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Opened 2 years ago
Closed 2 years ago
#9962 closed defect (can't reproduce)
Syntax error reading marker file
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
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
[deleted to fit within ticket limits]
> 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
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Volume Data |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Syntax error reading marker file |
comment:2 by , 2 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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Bad marker file, maybe it is empty (syntax error at column 0 of line 1). Not sure what software wrote it.
xml.parsers.expat.ExpatError: syntax error: line 1, column 0