717 -0.43729696 0.00006690 120.07385845
0.43729316 0.89930997 0.00403296 -76.55366432
-0.00182377 -0.00359765 0.99999186 -88.69859925
Axis -0.00872443 0.00216169 0.99995960
Axis point 225.47620258 220.87480148 0.00000000
Rotation angle (degrees) 25.93254758
Shift along axis -89.90807785
> fitmap #6 inMap #2
Fit molecule 231009_Xl_14-3_dEMhcr_1dimer.pdb (#6) to map
Xl_14-3_refine07_deepemhancer.mrc (#2) using 13480 atoms
average map value = 0.2344, steps = 124
shifted from previous position = 9
rotated from previous position = 25.6 degrees
atoms outside contour = 6474, contour level = 0.13449
Position of 231009_Xl_14-3_dEMhcr_1dimer.pdb (#6) relative to
Xl_14-3_refine07_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90155080 0.43266440 -0.00276982 -73.17013711
-0.43267107 0.90154814 -0.00258765 119.02568432
0.00137754 0.00353132 0.99999282 7.61682568
Axis 0.00707095 -0.00479260 -0.99996352
Axis point 224.90516982 220.14827976 0.00000000
Rotation angle (degrees) 25.63798393
Shift along axis -8.70437262
> fitmap #7 inMap #2
Fit molecule 231009_Xl_14-3_dEMhcr_1dimer.pdb (#7) to map
Xl_14-3_refine07_deepemhancer.mrc (#2) using 13480 atoms
average map value = 0.26, steps = 40
shifted from previous position = 0.00336
rotated from previous position = 0.0159 degrees
atoms outside contour = 6090, contour level = 0.13449
Position of 231009_Xl_14-3_dEMhcr_1dimer.pdb (#7) relative to
Xl_14-3_refine07_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.99999998 -0.00002896 -0.00020502 0.04495952
0.00002900 0.99999998 0.00018596 -0.04549527
0.00020501 -0.00018597 0.99999996 -0.01428046
Axis -0.66820833 -0.73665053 0.10413270
Axis point 70.70732083 0.00000000 225.75859353
Rotation angle (degrees) 0.01594572
Shift along axis 0.00198473
> fitmap #8 inMap #2
Fit molecule 231009_Xl_14-3_dEMhcr_1dimer.pdb (#8) to map
Xl_14-3_refine07_deepemhancer.mrc (#2) using 13480 atoms
average map value = 0.2294, steps = 68
shifted from previous position = 2.75
rotated from previous position = 5.33 degrees
atoms outside contour = 6538, contour level = 0.13449
Position of 231009_Xl_14-3_dEMhcr_1dimer.pdb (#8) relative to
Xl_14-3_refine07_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.90317004 -0.42928122 0.00123155 116.78957365
0.42927400 0.90316597 0.00388147 -75.08418201
-0.00277854 -0.00297696 0.99999171 -7.49317137
Axis -0.00798800 0.00467053 0.99995719
Axis point 224.71349292 221.20806271 0.00000000
Rotation angle (degrees) 25.42289021
Shift along axis -8.77644909
> select clear
> transparency #2-8 50
> select clear
> combine #3-8
Remapping chain ID 'A' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #4 to 'B'
Remapping chain ID 'M' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #4 to 'N'
Remapping chain ID 'Nt' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #4 to 'Nu'
Remapping chain ID 'a' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #4 to 'b'
Remapping chain ID 'nt' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #4 to 'nu'
Remapping chain ID 'A' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #5 to 'C'
Remapping chain ID 'M' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #5 to 'O'
Remapping chain ID 'Nt' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #5 to 'Nv'
Remapping chain ID 'a' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #5 to 'c'
Remapping chain ID 'nt' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #5 to 'nv'
Remapping chain ID 'A' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #6 to 'D'
Remapping chain ID 'M' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #6 to 'P'
Remapping chain ID 'Nt' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #6 to 'Nw'
Remapping chain ID 'a' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #6 to 'd'
Remapping chain ID 'nt' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #6 to 'nw'
Remapping chain ID 'A' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #7 to 'E'
Remapping chain ID 'M' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #7 to 'Q'
Remapping chain ID 'Nt' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #7 to 'Nx'
Remapping chain ID 'a' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #7 to 'e'
Remapping chain ID 'nt' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #7 to 'nx'
Remapping chain ID 'A' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #8 to 'F'
Remapping chain ID 'M' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #8 to 'R'
Remapping chain ID 'Nt' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #8 to 'Ny'
Remapping chain ID 'a' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #8 to 'f'
Remapping chain ID 'nt' in 231009_Xl_14-3_dEMhcr_1dimer.pdb #8 to 'ny'
> save /d/emr214/u/tl002/Xlaevis_2303/Isolde/231009_Xl_14-3_dEMhcr_6dimer.pdb
> models #9 relModel #2
> open /d/emr214/u/tl002/Xlaevis_2303/Isolde/231009_Xl_14-3_dEMhcr_6dimer.pdb
Chain information for 231009_Xl_14-3_dEMhcr_6dimer.pdb #10
---
Chain | Description
A B C D E F | No description available
a b c d e f | No description available
> close #1-9
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_6dimers_hybrid_dock.pdb
Chain information for 231009_Xt_14-3_dEMhcr_6dimers_hybrid_dock.pdb #1
---
Chain | Description
A B C D E F | No description available
a b c d e f | No description available
> select add #10
80880 atoms, 81810 bonds, 12 pseudobonds, 5226 residues, 2 models selected
> select subtract #10
Nothing selected
> select add #1
80898 atoms, 81828 bonds, 24 pseudobonds, 5226 residues, 2 models selected
> view matrix models
> #1,0.91365,-0.40607,-0.018901,79.548,0.40317,0.91111,-0.085582,-25.923,0.051973,0.070571,0.99615,-17.62
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.91365,-0.40607,-0.018901,113.09,0.40317,0.91111,-0.085582,-54.397,0.051973,0.070571,0.99615,-28.807
> molmap #10 6
Opened 231009_Xl_14-3_dEMhcr_6dimer.pdb map 6 as #2, grid size 96,77,117,
pixel 2, shown at level 0.134, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_6dimers_hybrid_dock.pdb (#1) to map
231009_Xl_14-3_dEMhcr_6dimer.pdb map 6 (#2) using 80898 atoms
average map value = 0.4164, steps = 68
shifted from previous position = 4.93
rotated from previous position = 5.04 degrees
atoms outside contour = 2137, contour level = 0.13384
Position of 231009_Xt_14-3_dEMhcr_6dimers_hybrid_dock.pdb (#1) relative to
231009_Xl_14-3_dEMhcr_6dimer.pdb map 6 (#2) coordinates:
Matrix rotation and translation
0.90628862 -0.42262510 0.00538355 114.42440979
0.42264513 0.90628915 -0.00332994 -73.85645112
-0.00347174 0.00529322 0.99997997 -8.35693681
Axis 0.01020057 0.01047516 0.99989310
Axis point 223.63002178 221.35210225 0.00000000
Rotation angle (degrees) 25.00392131
Shift along axis -7.96250743
> fitmap #1 inMap #2
Fit molecule 231009_Xt_14-3_dEMhcr_6dimers_hybrid_dock.pdb (#1) to map
231009_Xl_14-3_dEMhcr_6dimer.pdb map 6 (#2) using 80898 atoms
average map value = 0.4164, steps = 48
shifted from previous position = 0.0101
rotated from previous position = 0.0266 degrees
atoms outside contour = 2139, contour level = 0.13384
Position of 231009_Xt_14-3_dEMhcr_6dimers_hybrid_dock.pdb (#1) relative to
231009_Xl_14-3_dEMhcr_6dimer.pdb map 6 (#2) coordinates:
Matrix rotation and translation
0.90629806 -0.42260976 0.00498414 114.48851282
0.42262696 0.90629846 -0.00309339 -73.89173285
-0.00320982 0.00490997 0.99998281 -8.33671715
Axis 0.00946791 0.00969338 0.99990819
Axis point 223.75993884 221.47433433 0.00000000
Rotation angle (degrees) 25.00245868
Shift along axis -7.96824563
> hide #!10 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!10 models
> hide #!10 models
> hide #!1 models
> show #!1 models
> show #!10 models
> select add #10
161778 atoms, 163638 bonds, 36 pseudobonds, 10452 residues, 4 models selected
