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Opened 4 years ago
Closed 4 years ago
#6242 closed defect (duplicate)
wrapped C/C++ object of type QScreen has been deleted
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/modeling.cxs
Opened run_class001.mrc z flip as #8, grid size 220,220,220, pixel 1.67, shown
at level 0.023, step 1, values float32
Log from Thu Feb 24 10:30:24 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/modeling.cxs
Opened run_class001.mrc z flip as #8, grid size 220,220,220, pixel 1.67, shown
at level 0.023, step 1, values float32
Log from Wed Feb 23 13:58:39 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/modeling.cxs
Opened run_class001.mrc z flip as #8, grid size 220,220,220, pixel 1.67, shown
at level 0.0213, step 1, values float32
Log from Tue Feb 22 15:23:29 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/modeling.cxs
Opened run_class001.mrc z flip as #8, grid size 220,220,220, pixel 1.67, shown
at level 0.0213, step 1, values float32
Log from Tue Feb 22 11:44:31 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/1Crm1_loop.cxs
Opened run_class001.mrc as #1, grid size 220,220,220, pixel 1.67, shown at
level 0.0252, step 1, values float32
Opened mask.mrc as #2, grid size 220,220,220, pixel 1.67, shown at level 1,
step 1, values float32
Opened mask.mrc as #3, grid size 220,220,220, pixel 1.67, shown at level 1,
step 1, values float32
Opened run_class001.mrc z flip as #4, grid size 220,220,220, pixel 1.67, shown
at level 0.02, step 1, values float32
Opened mask.mrc z flip as #5, grid size 220,220,220, pixel 1.67, shown at
level 1, step 1, values float32
Opened mask.mrc z flip as #6, grid size 220,220,220, pixel 1.67, shown at
level 1, step 1, values float32
Opened run_class001.mrc as #7, grid size 220,220,220, pixel 1.67, shown at
level 0.0252, step 1, values float32
Opened run_class001.mrc z flip as #8, grid size 220,220,220, pixel 1.67, shown
at level 0.0196, step 1, values float32
Log from Tue Feb 22 10:41:40 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/021822.cxs
Opened run_class001.mrc as #1, grid size 220,220,220, pixel 1.67, shown at
level 0.0164, step 1, values float32
Opened mask.mrc as #2, grid size 220,220,220, pixel 1.67, shown at level 1,
step 1, values float32
Opened mask.mrc as #3, grid size 220,220,220, pixel 1.67, shown at level 1,
step 1, values float32
Opened run_class001.mrc z flip as #4, grid size 220,220,220, pixel 1.67, shown
at level 0.02, step 1, values float32
Opened mask.mrc z flip as #5, grid size 220,220,220, pixel 1.67, shown at
level 1, step 1, values float32
Opened mask.mrc z flip as #6, grid size 220,220,220, pixel 1.67, shown at
level 1, step 1, values float32
Opened run_class001.mrc as #7, grid size 220,220,220, pixel 1.67, shown at
level 0.012, step 1, values float32
Opened run_class001.mrc z flip as #8, grid size 220,220,220, pixel 1.67, shown
at level 0.0196, step 1, values float32
Log from Fri Feb 18 11:41:53 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/amberms/Desktop/wynton/Refine3D/job256/run_class001.mrc
Opened run_class001.mrc as #1, grid size 220,220,220, pixel 1.67, shown at
level 0.0113, step 1, values float32
> open /Users/amberms/Desktop/wynton/MaskCreate/job241/mask.mrc
Opened mask.mrc as #2, grid size 220,220,220, pixel 1.67, shown at level 1,
step 1, values float32
> open /Users/amberms/Desktop/wynton/MaskCreate/job242/mask.mrc
Opened mask.mrc as #3, grid size 220,220,220, pixel 1.67, shown at level 1,
step 1, values float32
> volume #2 level 0.9879
> volume #3 level 1
> volume #2 level 1
> transparency 50
> transparency 0
> hide #!1 models
> volume #!2-3 style image
> volume #!2-3 style image
> volume #!2-3 style surface
> transparency #2.1#3.1 50
> show #!1 models
> hide #!2 models
> hide #!3 models
> volume #1 level 0.01639
> set bgColor white
> volume flip #1-3
Opened run_class001.mrc z flip as #4, grid size 220,220,220, pixel 1.67, shown
at step 1, values float32
Opened mask.mrc z flip as #5, grid size 220,220,220, pixel 1.67, shown at step
1, values float32
Opened mask.mrc z flip as #6, grid size 220,220,220, pixel 1.67, shown at step
1, values float32
> hide #!5 models
> hide #!6 models
> volume #4 level 0.015
> volume #4 level 0.01
> volume #4 level 0.02
> save
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/job310_front.png
> turn x 180
> turn x 180
> turn y 180
> save
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/job310_back.png
> show #!5 models
> hide #!5 models
> turn y 180
> show #!5 models
> save
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/job310_1stCrm.png
> hide #!5 models
> show #!6 models
> save
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/job310_2ndCrm.png
> open /Users/amberms/Desktop/wynton/Refine3D/job310/run_class001.mrc
Opened run_class001.mrc as #7, grid size 220,220,220, pixel 1.67, shown at
level 0.012, step 1, values float32
> volume flip #7
Opened run_class001.mrc z flip as #8, grid size 220,220,220, pixel 1.67, shown
at step 1, values float32
> hide #!6 models
> hide #!4 models
> volume #8 level 0.01957
> save
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/job310_front.png
> turn y 180
> save
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/job310_back.png
> save /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/021822.cxs
——— End of log from Fri Feb 18 11:41:53 2022 ———
opened ChimeraX session
> show #!2 models
> hide #!2 models
> hide #!8 models
> show #!7 models
> show #!1 models
> hide #!7 models
> show #!7 models
> volume #7 level 0.02519
> hide #!7 models
> show #!7 models
> hide #!1 models
> volume #1 level 0.0264
> volume #1 level 0.0252
> show #!1 models
> hide #!7 models
> show #!7 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!7 models
> show #!8 models
> show #!4 models
> hide #!4 models
> open "/Users/amberms/Downloads/AF-O14980-F1-model_v2 (1).pdb"
AF-O14980-F1-model_v2 (1).pdb title:
Alphafold monomer V2.0 prediction for exportin-1 (O14980) [more info...]