> style sel stick
Changed 161778 atom styles
> hide sel atoms
> show sel cartoons
> select clear
> hide #!1 models
> select up
7192 atoms, 7270 bonds, 461 residues, 1 model selected
> select up
13395 atoms, 13547 bonds, 868 residues, 1 model selected
> select up
80880 atoms, 81810 bonds, 5226 residues, 1 model selected
> select down
13395 atoms, 13547 bonds, 868 residues, 1 model selected
> style sel stick
Changed 13395 atom styles
> style sel stick
Changed 13395 atom styles
> show sel atoms
> select up
11449 atoms, 11539 bonds, 748 residues, 1 model selected
> select up
11649 atoms, 11757 bonds, 748 residues, 1 model selected
> select up
12838 atoms, 12981 bonds, 831 residues, 1 model selected
> select up
13395 atoms, 13547 bonds, 868 residues, 1 model selected
> molmap sel 4
Opened 231009_Xl_14-3_dEMhcr_6dimer.pdb map 4 as #3, grid size 69,65,94, pixel
1.33, shown at level 0.119, step 1, values float32
> fitmap #1 inMap #3
Fit molecule 231009_Xt_14-3_dEMhcr_6dimers_hybrid_dock.pdb (#1) to map
231009_Xl_14-3_dEMhcr_6dimer.pdb map 4 (#3) using 80898 atoms
average map value = 0.3046, steps = 2000
shifted from previous position = 0.635
rotated from previous position = 0.542 degrees
atoms outside contour = 68173, contour level = 0.11937
Position of 231009_Xt_14-3_dEMhcr_6dimers_hybrid_dock.pdb (#1) relative to
231009_Xl_14-3_dEMhcr_6dimer.pdb map 4 (#3) coordinates:
Matrix rotation and translation
0.90599884 -0.42326002 -0.00413317 116.34011909
0.42326096 0.90600756 -0.00068781 -74.47051877
0.00403580 -0.00112625 0.99999123 -7.74305406
Axis -0.00051790 -0.00964960 0.99995331
Axis point 225.99734863 224.66671144 0.00000000
Rotation angle (degrees) 25.04185701
Shift along axis -7.08433461
> show #!1 models
> fitmap #10 inMap #3
Fit molecule 231009_Xl_14-3_dEMhcr_6dimer.pdb (#10) to map
231009_Xl_14-3_dEMhcr_6dimer.pdb map 4 (#3) using 80880 atoms
average map value = 0.3487, steps = 2000
shifted from previous position = 0.753
rotated from previous position = 0.504 degrees
atoms outside contour = 67478, contour level = 0.11937
Position of 231009_Xl_14-3_dEMhcr_6dimer.pdb (#10) relative to
231009_Xl_14-3_dEMhcr_6dimer.pdb map 4 (#3) coordinates:
Matrix rotation and translation
0.99997966 0.00614213 0.00171618 -1.03903856
-0.00615243 0.99996268 0.00606472 -0.75829990
-0.00167886 -0.00607515 0.99998014 1.14769770
Axis -0.68943298 0.19280710 -0.69821744
Axis point -117.18778474 194.72948519 0.00000000
Rotation angle (degrees) 0.50445257
Shift along axis -0.23120071
> ui tool show Matchmaker
> hide #!3 models
> matchmaker #10/D to #1/D pairing ss
Parameters
---
Chain pairing | ss
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 231009_Xt_14-3_dEMhcr_6dimers_hybrid_dock.pdb, chain D (#1) with
231009_Xl_14-3_dEMhcr_6dimer.pdb, chain D (#10), sequence alignment score =
2180.6
RMSD between 424 pruned atom pairs is 0.606 angstroms; (across all 430 pairs:
0.667)
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide sel atoms
> select clear
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Isolde/231009_Xt_14-3_dEMhcr_6dimers.pdb
Chain information for 231009_Xt_14-3_dEMhcr_6dimers.pdb #4
---
Chain | Description
A B C D E F | No description available
a b c d e f | No description available
> matchmaker #4/D to #1/D pairing ss
Parameters
---
Chain pairing | ss
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 231009_Xt_14-3_dEMhcr_6dimers_hybrid_dock.pdb, chain D (#1) with
231009_Xt_14-3_dEMhcr_6dimers.pdb, chain D (#4), sequence alignment score =
2272.9
RMSD between 430 pruned atom pairs is 0.001 angstroms; (across all 430 pairs:
0.001)
> matchmaker #4/D to #10/D pairing ss
Parameters
---
Chain pairing | ss
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 231009_Xl_14-3_dEMhcr_6dimer.pdb, chain D (#10) with
231009_Xt_14-3_dEMhcr_6dimers.pdb, chain D (#4), sequence alignment score =
2180.6
RMSD between 424 pruned atom pairs is 0.606 angstroms; (across all 430 pairs:
0.667)
> matchmaker #1/D to #10/D pairing ss
Parameters
---
Chain pairing | ss
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 231009_Xl_14-3_dEMhcr_6dimer.pdb, chain D (#10) with
231009_Xt_14-3_dEMhcr_6dimers_hybrid_dock.pdb, chain D (#1), sequence
alignment score = 2180.6
RMSD between 424 pruned atom pairs is 0.606 angstroms; (across all 430 pairs:
0.667)
> matchmaker #4/D to #10/D pairing ss
Parameters
---
Chain pairing | ss
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 231009_Xl_14-3_dEMhcr_6dimer.pdb, chain D (#10) with
231009_Xt_14-3_dEMhcr_6dimers.pdb, chain D (#4), sequence alignment score =
2180.6
RMSD between 424 pruned atom pairs is 0.606 angstroms; (across all 430 pairs:
0.667)
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> matchmaker #4/E to #10/D pairing ss
Parameters
---
Chain pairing | ss
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 231009_Xl_14-3_dEMhcr_6dimer.pdb, chain D (#10) with
231009_Xt_14-3_dEMhcr_6dimers.pdb, chain E (#4), sequence alignment score =
2180.6
RMSD between 424 pruned atom pairs is 0.606 angstroms; (across all 430 pairs:
0.667)
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> style stick
Changed 242676 atom styles
> hide atoms
> show cartoons
> hide #!10 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!10 models
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> ui tool show "Render By Attribute"
> color byattribute a:bfactor #!1 target scab palette
> 0,blue:34.775,white:69.55,red
80898 atoms, 5226 residues, atom bfactor range -0 to 69.6
> color byattribute a:bfactor #!1 target scab palette
> 0,blue:34.775,white:69.55,red
80898 atoms, 5226 residues, atom bfactor range -0 to 69.6
> hide #!10 models
> color byattribute r:seq_conservation #!1 target scab palette
> 0,blue:34.775,white:69.55,red
All 'seq_conservation' values are None
> ui tool show "Ramachandran Plot"
> view matrix models
> #10,0.9999,-0.0066835,-0.012795,3.0564,0.0067868,0.99994,0.0080525,-1.7249,0.01274,-0.0081385,0.99989,-6.3797
> hide #!1 models
> close #1-4,10
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Phenix02/Xtropicalis/231010_Xt_14-3_deepEMhcr_refine42.pdb
> /d/emr214/u/tl002/Xtropicalis_2209/Phenix02/Xtropicalis/Xt_14-3_refine10repeated_deepemhancer.mrc
Chain information for 231010_Xt_14-3_deepEMhcr_refine42.pdb #1
---
Chain | Description
A B C D E F | No description available
a b c d e f | No description available
Opened Xt_14-3_refine10repeated_deepemhancer.mrc as #2, grid size 416,416,416,
pixel 1.07, shown at level 0.085, step 2, values float32
> open
> /d/emr214/u/tl002/Xtropicalis_2209/Phenix02/Xlaevis/231010_Xl_14-3_deepEMhcr_refine43.pdb
> /d/emr214/u/tl002/Xtropicalis_2209/Phenix02/Xlaevis/Xl_14-3_refine07_deepemhancer.mrc
Chain information for 231010_Xl_14-3_deepEMhcr_refine43.pdb #3
---
Chain | Description
A B C D E F | No description available
a b c d e f | No description available
Opened Xl_14-3_refine07_deepemhancer.mrc as #4, grid size 416,416,416, pixel
1.07, shown at level 0.134, step 2, values float32
> select add #1
80898 atoms, 81828 bonds, 36 pseudobonds, 5226 residues, 2 models selected
> select add #2
80898 atoms, 81828 bonds, 36 pseudobonds, 5226 residues, 5 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,1,0,0,45.053,0,1,0,-39.188,0,0,1,-3.0916,#2,1,0,0,45.053,0,1,0,-39.188,0,0,1,-3.0916
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.93561,-0.32252,-0.14355,160.27,0.31455,0.94621,-0.075752,-80.141,0.16026,0.025719,0.98674,-40.976,#2,0.93561,-0.32252,-0.14355,160.27,0.31455,0.94621,-0.075752,-80.141,0.16026,0.025719,0.98674,-40.976
> ui mousemode right "rotate selected models"