Chain information for AF-O14980-F1-model_v2 (1).pdb #9
---
Chain | Description
A | exportin-1
> select #9
8669 atoms, 8851 bonds, 1071 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #9,1,0,0,-7.4513,0,1,0,-10.983,0,0,1,-14.082
> view matrix models #9,1,0,0,158.95,0,1,0,224.34,0,0,1,208.83
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.097642,-0.94633,0.3081,144.05,0.93196,0.19556,0.3053,233.81,-0.34917,0.25733,0.90103,205.14
> hide #!8 models
> show #!8 models
> view matrix models
> #9,0.13269,-0.95497,0.26537,144.53,0.87863,0.23724,0.41439,233.12,-0.45869,0.17818,0.87055,203.51
> view matrix models
> #9,0.34794,-0.91422,0.20769,147.52,0.76858,0.40501,0.49523,232.11,-0.53686,-0.012684,0.84357,201.94
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.34794,-0.91422,0.20769,197.55,0.76858,0.40501,0.49523,204.88,-0.53686,-0.012684,0.84357,213.47
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.19552,-0.96532,0.17301,195.44,0.81395,0.25814,0.52043,205.01,-0.54704,0.039071,0.8362,213.5
> view matrix models
> #9,0.18562,-0.95995,0.20986,195.29,0.83238,0.26711,0.48558,205.32,-0.52219,0.08455,0.84863,213.95
> view matrix models
> #9,0.082858,-0.86158,0.50081,193.95,0.59573,0.44568,0.66819,202.58,-0.7989,0.24298,0.5502,211.1
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.082858,-0.86158,0.50081,187.27,0.59573,0.44568,0.66819,191.59,-0.7989,0.24298,0.5502,202.88
> fitmap #9 inMap #8
Fit molecule AF-O14980-F1-model_v2 (1).pdb (#9) to map run_class001.mrc z flip
(#8) using 8669 atoms
average map value = 0.02224, steps = 128
shifted from previous position = 6.39
rotated from previous position = 27.1 degrees
atoms outside contour = 4350, contour level = 0.01957
Position of AF-O14980-F1-model_v2 (1).pdb (#9) relative to run_class001.mrc z
flip (#8) coordinates:
Matrix rotation and translation
0.14284124 -0.69487007 0.70480633 185.20202593
0.21776045 0.71672339 0.66248619 191.63662295
-0.96549301 0.05884859 0.25369287 197.31096218
Axis -0.30230391 0.83649199 0.45704868
Axis point 195.81359294 0.00000000 -108.05176024
Rotation angle (degrees) 86.75367481
Shift along axis 194.49591973
> view matrix models
> #9,0.14284,-0.69487,0.70481,180.4,0.21776,0.71672,0.66249,199.02,-0.96549,0.058849,0.25369,194.17
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.54431,-0.62198,0.56291,186,-0.16065,0.58131,0.79766,193.55,-0.82336,-0.52461,0.21649,194.33
> view matrix models
> #9,0.52124,-0.74038,0.42443,185.48,-0.09317,0.44499,0.89067,193.93,-0.84831,-0.5038,0.16297,194.12
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.52124,-0.74038,0.42443,192.83,-0.09317,0.44499,0.89067,191.96,-0.84831,-0.5038,0.16297,196.04
> fitmap #9 inMap #8
Fit molecule AF-O14980-F1-model_v2 (1).pdb (#9) to map run_class001.mrc z flip
(#8) using 8669 atoms
average map value = 0.03539, steps = 104
shifted from previous position = 14.6
rotated from previous position = 8.44 degrees
atoms outside contour = 1766, contour level = 0.01957
Position of AF-O14980-F1-model_v2 (1).pdb (#9) relative to run_class001.mrc z
flip (#8) coordinates:
Matrix rotation and translation
0.59506461 -0.74363901 0.30479358 189.05159691
-0.06388358 0.33428093 0.94030588 194.29648253
-0.80113481 -0.57901406 0.15141243 210.48912210
Axis -0.76028003 0.55341554 0.34015514
Axis point 0.00000000 301.84627923 27.90119069
Rotation angle (degrees) 87.68582543
Shift along axis 35.39349689
> volume #!8 style mesh
> ~select #9
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 9/A
> select /A:386
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:386-397
80 atoms, 81 bonds, 12 residues, 1 model selected
> volume #!8 style surface
> volume #!8 style mesh
> open /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-308.772.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-308.876.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-310.183.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-311.144.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-311.71.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-314.181.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-314.863.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-316.493.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-316.938.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-316.966.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-317.003.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-317.538.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-318.064.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-318.637.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-320.31.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-320.545.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-320.951.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-321.575.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-322.189.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-322.97.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-323.465.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-323.602.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-323.859.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-325.068.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-327.409.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-332.377.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-336.852.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-340.818.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-344.22.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-346.136.pdb
> /Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-349.447.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-308.772.pdb
---
warnings | Ignored bad PDB record found on line 17119
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17120
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-308.772.pdb
Ignored bad PDB record found on line 17121
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17122
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17123
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1057 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-308.876.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-308.876.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1053 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-310.183.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-310.183.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1053 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-311.144.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-311.144.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1053 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-311.71.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-311.71.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1053 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-314.181.pdb
---
warnings | Ignored bad PDB record found on line 17119
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17120
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-314.181.pdb
Ignored bad PDB record found on line 17121
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17122
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17123
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1057 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-314.863.pdb
---
warnings | Ignored bad PDB record found on line 17119
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17120
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-314.863.pdb
Ignored bad PDB record found on line 17121
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17122
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17123
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
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Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-316.493.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-316.493.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
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Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-316.938.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-316.938.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1053 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-316.966.pdb
---
warnings | Ignored bad PDB record found on line 17119
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17120
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-316.966.pdb
Ignored bad PDB record found on line 17121
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17122
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17123
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1057 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-317.003.pdb
---
warnings | Ignored bad PDB record found on line 17119
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17120
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-317.003.pdb
Ignored bad PDB record found on line 17121
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17122
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17123
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1057 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-317.538.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-317.538.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1053 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-318.064.pdb
---
warnings | Ignored bad PDB record found on line 17119
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17120
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-318.064.pdb
Ignored bad PDB record found on line 17121
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17122
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17123
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1057 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-318.637.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-318.637.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1053 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-320.31.pdb
---
warnings | Ignored bad PDB record found on line 17119
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17120
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-320.31.pdb
Ignored bad PDB record found on line 17121
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17122
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17123
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1057 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-320.545.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-320.545.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1053 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-320.951.pdb
---
warnings | Ignored bad PDB record found on line 17119
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17120
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-320.951.pdb
Ignored bad PDB record found on line 17121
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17122
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17123
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1057 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-321.575.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-321.575.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1053 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-322.189.pdb
---
warnings | Ignored bad PDB record found on line 17159
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17160
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-322.189.pdb
Ignored bad PDB record found on line 17161
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17162
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17163
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1061 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-322.97.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-322.97.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1053 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-323.465.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-323.465.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1053 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-323.602.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-323.602.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1053 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-323.859.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-323.859.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1053 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-325.068.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-325.068.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1053 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-327.409.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-327.409.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1053 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-332.377.pdb
---
warnings | Ignored bad PDB record found on line 17119
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17120
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-332.377.pdb
Ignored bad PDB record found on line 17121
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17122
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17123
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1057 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-336.852.pdb
---
warnings | Ignored bad PDB record found on line 17119
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17120
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-336.852.pdb
Ignored bad PDB record found on line 17121
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17122
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17123
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1057 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-340.818.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-340.818.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1053 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-344.22.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-344.22.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1053 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-346.136.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-346.136.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1053 messages similar to the above omitted
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/after_filter_17__0_-349.447.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-349.447.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.93 378.812 9.84824 -130.021 -1748.66 76.4932 -683.773 -12.037
-73.3896 -77.5088 0 0 195.195 1717.72 -67.1407 0 368.612 25.5312 -6478.25
1053 messages similar to the above omitted
Chain information for after_filter_17__0_-308.772.pdb #10
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Chain information for after_filter_17__0_-308.876.pdb #11
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Chain information for after_filter_17__0_-314.863.pdb #16
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Chain information for after_filter_17__0_-316.493.pdb #17
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Chain information for after_filter_17__0_-317.003.pdb #20
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Chain information for after_filter_17__0_-318.637.pdb #23
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Chain information for after_filter_17__0_-320.31.pdb #24
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Chain information for after_filter_17__0_-320.545.pdb #25
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Chain information for after_filter_17__0_-320.951.pdb #26
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Chain information for after_filter_17__0_-321.575.pdb #27
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Chain information for after_filter_17__0_-322.189.pdb #28
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Chain information for after_filter_17__0_-322.97.pdb #29
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Chain information for after_filter_17__0_-323.465.pdb #30
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Chain information for after_filter_17__0_-323.602.pdb #31
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Chain information for after_filter_17__0_-323.859.pdb #32
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Chain information for after_filter_17__0_-325.068.pdb #33
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A | No description available
Chain information for after_filter_17__0_-327.409.pdb #34
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A | No description available
Chain information for after_filter_17__0_-332.377.pdb #35
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B | No description available
Chain information for after_filter_17__0_-336.852.pdb #36
---
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A | No description available
B | No description available
Chain information for after_filter_17__0_-340.818.pdb #37
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A | No description available
Chain information for after_filter_17__0_-344.22.pdb #38
---
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A | No description available
Chain information for after_filter_17__0_-346.136.pdb #39
---
Chain | Description
A | No description available
Chain information for after_filter_17__0_-349.447.pdb #40
---
Chain | Description
A | No description available
> volume #!8 style surface
> volume #!8 style surface
> volume #!8 style mesh
> hide #9 models
> hide #10 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #18 models
> hide #19 models
> hide #20 models
> hide #21 models
> hide #22 models
> hide #23 models
> hide #24 models
> hide #26 models
> hide #25 models
> hide #27 models
> hide #28 models
> hide #29 models
> hide #30 models
> hide #31 models
> hide #32 models
> hide #33 models
> hide #34 models
> hide #35 models
> hide #36 models
> hide #37 models
> hide #38 models
> hide #39 models
> hide #40 models
> volume #!8 style surface
> transparency #8.1 50
> show #40 models
> show #39 models
> show #38 models
> show #37 models
> show #36 models
> hide #36 models
> close #36
> show #35 models
> hide #35,37-40 atoms
> show #34 models
> show #33 models
> show #32 models
> show #31 models
> show #30 models
> show #29 models
> show #28 models
> hide #28 models
> show #28 models
> close #28
> show #10 models
> close #10
> show #11 models
> close #11
> show #12 models
> close #12
> show #13 models
> close #13
> show #14 models
> show #15 models
> close #15
> show #16 models
> close #16
> show #17 models
> close #17
> show #18 models
> show #19 models
> show #20 models
> close #20
> show #21 models
> show #22 models
> hide #21 models
> hide #19 models
> hide #18 models
> hide #14 models
> hide #22 models
> show #22 models
> close #22
> show #23 models
> show #24 models
> close #24
> show #25 models
> show #26 models
> close #26
> show #27 models
> hide #38 models
> show #38 models
> hide #40 models
> show #40 models
> hide #38 models
> show #38 models
> hide #35 models
> show #35 models
> hide #29 models
> show #29 models
> hide #29 models
> close #29
> transparency #8.1 0
> transparency #8.1 50
> save /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/1Crm1_loop.cxs
——— End of log from Tue Feb 22 10:41:40 2022 ———
opened ChimeraX session
> open /Users/amberms/Desktop/wynton/refmodels/NEC_4PMI.pdb
Chain information for NEC_4PMI.pdb #10
---
Chain | Description
A C | No description available
B I | No description available
D H | No description available
G | No description available
J | No description available
K | No description available
> hide #23,25,27,30-35,37-40#!10 atoms
> hide #23 models
> hide #27 models
> hide #25 models
> hide #30 models
> hide #32 models
> hide #33 models
> hide #31 models
> hide #34 models
> hide #35 models
> hide #37 models
> hide #38 models
> hide #39 models
> hide #40 models
> hide #!10 models
> show #!10 models
> show #!10 cartoons
> show #14 models
> hide #14 models
> show #14 models
> hide #!10 models
> show #!10 models
> hide #14 models
> hide #!8 models
> select #10/C
8377 atoms, 8545 bonds, 1 pseudobond, 1036 residues, 2 models selected
> delete sel
> select #10/G
855 atoms, 953 bonds, 42 residues, 1 model selected
> select #10/A
8377 atoms, 8545 bonds, 1 pseudobond, 1036 residues, 2 models selected
> delete sel
> show #!8 models
> show #14 models
> hide #14 models
> hide #!8 models
> select #10/H
1440 atoms, 1466 bonds, 6 pseudobonds, 183 residues, 2 models selected
> save
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2021/RanQ69L180_1.pdb
> models #10/H relModel#8
Expected a keyword
> save
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2021/RanQ69L180_1.pdb
> models #10/H relModel #8
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/pdb/__init__.py", line 73, in save
pdb.save_pdb(session, path, **kw)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/pdb/pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
OSError: Unable to open file
'/Users/amberms/Desktop/wynton/figures/groupmtg_March2021/RanQ69L180_1.pdb'
for writing
OSError: Unable to open file
'/Users/amberms/Desktop/wynton/figures/groupmtg_March2021/RanQ69L180_1.pdb'
for writing
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/pdb/pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
See log for complete Python traceback.