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.93561,-0.32252,-0.14355,125.23,0.31455,0.94621,-0.075752,-51.823,0.16026,0.025719,0.98674,-30.095,#2,0.93561,-0.32252,-0.14355,125.23,0.31455,0.94621,-0.075752,-51.823,0.16026,0.025719,0.98674,-30.095
> fitmap #1 inMap #4
Fit molecule 231010_Xt_14-3_deepEMhcr_refine42.pdb (#1) to map
Xl_14-3_refine07_deepemhancer.mrc (#4) using 80898 atoms
average map value = 0.2294, steps = 148
shifted from previous position = 2.95
rotated from previous position = 11.4 degrees
atoms outside contour = 38486, contour level = 0.13449
Position of 231010_Xt_14-3_deepEMhcr_refine42.pdb (#1) relative to
Xl_14-3_refine07_deepemhancer.mrc (#4) coordinates:
Matrix rotation and translation
0.90638291 -0.42242630 0.00510278 114.43315759
0.42244521 0.90638193 -0.00344095 -73.82405284
-0.00317152 0.00527446 0.99998106 -8.39152077
Axis 0.01031462 0.00979257 0.99989885
Axis point 223.66158700 221.52134200 0.00000000
Rotation angle (degrees) 24.99116386
Shift along axis -7.93326481
> fitmap #1 inMap #2
Fit molecule 231010_Xt_14-3_deepEMhcr_refine42.pdb (#1) to map
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) using 80898 atoms
average map value = 0.212, steps = 144
shifted from previous position = 2.73
rotated from previous position = 11.4 degrees
atoms outside contour = 29702, contour level = 0.085003
Position of 231010_Xt_14-3_deepEMhcr_refine42.pdb (#1) relative to
Xt_14-3_refine10repeated_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00009727 0.00000735 -0.24757486
-0.00009727 0.99999999 0.00011096 -0.06530586
-0.00000734 -0.00011096 0.99999999 0.01018811
Axis -0.75103131 0.04972326 -0.65839165
Axis point 0.00000000 1135.99705695 667.53750850
Rotation angle (degrees) 0.00846495
Shift along axis 0.17598149
> select subtract #2
80898 atoms, 81828 bonds, 36 pseudobonds, 5226 residues, 2 models selected
> molmap #1 4
Opened 231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 as #5, grid size
115,127,167, pixel 1.33, shown at level 0.121, step 1, values float32
> fitmap #2 inMap #5
Fit map Xt_14-3_refine10repeated_deepemhancer.mrc in map
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 using 89984 points
correlation = 0.5923, correlation about mean = 0.3417, overlap = 5965
steps = 40, shift = 0.0541, angle = 0.0222 degrees
Position of Xt_14-3_refine10repeated_deepemhancer.mrc (#2) relative to
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 (#5) coordinates:
Matrix rotation and translation
0.99999996 0.00019657 -0.00022150 0.26990599
-0.00019657 0.99999998 0.00002267 0.08604357
0.00022150 -0.00002263 0.99999998 0.02688364
Axis -0.07625115 -0.74576680 -0.66182901
Axis point 185.14615819 0.00000000 1183.20369545
Rotation angle (degrees) 0.01701753
Shift along axis -0.10254145
> fitmap #3 inMap #5
Fit molecule 231010_Xl_14-3_deepEMhcr_refine43.pdb (#3) to map
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 (#5) using 80880 atoms
average map value = 0.5606, steps = 128
shifted from previous position = 2.74
rotated from previous position = 11.4 degrees
atoms outside contour = 3578, contour level = 0.12067
Position of 231010_Xl_14-3_deepEMhcr_refine43.pdb (#3) relative to
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 (#5) coordinates:
Matrix rotation and translation
0.90666827 0.42183170 -0.00326484 -72.49908331
-0.42181155 0.90666714 0.00545147 115.16500424
0.00525972 -0.00356552 0.99997981 7.56817652
Axis -0.01068700 -0.01010337 -0.99989185
Axis point 223.80451286 221.58640924 0.00000000
Rotation angle (degrees) 24.95253095
Shift along axis -7.95611479
> fitmap #4 inMap #5
Fit map Xl_14-3_refine07_deepemhancer.mrc in map
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 using 89894 points
correlation = 0.5245, correlation about mean = 0.2876, overlap = 5867
steps = 220, shift = 5.88, angle = 11.4 degrees
Position of Xl_14-3_refine07_deepemhancer.mrc (#4) relative to
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 (#5) coordinates:
Matrix rotation and translation
0.90678321 0.42158191 -0.00359249 -72.46439159
-0.42156012 0.90678354 0.00553824 115.06701788
0.00559243 -0.00350753 0.99997821 7.50263325
Axis -0.01072740 -0.01089240 -0.99988313
Axis point 223.75602728 221.56498973 0.00000000
Rotation angle (degrees) 24.93692528
Shift along axis -7.97775853
> select subtract #1
Nothing selected
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> show #!2 models
> show #!1 models
> close #5
> hide #!2 models
> hide #!4 models
> select up
7173 atoms, 7061 bonds, 6 pseudobonds, 559 residues, 2 models selected
> select up
8716 atoms, 8769 bonds, 6 pseudobonds, 559 residues, 2 models selected
> select up
11564 atoms, 11683 bonds, 6 pseudobonds, 748 residues, 2 models selected
> select up
13483 atoms, 13638 bonds, 6 pseudobonds, 871 residues, 2 models selected
> molmap sel 4
Opened 231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 as #5, grid size 68,63,94,
pixel 1.33, shown at level 0.119, step 1, values float32
> show #!2 models
> fitmap #1 inMap #5
Fit molecule 231010_Xt_14-3_deepEMhcr_refine42.pdb (#1) to map
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 (#5) using 80898 atoms
average map value = 0.2777, steps = 564
shifted from previous position = 0.0377
rotated from previous position = 0.0537 degrees
atoms outside contour = 67413, contour level = 0.11936
Position of 231010_Xt_14-3_deepEMhcr_refine42.pdb (#1) relative to
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 (#5) coordinates:
Matrix rotation and translation
0.99999967 -0.00072295 -0.00037233 0.19712915
0.00072313 0.99999963 0.00046448 -0.19763152
0.00037200 -0.00046475 0.99999982 0.05271624
Axis -0.49608459 -0.39736941 0.77200883
Axis point 261.66803682 287.26246261 0.00000000
Rotation angle (degrees) 0.05366149
Shift along axis 0.02143739
> fitmap #2 inMap #5
Fit map Xt_14-3_refine10repeated_deepemhancer.mrc in map
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 using 89984 points
correlation = 0.2533, correlation about mean = 0.1376, overlap = 1071
steps = 40, shift = 0.0538, angle = 0.113 degrees
Position of Xt_14-3_refine10repeated_deepemhancer.mrc (#2) relative to
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 (#5) coordinates:
Matrix rotation and translation
0.99999943 -0.00092962 -0.00052003 0.48457231
0.00093045 0.99999828 0.00160281 -0.43151675
0.00051854 -0.00160329 0.99999858 0.23247479
Axis -0.83289167 -0.26980272 0.48321626
Axis point 0.00000000 197.42800587 298.86774001
Rotation angle (degrees) 0.11027596
Shift along axis -0.17483625
> fitmap #2 inMap #5
Fit map Xt_14-3_refine10repeated_deepemhancer.mrc in map
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 using 89984 points
correlation = 0.2533, correlation about mean = 0.1376, overlap = 1071
steps = 48, shift = 0.0246, angle = 0.044 degrees
Position of Xt_14-3_refine10repeated_deepemhancer.mrc (#2) relative to
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 (#5) coordinates:
Matrix rotation and translation
0.99999942 -0.00036964 -0.00100862 0.50411543
0.00037106 0.99999894 0.00140722 -0.31854009
0.00100810 -0.00140759 0.99999850 0.14544747
Axis -0.79491143 -0.56952770 0.20917460
Axis point 0.00000000 131.07779706 302.90651208
Rotation angle (degrees) 0.10144303
Shift along axis -0.18888579
> fitmap #2 inMap #5
Fit map Xt_14-3_refine10repeated_deepemhancer.mrc in map
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 using 89984 points
correlation = 0.2533, correlation about mean = 0.1376, overlap = 1071
steps = 48, shift = 0.0395, angle = 0.0231 degrees
Position of Xt_14-3_refine10repeated_deepemhancer.mrc (#2) relative to
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 (#5) coordinates:
Matrix rotation and translation
0.99999963 -0.00053233 -0.00067374 0.45922855
0.00053338 0.99999864 0.00156060 -0.35778742
0.00067291 -0.00156096 0.99999856 0.18410609