> save
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/RanQ69L180_1.pdb
> models #10/H relModel #8
> save
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/RanQ69L180_2.pdb
> models #10/D relModel #8
> select clear
> save
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/RevHIV1NS2Val_2.pdb
> models #10/K relModel #8
> save /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/NES_2.pdb
> models #10/B relModel #8
> close #1
> close #2
> close #3
> close #4
> close #5
> close #6
> close #7
> close #9
> save /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/modeling.cxs
> show #!8 models
> hide #!10 models
> open /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/NES_2.pdb
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/RevHIV1NS2Val_2.pdb
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/RanQ69L180_2.pdb
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/RanQ69L180_1.pdb
Chain information for NES_2.pdb #1
---
Chain | Description
B I | No description available
D H | No description available
G | No description available
J | No description available
K | No description available
Chain information for RevHIV1NS2Val_2.pdb #2
---
Chain | Description
B I | No description available
D H | No description available
G | No description available
J | No description available
K | No description available
Chain information for RanQ69L180_2.pdb #3
---
Chain | Description
B I | No description available
D H | No description available
G | No description available
J | No description available
K | No description available
Chain information for RanQ69L180_1.pdb #4
---
Chain | Description
B I | No description available
D H | No description available
G | No description available
J | No description available
K | No description available
> hide #!1-4 atoms
> hide #!1-4 cartoons
> show #!1-4 cartoons
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!8 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> select #1/H,D,I
2976 atoms, 3027 bonds, 12 pseudobonds, 379 residues, 2 models selected
> select #1/H,D,I,J,K,G
4693 atoms, 4859 bonds, 12 pseudobonds, 526 residues, 2 models selected
> delete sel
> save /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/NES_2.pdb
> models #1 relModel #8
> hide #!1 models
> show #!2 models
> select #2/H,B,I,J,K,G
3349 atoms, 3488 bonds, 6 pseudobonds, 356 residues, 2 models selected
> delete sel
> save
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/RanQ69L180_2.pdb
> models #2 relModel #8
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> select #3/H,B,I,J,D,G
4351 atoms, 4507 bonds, 12 pseudobonds, 487 residues, 2 models selected
> delete sel
> save
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/RevHIV1NS2Val_2.pdb
> models #3 relModel #8
> show #!4 models
> hide #!3 models
> select #4/B,I,J,D,G
2911 atoms, 3041 bonds, 6 pseudobonds, 304 residues, 2 models selected
> select #4/B,I,J,D,G,K
3349 atoms, 3488 bonds, 6 pseudobonds, 356 residues, 2 models selected
> delete sel
> save
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/RanQ69L180_1.pdb
> models #4 relModel #8
> close #1
> close #2
> close #3
> close #4
> open
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/RanQ69L180_1.pdb
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/RevHIV1NS2Val_2.pdb
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/RanQ69L180_2.pdb
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/NES_2.pdb
Chain information for RanQ69L180_1.pdb #1
---
Chain | Description
H | No description available
Chain information for RevHIV1NS2Val_2.pdb #2
---
Chain | Description
K | No description available
Chain information for RanQ69L180_2.pdb #3
---
Chain | Description
D | No description available
Chain information for NES_2.pdb #4
---
Chain | Description
B | No description available
> hide #2,4#!1,3 atoms
> show #2,4#!1,3 cartoons
> show #!10 models
> hide #!10 models
> open /Users/amberms/Desktop/wynton/Rosetta/grower_prep.txt
Unrecognized file suffix '.txt'
> open /Users/amberms/Desktop/wynton/Rosetta/RevNS2Val_1.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/RevNS2Val_1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN I 2
ALA I 9 1 8
PDB SEQRES record for chain J is incomplete. Ignoring input sequence records
as basis for sequence.
Chain information for RevNS2Val_1.pdb #5
---
Chain | Description
J | No description available
> open
> /Users/amberms/Desktop/wynton/drrafter/drrafter_amber/out_NEC_R3/topten/NEC_R3_3650.out.1.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/drrafter/drrafter_amber/out_NEC_R3/topten/NEC_R3_3650.out.1.pdb
---
warnings | Ignored bad PDB record found on line 20876
N_BS 33
Ignored bad PDB record found on line 20877
N_NWC 4
Ignored bad PDB record found on line 20878
N_WC 12
Ignored bad PDB record found on line 20879
score -665.162
Ignored bad PDB record found on line 20880
silent_score -665.162
1 messages similar to the above omitted
Chain information for NEC_R3_3650.out.1.pdb #6
---
Chain | Description
A | No description available
G | No description available
H | No description available
> hide #!5 models
> hide #4 models
> hide #!3 models
> hide #2 models
> hide #!1 models
> show #!8 models
> select #6
20863 atoms, 21166 bonds, 1 pseudobond, 1243 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,48.77,0,1,0,33.41,0,0,1,-3.8945
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.77904,-0.4175,0.46776,50.307,0.20864,0.87616,0.43454,-69.017,-0.59124,-0.24093,0.76966,171
> view matrix models
> #6,0.059912,-0.031719,0.9977,-26.201,0.85937,0.51012,-0.035388,1.0109,-0.50783,0.85952,0.057821,126.14
> view matrix models
> #6,0.021043,0.25099,0.96776,-62.026,0.97742,0.1984,-0.072706,44.901,-0.21025,0.94744,-0.24114,133.06
> view matrix models
> #6,-0.24686,-0.088635,0.96499,34.339,0.96599,-0.10165,0.23777,30.46,0.077012,0.99086,0.11071,8.894
> hide #!8 models
> view matrix models
> #6,-0.31755,-0.19815,0.92731,71.09,0.9419,-0.17884,0.28434,36.942,0.1095,0.96372,0.24343,-19.729
> view matrix models
> #6,-0.010793,-0.32889,0.94431,45.68,0.96079,-0.26508,-0.081343,127.55,0.27707,0.9064,0.31885,-50.233
> view matrix models
> #6,-0.24631,-0.26014,0.93363,70.029,0.96596,-0.14443,0.2146,42.691,0.079019,0.95471,0.28686,-23.196
> show #!8 models
> hide #!8 models
> hide #!6 models
> show #!8 models
> transparency 0
> show #!6 models
> hide #!8 models
> view matrix models
> #6,0.017502,0.15001,0.98853,-48.907,0.97422,0.21987,-0.050614,36.971,-0.22494,0.96393,-0.14229,111.1
> show #!8 models
> fitmap #6 inMap #8
Fit molecule NEC_R3_3650.out.1.pdb (#6) to map run_class001.mrc z flip (#8)
using 20863 atoms
average map value = 0.03181, steps = 160
shifted from previous position = 11.5
rotated from previous position = 37.6 degrees
atoms outside contour = 5055, contour level = 0.01957
Position of NEC_R3_3650.out.1.pdb (#6) relative to run_class001.mrc z flip
(#8) coordinates:
Matrix rotation and translation
0.43636023 -0.09781756 0.89443920 -51.50095394
0.74638680 0.59450550 -0.29911529 49.61583305
-0.50249029 0.79811963 0.33242830 83.96361253
Axis 0.55789877 0.71028112 0.42924316
Axis point 10.33828275 0.00000000 90.63381181
Rotation angle (degrees) 79.53429162
Shift along axis 42.54967679
> ~select #6
Nothing selected
> transparency 50
> show #14 models
> hide #14 models
> hide #!6 models
> show #!6 models
> show #!5 models
> show #2 models
> hide #2 models
> hide #!5 models
> hide #!8 models
> select #6/A,H
19617 atoms, 19822 bonds, 1 pseudobond, 1204 residues, 2 models selected
> delete sel
> show #!8 models
> nucleotides #!6 ladder
> nucleotides #!6 stubs
> nucleotides #!6 tube/slab shape muffler
> nucleotides #!6 tube/slab shape ellipsoid
> nucleotides #!6 tube/slab shape box
> nucleotides #!6 atoms
> style nucleic & #!6 stick
Changed 1246 atom styles
> nucleotides #!6 ladder
> show #!5 models
> show #2 models
> hide #!5 models
> hide #!6 models
> fitmap #2 inMap #8
Fit molecule RevHIV1NS2Val_2.pdb (#2) to map run_class001.mrc z flip (#8)
using 484 atoms
average map value = 0.01964, steps = 100
shifted from previous position = 7.83
rotated from previous position = 2.27 degrees
atoms outside contour = 341, contour level = 0.01957
Position of RevHIV1NS2Val_2.pdb (#2) relative to run_class001.mrc z flip (#8)
coordinates:
Matrix rotation and translation
0.99927816 0.01685923 0.03404311 -16.73996329
-0.01648693 0.99980149 -0.01118750 2.65326063
-0.03422496 0.01061816 0.99935775 4.84678569
Axis 0.27586680 0.86366976 -0.42186734
Axis point 79.14088322 0.00000000 457.98498119
Rotation angle (degrees) 2.26503906
Shift along axis -4.37115980
> undo
> close #2
> open
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/RevHIV1NS2Val_2.pdb
Chain information for RevHIV1NS2Val_2.pdb #2
---
Chain | Description
K | No description available
> select #2
484 atoms, 495 bonds, 56 residues, 1 model selected
> view matrix models
> #2,0.99647,-0.011891,-0.083133,18.504,-0.0027614,0.98475,-0.17395,36.249,0.083934,0.17357,0.98124,-40.708
> view matrix models
> #2,0.99746,-0.0099879,-0.070455,15.613,-0.0030371,0.98322,-0.18238,38.144,0.071095,0.18213,0.9807,-39.752
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99746,-0.0099879,-0.070455,12.647,-0.0030371,0.98322,-0.18238,35.353,0.071095,0.18213,0.9807,-40.509
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.99998,0.0012905,0.005506,-4.1243,-0.00029075,0.98406,-0.17784,33.86,-0.0056477,0.17783,0.98404,-26.689
> close #2
> open
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/RevHIV1NS2Val_2.pdb
Chain information for RevHIV1NS2Val_2.pdb #2
---
Chain | Description
K | No description available
> hide #!6 models
> hide #!8 models
> select #2/E
23 atoms, 24 bonds, 2 residues, 1 model selected
> 123angle
123angle is provided by the uninstalled bundle SEQCROW versions 0.13 – 0.15
> delete sel
> select #2/F
23 atoms, 24 bonds, 2 residues, 1 model selected
> 123angle
123angle is provided by the uninstalled bundle SEQCROW versions 0.13 – 0.15
> delete sel
> hide #2 models
> show #!5 models
> show #2 models
> show #!3 models
> hide #!5 models
> hide #2 models
> show #!8 models
> fitmap #3 inMap #8
Fit molecule RanQ69L180_2.pdb (#3) to map run_class001.mrc z flip (#8) using
1486 atoms
average map value = 0.03301, steps = 52
shifted from previous position = 1.09
rotated from previous position = 3.42 degrees
atoms outside contour = 217, contour level = 0.01957
Position of RanQ69L180_2.pdb (#3) relative to run_class001.mrc z flip (#8)