Axis -0.87616111 -0.37797732 0.29912347
Axis point 0.00000000 158.31932570 280.75937652
Rotation angle (degrees) 0.10206597
Shift along axis -0.21205221
> fitmap #2 inMap #5
Fit map Xt_14-3_refine10repeated_deepemhancer.mrc in map
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 using 89984 points
correlation = 0.2533, correlation about mean = 0.1376, overlap = 1071
steps = 48, shift = 0.0213, angle = 0.0439 degrees
Position of Xt_14-3_refine10repeated_deepemhancer.mrc (#2) relative to
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 (#5) coordinates:
Matrix rotation and translation
0.99999924 -0.00119362 -0.00030597 0.47731071
0.00119413 0.99999788 0.00167527 -0.47646147
0.00030397 -0.00167564 0.99999855 0.26550438
Axis -0.80559159 -0.14663577 0.57403844
Axis point 0.00000000 213.77180680 298.87933029
Rotation angle (degrees) 0.11916278
Shift along axis -0.16224148
> fitmap #2 inMap #5
Fit map Xt_14-3_refine10repeated_deepemhancer.mrc in map
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 using 89984 points
correlation = 0.2533, correlation about mean = 0.1376, overlap = 1071
steps = 48, shift = 0.0335, angle = 0.052 degrees
Position of Xt_14-3_refine10repeated_deepemhancer.mrc (#2) relative to
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 (#5) coordinates:
Matrix rotation and translation
0.99999955 -0.00047773 -0.00082344 0.49397824
0.00047894 0.99999881 0.00146519 -0.32633362
0.00082273 -0.00146558 0.99999859 0.15320755
Axis -0.83857840 -0.47101773 0.27373083
Axis point 0.00000000 145.08200974 293.11451201
Rotation angle (degrees) 0.10012214
Shift along axis -0.21859293
> fitmap #2 inMap #5
Fit map Xt_14-3_refine10repeated_deepemhancer.mrc in map
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 using 89984 points
correlation = 0.2533, correlation about mean = 0.1376, overlap = 1071
steps = 48, shift = 0.0303, angle = 0.0421 degrees
Position of Xt_14-3_refine10repeated_deepemhancer.mrc (#2) relative to
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 (#5) coordinates:
Matrix rotation and translation
0.99999939 -0.00103766 -0.00038570 0.47124794
0.00103830 0.99999809 0.00165420 -0.45295499
0.00038399 -0.00165460 0.99999856 0.25398534
Axis -0.83109916 -0.19332990 0.52143814
Axis point 0.00000000 207.33965636 294.12096844
Rotation angle (degrees) 0.11405398
Shift along axis -0.17164638
> fitmap #2 inMap #5
Fit map Xt_14-3_refine10repeated_deepemhancer.mrc in map
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 using 89984 points
correlation = 0.2533, correlation about mean = 0.1376, overlap = 1071
steps = 60, shift = 0.0117, angle = 0.0383 degrees
Position of Xt_14-3_refine10repeated_deepemhancer.mrc (#2) relative to
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 (#5) coordinates:
Matrix rotation and translation
0.99999965 -0.00045779 -0.00070184 0.44638501
0.00045888 0.99999868 0.00155653 -0.35568776
0.00070112 -0.00155685 0.99999854 0.19324954
Axis -0.88053604 -0.39679020 0.25925629
Axis point 0.00000000 157.47528360 280.09569227
Rotation angle (degrees) 0.10129253
Shift along axis -0.20182351
> fitmap #2 inMap #5
Fit map Xt_14-3_refine10repeated_deepemhancer.mrc in map
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 using 89984 points
correlation = 0.2533, correlation about mean = 0.1376, overlap = 1071
steps = 56, shift = 0.00811, angle = 0.0105 degrees
Position of Xt_14-3_refine10repeated_deepemhancer.mrc (#2) relative to
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 (#5) coordinates:
Matrix rotation and translation
0.99999955 -0.00063978 -0.00069455 0.47436771
0.00064085 0.99999861 0.00153768 -0.38101474
0.00069356 -0.00153812 0.99999858 0.19868153
Axis -0.85217488 -0.38458875 0.35480905
Axis point 0.00000000 172.08541542 294.76624997
Rotation angle (degrees) 0.10340024
Shift along axis -0.18721626
> fitmap #2 inMap #5
Fit map Xt_14-3_refine10repeated_deepemhancer.mrc in map
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 using 89984 points
correlation = 0.2533, correlation about mean = 0.1376, overlap = 1071
steps = 28, shift = 0.0087, angle = 0.00844 degrees
Position of Xt_14-3_refine10repeated_deepemhancer.mrc (#2) relative to
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 (#5) coordinates:
Matrix rotation and translation
0.99999955 -0.00052764 -0.00078943 0.47678814
0.00052885 0.99999869 0.00152782 -0.36759230
0.00078862 -0.00152824 0.99999852 0.19007247
Axis -0.84936693 -0.43858705 0.29362767
Axis point 0.00000000 160.19761823 294.68647697
Rotation angle (degrees) 0.10307638
Shift along axis -0.18793632
> fitmap #2 inMap #5
Fit map Xt_14-3_refine10repeated_deepemhancer.mrc in map
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 using 89984 points
correlation = 0.2533, correlation about mean = 0.1376, overlap = 1071
steps = 28, shift = 0.039, angle = 0.00732 degrees
Position of Xt_14-3_refine10repeated_deepemhancer.mrc (#2) relative to
231010_Xt_14-3_deepEMhcr_refine42.pdb map 4 (#5) coordinates:
Matrix rotation and translation
0.99999957 -0.00061192 -0.00069364 0.49033002
0.00061298 0.99999865 0.00152316 -0.35403104
0.00069271 -0.00152359 0.99999860 0.17967531
Axis -0.85477006 -0.38894121 0.34364644
Axis point 0.00000000 167.21214865 288.67429453
Rotation angle (degrees) 0.10211286
Shift along axis -0.21967738
> ui tool show Matchmaker
Traceback (most recent call last):
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 79, in showEvent
self._items_change()
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 389, in _items_change
item_names = self._item_names()
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in _item_names
values = [v for v in self.list_func() if self.filter_func(v)]
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in <listcomp>
values = [v for v in self.list_func() if self.filter_func(v)]
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 497, in <lambda>
filter_func=lambda c, ref=chain: c.structure != ref.structure)
AttributeError: 'Sequence' object has no attribute 'structure'
AttributeError: 'Sequence' object has no attribute 'structure'
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 497, in
filter_func=lambda c, ref=chain: c.structure != ref.structure)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 54, in proxy_handler
pself._callback(pself)
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 368, in _pairing_change
self.bring_model_list.refresh()
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 72, in refresh
self._items_change()
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 169, in _items_change
item_names = self._item_names()
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in _item_names
values = [v for v in self.list_func() if self.filter_func(v)]
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in <listcomp>
values = [v for v in self.list_func() if self.filter_func(v)]
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 22, in <lambda>
filter_func = lambda x, ff=filter_func, cf=class_filter: ff(x) and
isinstance(x, cf)
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 308, in _filter_bring_models
match_value = match_widget.value
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 520, in value
match_chain = match_menu.value
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 333, in value
return self.get_value()
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 347, in get_value
return self.item_map[text]
KeyError: '231009_Xt_14-3_dEMhcr_6dimers.pdb #4/E'
Error processing trigger "setting changed":
KeyError: '231009_Xt_14-3_dEMhcr_6dimers.pdb #4/E'
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 347, in get_value
return self.item_map[text]
See log for complete Python traceback.
> matchmaker #3/E to #1/E pairing ss
Parameters
---
Chain pairing | ss
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 231010_Xt_14-3_deepEMhcr_refine42.pdb, chain E (#1) with
231010_Xl_14-3_deepEMhcr_refine43.pdb, chain E (#3), sequence alignment score
= 2171
RMSD between 424 pruned atom pairs is 0.599 angstroms; (across all 430 pairs:
0.662)
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> matchmaker #3/E to #1/E pairing ss
Parameters
---
Chain pairing | ss
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 231010_Xt_14-3_deepEMhcr_refine42.pdb, chain E (#1) with
231010_Xl_14-3_deepEMhcr_refine43.pdb, chain E (#3), sequence alignment score
= 2171
RMSD between 424 pruned atom pairs is 0.599 angstroms; (across all 430 pairs:
0.662)
> hide #!1 models
> hide #!2 models
> hide #!4 models
> hide #!5 models
> select up
10339 atoms, 10304 bonds, 3 pseudobonds, 730 residues, 2 models selected
> select up
11381 atoms, 11475 bonds, 3 pseudobonds, 730 residues, 2 models selected
> select up
13205 atoms, 13349 bonds, 3 pseudobonds, 853 residues, 2 models selected
> select up
26875 atoms, 27182 bonds, 3 pseudobonds, 1739 residues, 2 models selected
> select down
13205 atoms, 13349 bonds, 3 pseudobonds, 853 residues, 2 models selected
> select down
11381 atoms, 11475 bonds, 3 pseudobonds, 730 residues, 2 models selected
> select up
13205 atoms, 13349 bonds, 3 pseudobonds, 853 residues, 2 models selected
> select up
26875 atoms, 27182 bonds, 3 pseudobonds, 1739 residues, 2 models selected
> select up
80880 atoms, 81810 bonds, 18 pseudobonds, 5226 residues, 2 models selected
> select down
26875 atoms, 27182 bonds, 3 pseudobonds, 1739 residues, 2 models selected
> select down
13205 atoms, 13349 bonds, 3 pseudobonds, 853 residues, 2 models selected
> select down
11381 atoms, 11475 bonds, 3 pseudobonds, 730 residues, 2 models selected
> select down
10339 atoms, 10304 bonds, 3 pseudobonds, 730 residues, 2 models selected
> select clear
> select up
4933 atoms, 4804 bonds, 3 pseudobonds, 418 residues, 2 models selected
> select up
6499 atoms, 6537 bonds, 3 pseudobonds, 418 residues, 2 models selected
> select up
10693 atoms, 10806 bonds, 3 pseudobonds, 692 residues, 2 models selected
> select up
13480 atoms, 13635 bonds, 3 pseudobonds, 871 residues, 2 models selected
> select up
80880 atoms, 81810 bonds, 18 pseudobonds, 5226 residues, 2 models selected
> select down
13480 atoms, 13635 bonds, 3 pseudobonds, 871 residues, 2 models selected
> molmap sel 4
Opened 231010_Xl_14-3_deepEMhcr_refine43.pdb map 4 as #6, grid size 68,67,93,
pixel 1.33, shown at level 0.121, step 1, values float32
> show #!4 models
> fitmap #4 inMap #6
Fit map Xl_14-3_refine07_deepemhancer.mrc in map
231010_Xl_14-3_deepEMhcr_refine43.pdb map 4 using 89894 points
correlation = 0.2299, correlation about mean = 0.1346, overlap = 1082
steps = 76, shift = 0.263, angle = 0.503 degrees
Position of Xl_14-3_refine07_deepemhancer.mrc (#4) relative to
231010_Xl_14-3_deepEMhcr_refine43.pdb map 4 (#6) coordinates:
Matrix rotation and translation
0.99999837 -0.00180536 -0.00001957 0.24167434
0.00180536 0.99999837 0.00004408 -0.31615025
0.00001949 -0.00004411 1.00000000 -0.00116392
Axis -0.02441701 -0.01081256 0.99964339
Axis point 175.25975753 133.65715046 0.00000000
Rotation angle (degrees) 0.10347666
Shift along axis -0.00364608
> fitmap #4 inMap #6
Fit map Xl_14-3_refine07_deepemhancer.mrc in map
231010_Xl_14-3_deepEMhcr_refine43.pdb map 4 using 89894 points
correlation = 0.2299, correlation about mean = 0.1346, overlap = 1082
steps = 28, shift = 0.00743, angle = 0.0154 degrees
Position of Xl_14-3_refine07_deepemhancer.mrc (#4) relative to
231010_Xl_14-3_deepEMhcr_refine43.pdb map 4 (#6) coordinates:
Matrix rotation and translation
0.99999807 -0.00196183 -0.00010676 0.28185510
0.00196182 0.99999806 -0.00015536 -0.30203935
0.00010706 0.00015515 0.99999998 -0.03975994
Axis 0.07877538 -0.05424440 0.99541548
Axis point 154.12811343 143.55739894 0.00000000
Rotation angle (degrees) 0.11292204
Shift along axis -0.00099047
> fitmap #4 inMap #6
Fit map Xl_14-3_refine07_deepemhancer.mrc in map
231010_Xl_14-3_deepEMhcr_refine43.pdb map 4 using 89894 points
correlation = 0.2299, correlation about mean = 0.1346, overlap = 1082
steps = 28, shift = 0.0112, angle = 0.0144 degrees
Position of Xl_14-3_refine07_deepemhancer.mrc (#4) relative to
231010_Xl_14-3_deepEMhcr_refine43.pdb map 4 (#6) coordinates:
Matrix rotation and translation
0.99999849 -0.00172715 -0.00016423 0.26519548
0.00172712 0.99999848 -0.00022156 -0.24779069
0.00016461 0.00022128 0.99999996 -0.05133746
Axis 0.12659850 -0.09400507 0.98748968
Axis point 143.26902605 152.96758112 0.00000000
Rotation angle (degrees) 0.10021130
Shift along axis 0.00617171
> fitmap #4 inMap #6
Fit map Xl_14-3_refine07_deepemhancer.mrc in map
231010_Xl_14-3_deepEMhcr_refine43.pdb map 4 using 89894 points
correlation = 0.2299, correlation about mean = 0.1346, overlap = 1082
steps = 28, shift = 0.00455, angle = 0.00314 degrees
Position of Xl_14-3_refine07_deepemhancer.mrc (#4) relative to
231010_Xl_14-3_deepEMhcr_refine43.pdb map 4 (#6) coordinates:
Matrix rotation and translation
0.99999858 -0.00167584 -0.00016388 0.26108380
0.00167581 0.99999858 -0.00020233 -0.24454737
0.00016422 0.00020206 0.99999997 -0.05021579
Axis 0.11922297 -0.09673320 0.98814400
Axis point 145.76173261 155.30175846 0.00000000
Rotation angle (degrees) 0.09716998
Shift along axis 0.00516261
> fitmap #4 inMap #6
Fit map Xl_14-3_refine07_deepemhancer.mrc in map
231010_Xl_14-3_deepEMhcr_refine43.pdb map 4 using 89894 points
correlation = 0.2299, correlation about mean = 0.1346, overlap = 1082
steps = 28, shift = 0.00399, angle = 0.00374 degrees
Position of Xl_14-3_refine07_deepemhancer.mrc (#4) relative to
231010_Xl_14-3_deepEMhcr_refine43.pdb map 4 (#6) coordinates:
Matrix rotation and translation
0.99999868 -0.00161270 -0.00017503 0.25737686
0.00161267 0.99999868 -0.00021419 -0.23214486
0.00017538 0.00021391 0.99999996 -0.05535572
Axis 0.13081776 -0.10707706 0.98560703
Axis point 143.81804552 159.15412870 0.00000000
Rotation angle (degrees) 0.09374946
Shift along axis 0.00396786
> hide #!6 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> close #5-6
> show #!4 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> volume #2 step 1
> volume #4 step 1
> mmaker #3 to #1 pair ss showAlignment true
Parameters
---
Chain pairing | ss
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 231010_Xt_14-3_deepEMhcr_refine42.pdb, chain A (#1) with
231010_Xl_14-3_deepEMhcr_refine43.pdb, chain A (#3), sequence alignment score
= 2171
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1:
231010_Xt_14-3_deepEMhcr_refine42.pdb #1/A,
231010_Xl_14-3_deepEMhcr_refine43.pdb #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
Matchmaker 231010_Xt_14-3_deepEMhcr_refine42.pdb, chain B (#1) with
231010_Xl_14-3_deepEMhcr_refine43.pdb, chain B (#3), sequence alignment score
= 2171
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2:
231010_Xt_14-3_deepEMhcr_refine42.pdb #1/B,