coordinates:
Matrix rotation and translation
0.99958909 -0.01656635 -0.02339227 6.56116311
0.01531874 0.99850122 -0.05254184 5.21454828
0.02422764 0.05216191 0.99834471 -13.08571646
Axis 0.87719797 -0.39895507 0.26713024
Axis point 0.00000000 254.74848931 93.34162045
Rotation angle (degrees) 3.42149107
Shift along axis 0.17947797
> hide #!3 models
> show #!1 models
> fitmap #1 inMap #8
Fit molecule RanQ69L180_1.pdb (#1) to map run_class001.mrc z flip (#8) using
1486 atoms
average map value = 0.03471, steps = 52
shifted from previous position = 0.819
rotated from previous position = 1.65 degrees
atoms outside contour = 215, contour level = 0.01957
Position of RanQ69L180_1.pdb (#1) relative to run_class001.mrc z flip (#8)
coordinates:
Matrix rotation and translation
0.99970933 0.00247486 0.02398169 -5.49281917
-0.00284887 0.99987466 0.01557422 -2.88291383
-0.02394014 -0.01563802 0.99959108 8.70980842
Axis -0.54341379 0.83433235 -0.09268758
Axis point 358.85976723 0.00000000 238.55188491
Rotation angle (degrees) 1.64568460
Shift along axis -0.22772565
> show #!3 models
> show #4 models
> show #!5 models
> show #2 models
> transparency 0
> transparency 50
> show #!6 models
> nucleotides #2,4#!1,3,5-6 stubs
> nucleotides #2,4#!1,3,5-6 stubs
> nucleotides #2,4#!1,3,5-6 ladder
> nucleotides #2,4#!1,3,5-6 stubs
> color #2,4#!1,3,5-6 bynucleotide
> color #2,4#!1,3,5-6 bynucleotide
> show #14 models
> transparency 0
> transparency 50
> volume #8 level 0.02134
> select #5
529 atoms, 537 bonds, 1 pseudobond, 66 residues, 2 models selected
> view matrix models
> #5,0.99924,0.019517,-0.033786,3.5764,-0.020298,0.99953,-0.022942,8.1889,0.033322,0.02361,0.99917,-9.621
> view matrix models
> #5,0.98269,0.080424,0.16688,-42.388,-0.076262,0.9966,-0.031208,20.312,-0.16882,0.017942,0.98548,30.222
> view matrix models
> #5,0.96966,0.16352,0.18172,-56.338,-0.13615,0.97863,-0.15411,57.909,-0.20304,0.12469,0.9712,21.938
> view matrix models
> #5,0.95222,0.16268,0.25849,-68.038,-0.088957,0.95737,-0.27484,76.404,-0.29218,0.23871,0.92609,28.342
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.95222,0.16268,0.25849,-67.748,-0.088957,0.95737,-0.27484,75.866,-0.29218,0.23871,0.92609,28.898
> undo
> undo
> undo
> undo
> undo
> select clear
> show #18 models
> show #19 models
> transparency 0
> transparency 50
> show #21 models
> hide #19 models
> hide #18 models
> hide #14 models
> show #23 models
> hide #21 models
> show #25 models
> hide #25 models
> show #27 models
> hide #27 models
> show #30 models
> hide #30 models
> show #31 models
> hide #31 models
> show #32 models
> hide #32 models
> show #33 models
> hide #33 models
> show #34 models
> hide #34 models
> show #35 models
> hide #35 models
> show #37 models
> hide #37 models
> show #38 models
> hide #38 models
> show #39 models
> hide #39 models
> show #40 models
> hide #40 models
> close #14
> close #18-21
> close #25-40
> save /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/modeling.cxs
——— End of log from Tue Feb 22 11:44:31 2022 ———
opened ChimeraX session
> hide #!1 models
> hide #2 models
> hide #!3 models
> hide #4 models
> hide #!5 models
> hide #!6 models
> hide #23 models
> transparency 0
> turn y 1 360
> turn y 1 360
> wait
> turn x 1 360
> turn y 1 360
> wait
> turn x 1 360
> movie encode
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/movie1.mp4
No frames have been recorded
> turn y 1 360
> wait
> movie encode
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/movie2.mp4
No frames have been recorded
> toolshed show
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/amberms/Desktop/movie1.mp4
Movie saved to /Users/amberms/Desktop/movie1.mp4
> movie encode
No frames have been recorded
> movie record
> turn y 1 360
> wait 60
> movie stop
> movie encode
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/movie2.mp4
Movie saved to /Users/amberms/.../groupmtg_March2022/movie2.mp4
> show #!10 models
> hide #!10 models
> volume #8 style mesh
> volume #8 style surface
> volume #8 style transparent surface
Invalid "style" argument: Should be one of 'image', 'mesh', 'solid', or
'surface'
> volume #8 style transparent
Invalid "style" argument: Should be one of 'image', 'mesh', 'solid', or
'surface'
> transparency #8 50 surfaces all
Expected ',' or a keyword
> transparency #8 50 surfaces
> transparency #8 30 surfaces
> transparency #8 80 surfaces
> transparency 0
> transparency #8 80 surfaces
> modeldisplay #23
Unknown command: modeldisplay #23
> transparency #8 80 surfaces
> display #23
Unknown command: modeller display #23
> display #23
Unknown command: modeller display #23
> show #23
> show #23 models
> hide #23 atoms
> show #23 cartoons
> hide #23 cartoons
> show #23 cartoons
> show #1-5 cartoons
> show #1-5 cartoons
> show #!1 models
> hide #!1 models
> show #1 cartoons
> show #1 cartoons
> show #!1 models
> show #2 models
> show #!3 models
> show #4 models
> show #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> volume style surface
> volume style surface
> transparency 0
> transparency 50
> transparency #8 80 surfaces
> display #23
Unknown command: modeller display #23
> save /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/modeling.cxs
——— End of log from Tue Feb 22 15:23:29 2022 ———
opened ChimeraX session
> open
> /Users/amberms/Desktop/wynton/drrafter/drrafter_amber/NEC_working_4/topten_pdb/NEC_R4_128.out.1.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/drrafter/drrafter_amber/NEC_working_4/topten_pdb/NEC_R4_128.out.1.pdb
---
warnings | Ignored bad PDB record found on line 20877
N_BS 33
Ignored bad PDB record found on line 20878
N_NWC 4
Ignored bad PDB record found on line 20879
N_WC 12
Ignored bad PDB record found on line 20880
score -10221.8
Ignored bad PDB record found on line 20881
silent_score -10221.8
1 messages similar to the above omitted
Chain information for NEC_R4_128.out.1.pdb #7
---
Chain | Description
A | No description available
G | No description available
H | No description available
> open
> /Users/amberms/Desktop/wynton/drrafter/drrafter_amber/NEC_working_4/topten_pdb/NEC_R4_182.out.1.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/drrafter/drrafter_amber/NEC_working_4/topten_pdb/NEC_R4_182.out.1.pdb
---
warnings | Ignored bad PDB record found on line 20877
N_BS 33
Ignored bad PDB record found on line 20878
N_NWC 4
Ignored bad PDB record found on line 20879
N_WC 12
Ignored bad PDB record found on line 20880
score -10221.8
Ignored bad PDB record found on line 20881
silent_score -10221.8
1 messages similar to the above omitted
Chain information for NEC_R4_182.out.1.pdb #9
---
Chain | Description
A | No description available
G | No description available
H | No description available
> open
> /Users/amberms/Desktop/wynton/drrafter/drrafter_amber/NEC_working_4/topten_pdb/NEC_R4_262.out.1.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/drrafter/drrafter_amber/NEC_working_4/topten_pdb/NEC_R4_262.out.1.pdb
---
warnings | Ignored bad PDB record found on line 20877
N_BS 33
Ignored bad PDB record found on line 20878
N_NWC 4
Ignored bad PDB record found on line 20879
N_WC 12
Ignored bad PDB record found on line 20880
score -10221.8
Ignored bad PDB record found on line 20881
silent_score -10221.8
1 messages similar to the above omitted
Chain information for NEC_R4_262.out.1.pdb #11
---
Chain | Description
A | No description available
G | No description available
H | No description available
> open
> /Users/amberms/Desktop/wynton/drrafter/drrafter_amber/NEC_working_4/topten_pdb/NEC_R4_1118.out.1.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/drrafter/drrafter_amber/NEC_working_4/topten_pdb/NEC_R4_1118.out.1.pdb
---
warnings | Ignored bad PDB record found on line 20877
N_BS 33
Ignored bad PDB record found on line 20878
N_NWC 4
Ignored bad PDB record found on line 20879
N_WC 12
Ignored bad PDB record found on line 20880
score -10221.8
Ignored bad PDB record found on line 20881
silent_score -10221.8
1 messages similar to the above omitted
Chain information for NEC_R4_1118.out.1.pdb #12
---
Chain | Description
A | No description available
G | No description available
H | No description available
> open
> /Users/amberms/Desktop/wynton/drrafter/drrafter_amber/NEC_working_4/topten_pdb/NEC_R4_1373.out.1.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/drrafter/drrafter_amber/NEC_working_4/topten_pdb/NEC_R4_1373.out.1.pdb
---
warnings | Ignored bad PDB record found on line 20877
N_BS 33
Ignored bad PDB record found on line 20878
N_NWC 4
Ignored bad PDB record found on line 20879
N_WC 12
Ignored bad PDB record found on line 20880
score -10221.8
Ignored bad PDB record found on line 20881
silent_score -10221.8
1 messages similar to the above omitted
Chain information for NEC_R4_1373.out.1.pdb #13
---
Chain | Description
A | No description available
G | No description available
H | No description available
> open
> /Users/amberms/Desktop/wynton/drrafter/drrafter_amber/NEC_working_4/topten_pdb/NEC_R4_1631.out.1.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/drrafter/drrafter_amber/NEC_working_4/topten_pdb/NEC_R4_1631.out.1.pdb
---
warnings | Ignored bad PDB record found on line 20877
N_BS 33
Ignored bad PDB record found on line 20878
N_NWC 4
Ignored bad PDB record found on line 20879
N_WC 12
Ignored bad PDB record found on line 20880
score -10221.8
Ignored bad PDB record found on line 20881
silent_score -10221.8
1 messages similar to the above omitted
Chain information for NEC_R4_1631.out.1.pdb #14
---
Chain | Description
A | No description available
G | No description available
H | No description available
> open
> /Users/amberms/Desktop/wynton/drrafter/drrafter_amber/NEC_working_4/topten_pdb/NEC_R4_2369.out.1.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/drrafter/drrafter_amber/NEC_working_4/topten_pdb/NEC_R4_2369.out.1.pdb
---
warnings | Ignored bad PDB record found on line 20877
N_BS 33
Ignored bad PDB record found on line 20878
N_NWC 4
Ignored bad PDB record found on line 20879
N_WC 12
Ignored bad PDB record found on line 20880
score -10221.8
Ignored bad PDB record found on line 20881
silent_score -10221.8
1 messages similar to the above omitted
Chain information for NEC_R4_2369.out.1.pdb #15
---
Chain | Description
A | No description available
G | No description available
H | No description available
> open
> /Users/amberms/Desktop/wynton/drrafter/drrafter_amber/NEC_working_4/topten_pdb/NEC_R4_2539.out.1.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/drrafter/drrafter_amber/NEC_working_4/topten_pdb/NEC_R4_2539.out.1.pdb
---
warnings | Ignored bad PDB record found on line 20877
N_BS 33
Ignored bad PDB record found on line 20878
N_NWC 4
Ignored bad PDB record found on line 20879
N_WC 12
Ignored bad PDB record found on line 20880
score -10221.8
Ignored bad PDB record found on line 20881
silent_score -10221.8
1 messages similar to the above omitted
Chain information for NEC_R4_2539.out.1.pdb #16
---
Chain | Description
A | No description available
G | No description available
H | No description available
> open
> /Users/amberms/Desktop/wynton/drrafter/drrafter_amber/NEC_working_4/topten_pdb/NEC_R4_2620.out.1.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/drrafter/drrafter_amber/NEC_working_4/topten_pdb/NEC_R4_2620.out.1.pdb
---
warnings | Ignored bad PDB record found on line 20877
N_BS 33
Ignored bad PDB record found on line 20878
N_NWC 4
Ignored bad PDB record found on line 20879
N_WC 12
Ignored bad PDB record found on line 20880
score -10221.8
Ignored bad PDB record found on line 20881
silent_score -10221.8
1 messages similar to the above omitted
Chain information for NEC_R4_2620.out.1.pdb #17
---
Chain | Description
A | No description available
G | No description available
H | No description available
> open
> /Users/amberms/Desktop/wynton/drrafter/drrafter_amber/NEC_working_4/topten_pdb/NEC_R4_2686.out.1.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/drrafter/drrafter_amber/NEC_working_4/topten_pdb/NEC_R4_2686.out.1.pdb
---
warnings | Ignored bad PDB record found on line 20877
N_BS 33
Ignored bad PDB record found on line 20878
N_NWC 4
Ignored bad PDB record found on line 20879
N_WC 12
Ignored bad PDB record found on line 20880
score -10221.8
Ignored bad PDB record found on line 20881
silent_score -10221.8
1 messages similar to the above omitted
Chain information for NEC_R4_2686.out.1.pdb #18
---
Chain | Description
A | No description available
G | No description available
H | No description available
> hide #!1 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> hide #23 models
> hide #!9 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!9 models
> show #!7 models
> hide #!9 models
> hide #!7 models
> show #!11 models
> show #!12 models
> show #!13 models
> show #!14 models
> show #!15 models
> show #!16 models
> show #!17 models
> show #!18 models
> show #23 models
> hide #23 models
> hide #!18 models
> hide #!17 models
> hide #!16 models
> hide #!15 models
> hide #!14 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> show #!6 models
> show #!1 models
> show #!10 models
> hide #!10 models
> show #23 models
> close #7
> close #9
> close #11-18
> transparency 0
> transparency 50
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> transparency 0
> transparency 50
> turn y 1 180
> turn y 1 180
> transparency #8 80
> transparency 0
> transparency #8 80
> transparency 0
> volume #8 level 0.01554
> transparency #8 80
> transparency 0
> transparency 50
> transparency #8 80
> ui tool show "Show Sequence Viewer"
> sequence chain #5/J
Alignment identifier is 5/J
> ui tool show "Show Sequence Viewer"
> sequence chain #2/K
Alignment identifier is 2/K
> transparency 0
> volume #8 level 0.01957
> transparency #8 80
> transparency 0
> transparency 50
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-308.847.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-308.847.pdb
---
warnings | Ignored bad PDB record found on line 17119
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17120
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-308.847.pdb
Ignored bad PDB record found on line 17121
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17122
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17123
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1057 messages similar to the above omitted
Chain information for after_filter_17__0_-308.847.pdb #7
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-309.72.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-309.72.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-309.72.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1053 messages similar to the above omitted
Chain information for after_filter_17__0_-309.72.pdb #9
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-309.472.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-309.472.pdb
---
warnings | Ignored bad PDB record found on line 17119
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17120
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-309.472.pdb
Ignored bad PDB record found on line 17121
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17122
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17123
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1057 messages similar to the above omitted
Chain information for after_filter_17__0_-309.472.pdb #11
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-310.782.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-310.782.pdb
---
warnings | Ignored bad PDB record found on line 17119
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17120
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-310.782.pdb
Ignored bad PDB record found on line 17121
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17122
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17123
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1057 messages similar to the above omitted
Chain information for after_filter_17__0_-310.782.pdb #12
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-311.073.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-311.073.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-311.073.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1053 messages similar to the above omitted
Chain information for after_filter_17__0_-311.073.pdb #13
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-312.306.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-312.306.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-312.306.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1053 messages similar to the above omitted
Chain information for after_filter_17__0_-312.306.pdb #14
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-312.683.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-312.683.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-312.683.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1053 messages similar to the above omitted
Chain information for after_filter_17__0_-312.683.pdb #15
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-313.6.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-313.6.pdb
---
warnings | Ignored bad PDB record found on line 17119
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17120
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-313.6.pdb
Ignored bad PDB record found on line 17121
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17122
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17123
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1057 messages similar to the above omitted
Chain information for after_filter_17__0_-313.6.pdb #16
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-313.072.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-313.072.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-313.072.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1053 messages similar to the above omitted
Chain information for after_filter_17__0_-313.072.pdb #17
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-313.265.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-313.265.pdb
---
warnings | Ignored bad PDB record found on line 17119
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17120
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-313.265.pdb
Ignored bad PDB record found on line 17121
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17122
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17123
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1057 messages similar to the above omitted
Chain information for after_filter_17__0_-313.265.pdb #18
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-314.38.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-314.38.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-314.38.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1053 messages similar to the above omitted
Chain information for after_filter_17__0_-314.38.pdb #19
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-314.385.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-314.385.pdb
---
warnings | Ignored bad PDB record found on line 17119
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17120
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-314.385.pdb
Ignored bad PDB record found on line 17121
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17122
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17123
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1057 messages similar to the above omitted
Chain information for after_filter_17__0_-314.385.pdb #20
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-315.456.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-315.456.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-315.456.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1053 messages similar to the above omitted
Chain information for after_filter_17__0_-315.456.pdb #21
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-315.487.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-315.487.pdb
---
warnings | Ignored bad PDB record found on line 17119
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17120
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-315.487.pdb
Ignored bad PDB record found on line 17121
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17122
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17123
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1057 messages similar to the above omitted
Chain information for after_filter_17__0_-315.487.pdb #22
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-316.001.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-316.001.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-316.001.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1053 messages similar to the above omitted