231010_Xl_14-3_deepEMhcr_refine43.pdb #3/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
Matchmaker 231010_Xt_14-3_deepEMhcr_refine42.pdb, chain C (#1) with
231010_Xl_14-3_deepEMhcr_refine43.pdb, chain C (#3), sequence alignment score
= 2171
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3:
231010_Xt_14-3_deepEMhcr_refine42.pdb #1/C,
231010_Xl_14-3_deepEMhcr_refine43.pdb #3/C
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
Matchmaker 231010_Xt_14-3_deepEMhcr_refine42.pdb, chain D (#1) with
231010_Xl_14-3_deepEMhcr_refine43.pdb, chain D (#3), sequence alignment score
= 2171
Alignment identifier is 4
Showing conservation header ("seq_conservation" residue attribute) for
alignment 4
Hiding conservation header for alignment 4
Chains used in RMSD evaluation for alignment 4:
231010_Xt_14-3_deepEMhcr_refine42.pdb #1/D,
231010_Xl_14-3_deepEMhcr_refine43.pdb #3/D
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 4
Matchmaker 231010_Xt_14-3_deepEMhcr_refine42.pdb, chain E (#1) with
231010_Xl_14-3_deepEMhcr_refine43.pdb, chain E (#3), sequence alignment score
= 2171
Alignment identifier is 5
Showing conservation header ("seq_conservation" residue attribute) for
alignment 5
Hiding conservation header for alignment 5
Chains used in RMSD evaluation for alignment 5:
231010_Xt_14-3_deepEMhcr_refine42.pdb #1/E,
231010_Xl_14-3_deepEMhcr_refine43.pdb #3/E
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 5
Matchmaker 231010_Xt_14-3_deepEMhcr_refine42.pdb, chain F (#1) with
231010_Xl_14-3_deepEMhcr_refine43.pdb, chain F (#3), sequence alignment score
= 2171
Alignment identifier is 6
Showing conservation header ("seq_conservation" residue attribute) for
alignment 6
Hiding conservation header for alignment 6
Chains used in RMSD evaluation for alignment 6:
231010_Xt_14-3_deepEMhcr_refine42.pdb #1/F,
231010_Xl_14-3_deepEMhcr_refine43.pdb #3/F
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 6
Matchmaker 231010_Xt_14-3_deepEMhcr_refine42.pdb, chain a (#1) with
231010_Xl_14-3_deepEMhcr_refine43.pdb, chain a (#3), sequence alignment score
= 2151.5
Alignment identifier is 7
Showing conservation header ("seq_conservation" residue attribute) for
alignment 7
Hiding conservation header for alignment 7
Chains used in RMSD evaluation for alignment 7:
231010_Xt_14-3_deepEMhcr_refine42.pdb #1/a,
231010_Xl_14-3_deepEMhcr_refine43.pdb #3/a
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 7
Matchmaker 231010_Xt_14-3_deepEMhcr_refine42.pdb, chain b (#1) with
231010_Xl_14-3_deepEMhcr_refine43.pdb, chain b (#3), sequence alignment score
= 2151.5
Alignment identifier is 8
Showing conservation header ("seq_conservation" residue attribute) for
alignment 8
Hiding conservation header for alignment 8
Chains used in RMSD evaluation for alignment 8:
231010_Xt_14-3_deepEMhcr_refine42.pdb #1/b,
231010_Xl_14-3_deepEMhcr_refine43.pdb #3/b
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 8
Matchmaker 231010_Xt_14-3_deepEMhcr_refine42.pdb, chain c (#1) with
231010_Xl_14-3_deepEMhcr_refine43.pdb, chain c (#3), sequence alignment score
= 2151.5
Alignment identifier is 9
Showing conservation header ("seq_conservation" residue attribute) for
alignment 9
Hiding conservation header for alignment 9
Chains used in RMSD evaluation for alignment 9:
231010_Xt_14-3_deepEMhcr_refine42.pdb #1/c,
231010_Xl_14-3_deepEMhcr_refine43.pdb #3/c
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 9
Matchmaker 231010_Xt_14-3_deepEMhcr_refine42.pdb, chain d (#1) with
231010_Xl_14-3_deepEMhcr_refine43.pdb, chain d (#3), sequence alignment score
= 2151.5
Alignment identifier is 10
Showing conservation header ("seq_conservation" residue attribute) for
alignment 10
Hiding conservation header for alignment 10
Chains used in RMSD evaluation for alignment 10:
231010_Xt_14-3_deepEMhcr_refine42.pdb #1/d,
231010_Xl_14-3_deepEMhcr_refine43.pdb #3/d
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 10
Matchmaker 231010_Xt_14-3_deepEMhcr_refine42.pdb, chain e (#1) with
231010_Xl_14-3_deepEMhcr_refine43.pdb, chain e (#3), sequence alignment score
= 2151.5
Alignment identifier is 11
Showing conservation header ("seq_conservation" residue attribute) for
alignment 11
Hiding conservation header for alignment 11
Chains used in RMSD evaluation for alignment 11:
231010_Xt_14-3_deepEMhcr_refine42.pdb #1/e,
231010_Xl_14-3_deepEMhcr_refine43.pdb #3/e
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 11
Matchmaker 231010_Xt_14-3_deepEMhcr_refine42.pdb, chain f (#1) with
231010_Xl_14-3_deepEMhcr_refine43.pdb, chain f (#3), sequence alignment score
= 2151.5
Alignment identifier is 12
Showing conservation header ("seq_conservation" residue attribute) for
alignment 12
Hiding conservation header for alignment 12
Chains used in RMSD evaluation for alignment 12:
231010_Xt_14-3_deepEMhcr_refine42.pdb #1/f,
231010_Xl_14-3_deepEMhcr_refine43.pdb #3/f
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 12
RMSD between 5108 pruned atom pairs is 0.669 angstroms; (across all 5208
pairs: 0.770)
> mmaker #3/E to #1/E pair ss showAlignment true
Parameters
---
Chain pairing | ss
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 231010_Xt_14-3_deepEMhcr_refine42.pdb, chain E (#1) with
231010_Xl_14-3_deepEMhcr_refine43.pdb, chain E (#3), sequence alignment score
= 2171
Alignment identifier is 13
Showing conservation header ("seq_conservation" residue attribute) for
alignment 13
Hiding conservation header for alignment 13
Chains used in RMSD evaluation for alignment 13:
231010_Xt_14-3_deepEMhcr_refine42.pdb #1/E,
231010_Xl_14-3_deepEMhcr_refine43.pdb #3/E
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 13
RMSD between 424 pruned atom pairs is 0.599 angstroms; (across all 430 pairs:
0.662)
> show #!2 models
> show #!3 models
> show #!4 models
> show #!1 models
> hide #!4 models
> hide #!2 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> molmap #1 3.5
Opened 231010_Xt_14-3_deepEMhcr_refine42.pdb map 3.5 as #5, grid size
129,143,188, pixel 1.17, shown at level 0.118, step 1, values float32
> molmap #3 3.0
Opened 231010_Xl_14-3_deepEMhcr_refine43.pdb map 3 as #6, grid size
172,135,216, pixel 1, shown at level 0.119, step 1, values float32
> fitmap #1 inMap #5
Fit molecule 231010_Xt_14-3_deepEMhcr_refine42.pdb (#1) to map
231010_Xt_14-3_deepEMhcr_refine42.pdb map 3.5 (#5) using 80898 atoms
average map value = 0.7582, steps = 40
shifted from previous position = 0.00988
rotated from previous position = 0.00954 degrees
atoms outside contour = 0, contour level = 0.11752
Position of 231010_Xt_14-3_deepEMhcr_refine42.pdb (#1) relative to
231010_Xt_14-3_deepEMhcr_refine42.pdb map 3.5 (#5) coordinates:
Matrix rotation and translation
0.99999999 -0.00010438 -0.00010438 0.04482416
0.00010439 0.99999999 0.00007683 -0.02759854
0.00010438 -0.00007684 0.99999999 0.00101700
Axis -0.46167345 -0.62722133 0.62725675
Axis point 280.90905379 417.24787774 0.00000000
Rotation angle (degrees) 0.00953503
Shift along axis -0.00274581
> fitmap #2 inMap #5