Chain information for after_filter_17__0_-316.001.pdb #24
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-316.048.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-316.048.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-316.048.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1053 messages similar to the above omitted
Chain information for after_filter_17__0_-316.048.pdb #25
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-316.365.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-316.365.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-316.365.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1053 messages similar to the above omitted
Chain information for after_filter_17__0_-316.365.pdb #26
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-318.077.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-318.077.pdb
---
warnings | Ignored bad PDB record found on line 17119
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17120
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-318.077.pdb
Ignored bad PDB record found on line 17121
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17122
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17123
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1057 messages similar to the above omitted
Chain information for after_filter_17__0_-318.077.pdb #27
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-318.764.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-318.764.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-318.764.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1053 messages similar to the above omitted
Chain information for after_filter_17__0_-318.764.pdb #28
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-318.772.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-318.772.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-318.772.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1053 messages similar to the above omitted
Chain information for after_filter_17__0_-318.772.pdb #29
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-319.087.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-319.087.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-319.087.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1053 messages similar to the above omitted
Chain information for after_filter_17__0_-319.087.pdb #30
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-319.567.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-319.567.pdb
---
warnings | Ignored bad PDB record found on line 17119
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17120
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-319.567.pdb
Ignored bad PDB record found on line 17121
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17122
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17123
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1057 messages similar to the above omitted
Chain information for after_filter_17__0_-319.567.pdb #31
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-320.178.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-320.178.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-320.178.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1053 messages similar to the above omitted
Chain information for after_filter_17__0_-320.178.pdb #32
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-325.293.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-325.293.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-325.293.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1053 messages similar to the above omitted
Chain information for after_filter_17__0_-325.293.pdb #33
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-325.783.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-325.783.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-325.783.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1053 messages similar to the above omitted
Chain information for after_filter_17__0_-325.783.pdb #34
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-325.996.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-325.996.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-325.996.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1053 messages similar to the above omitted
Chain information for after_filter_17__0_-325.996.pdb #35
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-326.59.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-326.59.pdb
---
warnings | Ignored bad PDB record found on line 17119
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17120
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-326.59.pdb
Ignored bad PDB record found on line 17121
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17122
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17123
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1057 messages similar to the above omitted
Chain information for after_filter_17__0_-326.59.pdb #36
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-332.887.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-332.887.pdb
---
warnings | Ignored bad PDB record found on line 17119
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17120
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-332.887.pdb
Ignored bad PDB record found on line 17121
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17122
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17123
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1057 messages similar to the above omitted
Chain information for after_filter_17__0_-332.887.pdb #37
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-336.109.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-336.109.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-336.109.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1053 messages similar to the above omitted
Chain information for after_filter_17__0_-336.109.pdb #38
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-338.15.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-338.15.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-338.15.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1053 messages similar to the above omitted
Chain information for after_filter_17__0_-338.15.pdb #39
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-338.356.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-338.356.pdb
---
warnings | Ignored bad PDB record found on line 17078
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17079
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-338.356.pdb
Ignored bad PDB record found on line 17080
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17081
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17082
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1053 messages similar to the above omitted
Chain information for after_filter_17__0_-338.356.pdb #40
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-342.664.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/2_Crm1_loop/after_filter_17__0_-342.664.pdb
---
warnings | Ignored bad PDB record found on line 17119
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 17120
#BEGIN_POSE_ENERGIES_TABLE after_filter_17__0_-342.664.pdb
Ignored bad PDB record found on line 17121
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 17122
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 17123
pose -6457.95 378.847 9.84807 -130.011 -1748.65 76.4985 -683.808 -12.0383
-73.3676 -77.5139 0 0 195.229 1717.75 -67.1434 0 368.612 25.59 -6478.1
1057 messages similar to the above omitted
Chain information for after_filter_17__0_-342.664.pdb #41
---
Chain | Description
A | No description available
B | No description available
> hide #2,4,7,9,11-41#!1,3,5-6 atoms
> transparency #8 80
> hide #28 models
> hide #27 models
> hide #26 models
> hide #25 models
> hide #24 models
> hide #23 models
> hide #22 models
> hide #21 models
> hide #20 models
> hide #19 models
> hide #18 models
> hide #17 models
> hide #16 models
> hide #15 models
> hide #13 models
> hide #14 models
> hide #12 models
> hide #11 models
> show #23 models
> hide #23 models
> show #23 models
> rename #23 1°Crm1
> hide #29 models
> hide #30 models
> hide #31 models
> hide #32 models
> hide #33 models
> hide #34 models
> hide #35 models
> hide #36 models
> hide #37 models
> hide #38 models
> hide #39 models
> hide #40 models
> hide #41 models
> hide #9 models
> hide #7 models
> show #7 models
> transparency 0
> transparency 50
> hide #7 models
> show #7 models
> transparency #8 80
> transparency 0
> transparency 50
> hide #7 models
> show #9 models
> show #11 models
> hide #11 models
> show #12 models
> hide #9 models
> transparency 0
> transparency 50
> hide #!5 models
> hide #12 models
> show #13 models
> hide #13 models
> show #14 models
> hide #14 models
> show #15 models
> hide #15 models
> show #16 models
> hide #16 models
> show #17 models
> hide #17 models
> show #18 models
> hide #18 models
> show #19 models
> hide #19 models
> show #20 models
> hide #20 models
> show #21 models
> hide #21 models
> show #22 models
> hide #22 models
> show #24 models
> hide #24 models
> show #25 models
> hide #25 models
> show #26 models
> hide #26 models
> show #27 models
> show #!5 models
> hide #27 models
> show #28 models
> hide #28 models
> show #29 models
> hide #29 models
> show #30 models
> transparency 0
> transparency 50
> show #31 models
> hide #30 models
> show #32 models
> hide #32 models
> show #33 models
> hide #31 models
> show #34 models
> hide #34 models
> show #34 models
> show #35 models
> hide #34 models
> hide #33 models
> show #36 models
> hide #36 models
> show #37 models
> hide #37 models
> show #38 models
> show #39 models
> hide #39 models
> show #39 models
> hide #39 models
> show #39 models
> hide #39 models
> show #40 models
> hide #40 models
> show #41 models
> hide #41 models
> volume #8 level 0.02118
> show #7 models
> hide #7 models
> show #9 models
> hide #9 models
> show #9 models
> hide #35 models
> hide #38 models
> show #35 models
> show #38 models
> show #11 models
> close #11
> close #7
> show #12 models
> close #12
> show #13 models
> close #13
> show #14 models
> close #14
> show #15 models
> hide #9 models
> hide #38 models
> hide #35 models
> close #15
> show #16 models
> close #16
> show #17 models
> close #17
> show #18 models
> close #18