Fit map Xt_14-3_refine10repeated_deepemhancer.mrc in map
231010_Xt_14-3_deepEMhcr_refine42.pdb map 3.5 using 719343 points
correlation = 0.5845, correlation about mean = 0.3482, overlap = 5.119e+04
steps = 40, shift = 0.051, angle = 0.0536 degrees
Position of Xt_14-3_refine10repeated_deepemhancer.mrc (#2) relative to
231010_Xt_14-3_deepEMhcr_refine42.pdb map 3.5 (#5) coordinates:
Matrix rotation and translation
0.99999991 0.00036320 -0.00022563 0.25195654
-0.00036316 0.99999992 0.00016355 0.07277050
0.00022569 -0.00016347 0.99999996 0.03361809
Axis -0.35719037 -0.49295136 -0.79335616
Axis point -6.55665626 -543.70151676 -0.00000000
Rotation angle (degrees) 0.02622865
Shift along axis -0.15253989
> fitmap #4 inMap #6
Fit map Xl_14-3_refine07_deepemhancer.mrc in map
231010_Xl_14-3_deepEMhcr_refine43.pdb map 3 using 715847 points
correlation = 0.5142, correlation about mean = 0.3011, overlap = 5.856e+04
steps = 48, shift = 0.0506, angle = 0.0902 degrees
Position of Xl_14-3_refine07_deepemhancer.mrc (#4) relative to
231010_Xl_14-3_deepEMhcr_refine43.pdb map 3 (#6) coordinates:
Matrix rotation and translation
0.99999993 -0.00004952 -0.00036332 0.08108190
0.00004946 0.99999998 -0.00017676 0.02436222
0.00036333 0.00017674 0.99999992 -0.04171967
Axis 0.43421587 -0.89256650 0.12157971
Axis point 117.68188089 0.00000000 213.12110929
Rotation angle (degrees) 0.02332252
Shift along axis 0.00838988
> close #5-6
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!4 models
> hide #!1 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> show #!3 models
> select clear
> show atoms
> style stick
Changed 161778 atom styles
> show cartoons
> hide atoms
> volume #2 level 0.1303
> volume #4 level 0.1345
> volume #4 level 0.1535
> ui tool show "Side View"
> transparency 50
> volume #4 level 0.201
> select add #4
4 models selected
> transparency #4.1 0
> select clear
> hide #!4 models
> volume #2 level 0.2245
> ui tool show "Render By Attribute"
> color byattribute r:seq_rmsd #!1 target scab palette
> 0.0299768,blue:2.25707,white:4.48416,red
80898 atoms, 5226 residues, atom seq_rmsd range 0.03 to 4.48
> volume #4 level 0.5353
> volume #2 level 0.2071
> select add #2
4 models selected
> select subtract #2
Nothing selected
> select add #3
80880 atoms, 81810 bonds, 18 pseudobonds, 5226 residues, 2 models selected
> select add #1
161778 atoms, 163638 bonds, 54 pseudobonds, 10452 residues, 4 models selected
> show sel atoms
> hide HC
> select clear
> volume #4 level 0.3339
> volume #2 level 0.1373
> color byattribute r:seq_rmsd #!1 target scab palette
> 0.0299768,blue:0.766017,white:1.50585,red
80898 atoms, 5226 residues, atom seq_rmsd range 0.03 to 4.48
> volume #4 level 0.1516
> volume #2 level 0.05884
> volume #4 level 0.275
> hide #!3 models
> volume #2 level 0.2629
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #2 level 0.4634
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> volume #2 level 0.2681
> volume #4 style mesh
> volume #4 style surface
> hide #!3 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> select up
1205 atoms, 1211 bonds, 74 residues, 2 models selected
> select up
13259 atoms, 13409 bonds, 860 residues, 2 models selected
> select down
1205 atoms, 1211 bonds, 74 residues, 2 models selected
> mmaker #3/sel to #1/sel pair ss showAlignment true
No 'to' chains specified
> mmaker #3/sel to #1 pair ss showAlignment true
No molecules/chains to match specified
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> molmap sel 3.0
Opened map 3 as #5, grid size 44,47,59, pixel 1, shown at level 0.19, step 1,
values float32
> molmap sel 3.5
Opened map 3.5 as #5, grid size 40,43,53, pixel 1.17, shown at level 0.172,
step 1, values float32
> fitmap #1 inMap #5
Fit molecule 231010_Xt_14-3_deepEMhcr_refine42.pdb (#1) to map map 3.5 (#5)
using 80898 atoms
average map value = 0.1467, steps = 2000
shifted from previous position = 2.73
rotated from previous position = 2.75 degrees
atoms outside contour = 80212, contour level = 0.17154
Position of 231010_Xt_14-3_deepEMhcr_refine42.pdb (#1) relative to map 3.5
(#5) coordinates:
Matrix rotation and translation
0.99951635 -0.03050639 -0.00603621 4.15754146
0.03070609 0.99886736 0.03634730 -11.59820298
0.00492055 -0.03651507 0.99932099 3.27632309
Axis -0.76063783 -0.11438170 0.63902028
Axis point 0.00000000 79.24786705 320.75193415
Rotation angle (degrees) 2.74526419
Shift along axis 0.25787570
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> fitmap #3 inMap #5
Fit molecule 231010_Xl_14-3_deepEMhcr_refine43.pdb (#3) to map map 3.5 (#5)
using 80880 atoms
average map value = 0.1557, steps = 880
shifted from previous position = 0.763
rotated from previous position = 0.754 degrees
atoms outside contour = 80181, contour level = 0.17154
Position of 231010_Xl_14-3_deepEMhcr_refine43.pdb (#3) relative to map 3.5
(#5) coordinates:
Matrix rotation and translation
0.90959710 0.41537640 -0.00977607 -71.71395479
-0.41525661 0.90962230 0.01221578 112.29571320
0.01396668 -0.00705186 0.99987759 6.25093914
Axis -0.02318064 -0.02856457 -0.99932313
Axis point 221.71630525 221.33750768 0.00000000
Rotation angle (degrees) 24.55696902
Shift along axis -7.79201097
> fitmap #3 inMap #5
Fit molecule 231010_Xl_14-3_deepEMhcr_refine43.pdb (#3) to map map 3.5 (#5)
using 80880 atoms
average map value = 0.1557, steps = 84
shifted from previous position = 0.115
rotated from previous position = 0.105 degrees
atoms outside contour = 80181, contour level = 0.17154
Position of 231010_Xl_14-3_deepEMhcr_refine43.pdb (#3) relative to map 3.5
(#5) coordinates:
Matrix rotation and translation
0.90944431 0.41569882 -0.01027319 -71.61849386
-0.41555012 0.90946347 0.01393910 112.05610653
0.01513756 -0.00840781 0.99985007 6.10854983
Axis -0.02686129 -0.03054407 -0.99917242
Axis point 220.96815272 220.91144473 0.00000000
Rotation angle (degrees) 24.58033609
Shift along axis -7.60237838
> fitmap #1 inMap #5
Fit molecule 231010_Xt_14-3_deepEMhcr_refine42.pdb (#1) to map map 3.5 (#5)
using 80898 atoms
average map value = 0.1527, steps = 1212
shifted from previous position = 2.91
rotated from previous position = 2.87 degrees
atoms outside contour = 80210, contour level = 0.17154
Position of 231010_Xt_14-3_deepEMhcr_refine42.pdb (#1) relative to map 3.5
(#5) coordinates:
Matrix rotation and translation
0.99996889 0.00787234 -0.00049900 -0.86125900
-0.00786987 0.99995764 0.00477394 0.30995799
0.00053656 -0.00476987 0.99998848 0.60594288
Axis -0.51760580 -0.05616360 -0.85377391
Axis point 38.12938397 115.40262049 0.00000000
Rotation angle (degrees) 0.52822802
Shift along axis -0.08895393
> color byattribute r:seq_rmsd #!1 target scab palette
> 0.0299768,blue:0.766017,white:1.50585,red
80898 atoms, 5226 residues, atom seq_rmsd range 0.0438 to 4.9
> select clear
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> undo
[Repeated 9 time(s)]
> select clear
> select up
188 atoms, 189 bonds, 13 residues, 1 model selected
> select up
6631 atoms, 6706 bonds, 430 residues, 1 model selected
> select down
188 atoms, 189 bonds, 13 residues, 1 model selected