> show #19 models
> close #19
> show #20 models
> close #20
> show #21 models
> close #21
> show #22 models
> close #22
> show #24 models
> close #24
> show #25 models
> close #25
> show #9 models
> hide #23 models
> show #23 models
> show #27 models
> close #27
> show #26 models
> hide #9 models
> show #35 models
> hide #26 models
> show #26 models
> hide #26 models
> show #26 models
> show #28 models
> hide #28 models
> show #28 models
> close #28
> show #29 models
> close #29
> show #30 models
> close #30
> show #31 models
> close #31
> show #32 models
> close #32
> show #33 models
> show #34 models
> close #34
> hide #35 models
> show #35 models
> show #36 models
> close #36
> show #37 models
> close #37
> show #38 models
> show #39 models
> close #39
> show #40 models
> show #41 models
> close #41
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> hide #26 models
> hide #33 models
> hide #35 models
> hide #38 models
> hide #40 models
> show #40 models
> show #38 models
> show #26 models
> hide #38 models
> hide #40 models
> show #9 models
> hide #9 models
> show #33 models
> hide #33 models
> show #33 models
> hide #33 models
> show #33 models
> hide #33 models
> show #33 models
> hide #33 models
> show #35 models
> hide #35 models
> show #38 models
> hide #38 models
> show #40 models
> hide #40 models
> rename #26 2°Crm1
> hide #4 models
> hide #!5 models
> hide #2 models
> volume #8 level 0.02505
> volume #8 orthoplanes xyz positionPlanes 110,110,110 style image region all
> mousemode rightMode "move planes"
> volume #8 orthoplanes xyz positionPlanes 110,110,110 style image region all
> mousemode rightMode "move planes"
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 5 atomic
models, 1 maps.
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 5 atomic
models, 1 maps.
> volume #8 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.5 tiltedSlabSpacing 1.668 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #8 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.5 tiltedSlabSpacing 1.668 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #8 orthoplanes xyz positionPlanes 110,110,110 style image region all
> mousemode rightMode "move planes"
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 5 atomic
models, 1 maps.
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 5 atomic
models, 1 maps.
> volume style surface
> volume #8 change image level -0.001531,0 level 0.01196,0.8 level 0.08844,1
> volume #8 level 0.0228
> set bgColor black
> show #23,26#!1,3,6 atoms
> hide #23,26#!1,3,6 atoms
> rename #6 StemIIB
> save /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/modeling.cxs
> set bgColor white
> nucleotides #23,26#!1,3,6 ladder
> nucleotides #23,26#!1,3,6 ladder
> nucleotides #23,26#!1,3,6 ladder
> hide #!3 models
> hide #!1 models
> hide #!8 models
> hide #23 models
> hide #26 models
> show #!6 atoms
> show #!1 models
> show #2 models
> show #!3 models
> show #4 models
> show #!5 models
> show #!8 models
> show #9 models
> hide #9 models
> show #23 models
> show #26 models
> volume #8 level 0.01602
> volume #8 level 0.01957
> ui tool show "Show Sequence Viewer"
> sequence chain #1/H
Alignment identifier is 1/H
> ui tool show "Show Sequence Viewer"
> sequence chain #5/J
Alignment identifier is 5/J
> hide #!8 models
> show #!8 models
> hide #!6 models
> hide #!5 models
> hide #4 models
> hide #!3 models
> hide #2 models
> hide #!1 models
> show #!10 models
> hide #!10 models
> show #2 models
> show #!1 models
> hide #2 models
> hide #!1 models
> show #!1 models
> show #2 models
> show #!3 models
> show #4 models
> show #!5 models
> show #!6 models
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-156.272.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-156.272.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-156.272.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-156.272.pdb #7
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-156.491.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-156.491.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-156.491.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-156.491.pdb #11
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-156.705.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-156.705.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-156.705.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-156.705.pdb #12
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-156.739.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-156.739.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-156.739.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-156.739.pdb #13
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-156.776.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-156.776.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-156.776.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-156.776.pdb #14
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-156.821.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-156.821.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-156.821.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-156.821.pdb #15
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-157.019.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-157.019.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-157.019.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-157.019.pdb #16
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-157.435.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-157.435.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-157.435.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-157.435.pdb #17
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-158.097.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-158.097.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-158.097.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-158.097.pdb #18
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-158.268.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-158.268.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-158.268.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-158.268.pdb #19
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-158.311.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-158.311.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-158.311.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-158.311.pdb #20
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-158.785.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-158.785.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-158.785.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-158.785.pdb #21
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-158.805.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-158.805.pdb
---
warnings | Ignored bad PDB record found on line 1387
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1388
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-158.805.pdb
Ignored bad PDB record found on line 1389
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1390
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1391
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
85 messages similar to the above omitted
Chain information for after_filter_13__0_-158.805.pdb #22
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-158.873.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-158.873.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-158.873.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-158.873.pdb #24
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-159.109.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-159.109.pdb
---
warnings | Ignored bad PDB record found on line 1387
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1388
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-159.109.pdb
Ignored bad PDB record found on line 1389
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1390
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1391
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
85 messages similar to the above omitted
Chain information for after_filter_13__0_-159.109.pdb #25
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-159.124.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-159.124.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-159.124.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-159.124.pdb #27
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-161.232.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-161.232.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-161.232.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-161.232.pdb #28
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-162.489.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-162.489.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-162.489.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-162.489.pdb #29
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-163.06.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-163.06.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-163.06.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-163.06.pdb #30
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-163.381.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-163.381.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-163.381.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-163.381.pdb #31
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-163.977.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-163.977.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-163.977.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-163.977.pdb #32
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-165.203.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-165.203.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-165.203.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-165.203.pdb #34
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-165.666.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-165.666.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-165.666.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-165.666.pdb #36
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-165.676.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-165.676.pdb
---