> select clear
> hide #!3 models
> matchmaker #1/D to #3/D pairing ss
Parameters
---
Chain pairing | ss
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 231010_Xl_14-3_deepEMhcr_refine43.pdb, chain D (#3) with
231010_Xt_14-3_deepEMhcr_refine42.pdb, chain D (#1), sequence alignment score
= 2171
RMSD between 424 pruned atom pairs is 0.599 angstroms; (across all 430 pairs:
0.662)
> color byattribute r:seq_rmsd #!1 target scab palette
> 0.0299768,blue:0.766017,white:1.50585,red
80898 atoms, 5226 residues, atom seq_rmsd range 0.0298 to 4.82
> hide #!1 cartoons
> hide #!1 atoms
> show #!1 atoms
> hide HC
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
160758 atoms, 162582 bonds, 10416 residues, 2 models selected
> hide (#!1 & sel) target a
> show (#!1 & sel) target ab
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & backbone) target ab
> hide HC
> select clear
> hide (#1 & (protein|nucleic)) target a
> cartoon hide #1
> show (#1 & ((protein&@ca)|(nucleic&@p))) target ab
> show #!3 models
> hide (#1,3 & (protein|nucleic)) target a
> cartoon hide #1,3
> show (#1,3 & ((protein&@ca)|(nucleic&@p))) target ab
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> matchmaker #1/d to #3/d pairing ss
Parameters
---
Chain pairing | ss
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 231010_Xl_14-3_deepEMhcr_refine43.pdb, chain d (#3) with
231010_Xt_14-3_deepEMhcr_refine42.pdb, chain d (#1), sequence alignment score
= 2151.5
RMSD between 429 pruned atom pairs is 0.624 angstroms; (across all 438 pairs:
0.747)
> color byattribute r:seq_rmsd #!1 target scab palette
> 0.0299768,blue:0.766017,white:1.50585,red
80898 atoms, 5226 residues, atom seq_rmsd range 0.0136 to 4.93
> show #!3 models
> hide #!3 models
> matchmaker #1/a to #3/a pairing ss
Parameters
---
Chain pairing | ss
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 231010_Xl_14-3_deepEMhcr_refine43.pdb, chain a (#3) with
231010_Xt_14-3_deepEMhcr_refine42.pdb, chain a (#1), sequence alignment score
= 2151.5
RMSD between 429 pruned atom pairs is 0.624 angstroms; (across all 438 pairs:
0.747)
> color byattribute r:seq_rmsd #!1 target scab palette
> 0.0299768,blue:0.766017,white:1.50585,red
80898 atoms, 5226 residues, atom seq_rmsd range 0.0248 to 4.65
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> matchmaker #1/D to #3/D pairing ss
Parameters
---
Chain pairing | ss
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 231010_Xl_14-3_deepEMhcr_refine43.pdb, chain D (#3) with
231010_Xt_14-3_deepEMhcr_refine42.pdb, chain D (#1), sequence alignment score
= 2171
RMSD between 424 pruned atom pairs is 0.599 angstroms; (across all 430 pairs:
0.662)
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> save
> /d/emr214/u/tl002/Xtropicalis_2209/Phenix02/Xtropicalis/231010_Xt_14-3_deepEMhcr_refine42_Xlmm-D.pdb
> models #1 relModel #3
> open /d/emr214/u/tl002/Xtropicalis_2209/Phenix02/displacement_markers.cmm
Traceback (most recent call last):
File "/usr/local/chimerax-1.6.1/lib/python3.9/xml/sax/expatreader.py", line
217, in feed
self._parser.Parse(data, isFinal)
xml.parsers.expat.ExpatError: syntax error: line 1, column 0
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open
return remember_data_format()
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/markers/__init__.py", line 51, in open
return cmmfiles.read_cmm(session, data)
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/markers/cmmfiles.py", line 7, in read_cmm
msets = load_markerset_xml(session, f)
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/markers/cmmfiles.py", line 181, in load_markerset_xml
xml_parser.parse(input)
File "/usr/local/chimerax-1.6.1/lib/python3.9/xml/sax/expatreader.py", line
111, in parse
xmlreader.IncrementalParser.parse(self, source)
File "/usr/local/chimerax-1.6.1/lib/python3.9/xml/sax/xmlreader.py", line 125,
in parse
self.feed(buffer)
File "/usr/local/chimerax-1.6.1/lib/python3.9/xml/sax/expatreader.py", line
221, in feed
self._err_handler.fatalError(exc)
File "/usr/local/chimerax-1.6.1/lib/python3.9/xml/sax/handler.py", line 38, in
fatalError
raise exception
xml.sax._exceptions.SAXParseException:
/d/emr214/u/tl002/Xtropicalis_2209/Phenix02/displacement_markers.cmm:1:0:
syntax error
xml.sax._exceptions.SAXParseException:
/d/emr214/u/tl002/Xtropicalis_2209/Phenix02/displacement_markers.cmm:1:0:
syntax error
File "/usr/local/chimerax-1.6.1/lib/python3.9/xml/sax/handler.py", line 38, in
fatalError
raise exception
See log for complete Python traceback.
> open /d/emr214/u/tl002/Xtropicalis_2209/Phenix02/displacement_markers2.cmm
Traceback (most recent call last):
File "/usr/local/chimerax-1.6.1/lib/python3.9/xml/sax/expatreader.py", line
217, in feed
self._parser.Parse(data, isFinal)
xml.parsers.expat.ExpatError: syntax error: line 1, column 0
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open
return remember_data_format()
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/markers/__init__.py", line 51, in open
return cmmfiles.read_cmm(session, data)
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/markers/cmmfiles.py", line 7, in read_cmm
msets = load_markerset_xml(session, f)
File "/usr/local/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/markers/cmmfiles.py", line 181, in load_markerset_xml
xml_parser.parse(input)
File "/usr/local/chimerax-1.6.1/lib/python3.9/xml/sax/expatreader.py", line
111, in parse
xmlreader.IncrementalParser.parse(self, source)
File "/usr/local/chimerax-1.6.1/lib/python3.9/xml/sax/xmlreader.py", line 125,
in parse
self.feed(buffer)
File "/usr/local/chimerax-1.6.1/lib/python3.9/xml/sax/expatreader.py", line
221, in feed
self._err_handler.fatalError(exc)
File "/usr/local/chimerax-1.6.1/lib/python3.9/xml/sax/handler.py", line 38, in
fatalError
raise exception
xml.sax._exceptions.SAXParseException:
/d/emr214/u/tl002/Xtropicalis_2209/Phenix02/displacement_markers2.cmm:1:0:
syntax error
xml.sax._exceptions.SAXParseException:
/d/emr214/u/tl002/Xtropicalis_2209/Phenix02/displacement_markers2.cmm:1:0:
syntax error
File "/usr/local/chimerax-1.6.1/lib/python3.9/xml/sax/handler.py", line 38, in
fatalError
raise exception
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 535.113.01
OpenGL renderer: NVIDIA GeForce RTX 2080 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_GB.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
DISPLAY=:1
Manufacturer: System manufacturer
Model: System Product Name
OS: AlmaLinux 8.8 Sapphire Caracal
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 AMD Ryzen 9 5950X 16-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 125Gi 13Gi 98Gi 145Mi 13Gi 110Gi
Swap: 255Gi 173Mi 255Gi
Graphics:
08:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104 [GeForce RTX 2080 SUPER] [10de:1e81] (rev a1)
Subsystem: PNY Device [196e:133f]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.21.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.6.0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
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