warnings | Ignored bad PDB record found on line 1387
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1388
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-165.676.pdb
Ignored bad PDB record found on line 1389
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1390
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1391
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
85 messages similar to the above omitted
Chain information for after_filter_13__0_-165.676.pdb #37
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-165.856.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-165.856.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-165.856.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-165.856.pdb #39
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-167.122.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-167.122.pdb
---
warnings | Ignored bad PDB record found on line 1387
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1388
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-167.122.pdb
Ignored bad PDB record found on line 1389
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1390
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1391
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
85 messages similar to the above omitted
Chain information for after_filter_13__0_-167.122.pdb #41
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-167.288.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-167.288.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-167.288.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-167.288.pdb #42
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-167.524.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-167.524.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-167.524.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-167.524.pdb #43
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-171.14.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-171.14.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-171.14.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-171.14.pdb #44
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-172.251.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-172.251.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-172.251.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-172.251.pdb #45
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-172.868.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-172.868.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-172.868.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-172.868.pdb #46
---
Chain | Description
A | No description available
> open
> /Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-175.99.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/Revstuff/after_filter_13__0_-175.99.pdb
---
warnings | Ignored bad PDB record found on line 1346
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 1347
#BEGIN_POSE_ENERGIES_TABLE after_filter_13__0_-175.99.pdb
Ignored bad PDB record found on line 1348
label fa_atr fa_rep fa_intra_rep lk_ball_wtd fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 1349
weights 1 0.3 0.005 1 1 1.25 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 1350
pose -339.226 148.191 0.98733 -12.8731 -85.4718 4.65581 -40.8162 0 -1.98092
-2.17415 0 0 8.79497 170.262 -10.643 0 7.25508 -0.45403 -153.493
81 messages similar to the above omitted
Chain information for after_filter_13__0_-175.99.pdb #47
---
Chain | Description
A | No description available
> hide #7 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #18 models
> hide #19 models
> hide #20 models
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> hide #27 models
> hide #25 models
> hide #24 models
> hide #28 models
> hide #29 models
> hide #30 models
> hide #31 models
> hide #32 models
> show #33 models
> hide #34 models
> hide #36 models
> hide #37 models
> hide #39 models
> hide #33 models
> hide #41 models
> hide #42 models
> hide #43 models
> hide #44 models
> hide #45 models
> hide #46 models
> hide #47 models
> hide #!5 models
> show #7 models
> hide #7 models
> show #11 models
> hide #11 models
> show #12 models
> close #12
> show #13 models
> hide #13 models
> show #14 models
> show #15 models
> hide #14 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #16 models
> hide #16 models
> show #17 models
> close #17
> show #11 models
> close #11
> show #13 models
> hide #13 models
> show #14 models
> hide #14 models
> show #16 models
> hide #16 models
> show #18 models
> close #18
> transparency #8 80
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #19 models
> hide #19 models
> show #19 models
> hide #19 models
> close #19
> rename #9 2°Crm_2
> rename #33 2°Crm_3
> rename #35 2°Crm_4
> rename #38 2°Crm_5
> rename #40 2°Crm_6
> show #7 models
> show #13 models
> close #13
> show #14 models
> show #16 models
> close #16
> show #20 models
> hide #20 models
> show #20 models
> hide #20 models
> show #20 models
> close #20
> show #21 models
> show #22 models
> close #22
> show #24 models
> hide #23 models
> hide #21 models
> show #23 models
> hide #15 models
> hide #14 models
> hide #7 models
> hide #24 models
> show #24 models
> close #24
> show #25 models
> close #25
> show #27 models
> close #27
> show #28 models
> close #28
> show #29 models
> close #29
> show #30 models
> show #14 models
> show #15 models
> show #21 models
> show #7 models
> hide #14 models
> show #14 models
> hide #2 models
> show #2 models
> show #31 models
> hide #31 models
> show #31 models
> hide #31 models
> show #31 models
> hide #30 models
> hide #21 models
> hide #15 models
> hide #14 models
> hide #7 models
> hide #31 models
> show #31 models
> show #14 models
> hide #14 models
> show #14 models
> show #7 models
> hide #7 models
> show #32 models
> show #34 models
> hide #34 models
> show #34 models
> close #34
> show #36 models
> hide #32 models
> hide #31 models
> hide #14 models
> show #37 models
> close #37
> show #39 models
> close #39
> show #41 models
> close #41
> show #42 models
> hide #36 models
> rename #42 RevNS2Val_1
> show #43 models
> hide #43 models
> show #43 models
> show #44 models
> show #45 models
> hide #44 models
> hide #43 models
> hide #42 models
> show #46 models
> hide #46 models
> show #47 models
> hide #47 models
> hide #45 models
> show #42 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> rename #7,14-15,21,30-32,36,43-47 id #20
> hide #42 models
> show #42 models
> show #33 models
> hide #33 models
> save /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/modeling.cxs
> volume #8 region 0,0,0,219,219,219
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> volume #8 level 0.02296
> transparency 0
> transparency 50
> save /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/modeling.cxs
——— End of log from Wed Feb 23 13:58:39 2022 ———
opened ChimeraX session
> X
Unknown command: X
> hide #!8 models
> save /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/NEC_022422.pdb
> models #1-4,6,23,26 relModel #8 displayedOnly true
> open /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/NEC_022422.pdb
Chain information for NEC_022422.pdb #7
---
Chain | Description
G | No description available
> hide #!6 models
> hide #4 models
> hide #!3 models
> hide #2 models
> hide #!1 models
> hide #!20 models
> hide #23 models
> hide #26 models
> hide #42 models
> hide #7 models
> show #7 models
> hide #7 models
> show #!1 models
> show #2 models
> show #!3 models
> show #4 models
> show #!5 models
> show #!6 models
> show #23 models
> show #26 models
> hide #!5 models
> show #42 models
> save /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/NEC_022422.pdb
> models #1-4,6,23,26 ,42 relModel #8
> close #7
> open /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/NEC_022422.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/figures/groupmtg_March2022/NEC_022422.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY H 22
THR H 32 1 11
Start residue of secondary structure not found: HELIX 2 2 LEU H 69 GLY H 73 1
5
Start residue of secondary structure not found: HELIX 3 3 LEU H 75 ILE H 81 1
7
Start residue of secondary structure not found: HELIX 4 4 SER H 94 CYS H 112 1
19
Start residue of secondary structure not found: HELIX 5 5 LYS H 132 ASN H 143
1 12
86 messages similar to the above omitted
Chain information for NEC_022422.pdb
---
Chain | Description
7.6/A 7.7/A | No description available
7.8/A | No description available
7.4/B | No description available
7.3/D 7.1/H | No description available
7.5/G | No description available
7.2/K | No description available
> hide #4 models
> hide #!3 models
> hide #!1 models
> hide #2 models
> hide #!6 models
> hide #23 models
> hide #26 models
> hide #42 models
> select #7.3/F
23 atoms, 24 bonds, 2 residues, 1 model selected
> delete sel
> select #7.2/F
Nothing selected
> select #7.1/F
23 atoms, 24 bonds, 2 residues, 1 model selected
> delete sel
> select #7.4/F
23 atoms, 24 bonds, 2 residues, 1 model selected
> delete sel
> select #7.1/E
23 atoms, 24 bonds, 2 residues, 1 model selected
> delete sel
> select #7.4/E
23 atoms, 24 bonds, 2 residues, 1 model selected
> delete sel
> select #7.2/E
Nothing selected
> select #7.3/E
23 atoms, 24 bonds, 2 residues, 1 model selected
> delete sel
> hide #7.2,4-8#!7.1,3 atoms
> show #7.2,4-8#!7.1,3 atoms
> hide #7.2,4-8#!7.1,3 atoms
> save /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/NEC_022422.pdb
> models #7 relModel #8
> close #7
> open /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/NEC_022422.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/figures/groupmtg_March2022/NEC_022422.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY H 22
THR H 32 1 11
Start residue of secondary structure not found: HELIX 2 2 LEU H 69 GLY H 73 1
5
Start residue of secondary structure not found: HELIX 3 3 LEU H 75 ILE H 81 1
7
Start residue of secondary structure not found: HELIX 4 4 SER H 94 CYS H 112 1
19
Start residue of secondary structure not found: HELIX 5 5 LYS H 132 ASN H 143
1 12
86 messages similar to the above omitted
Chain information for NEC_022422.pdb
---
Chain | Description
7.6/A 7.7/A | No description available
7.8/A | No description available
7.4/B | No description available
7.3/D 7.1/H | No description available
7.5/G | No description available
7.2/K | No description available
> select #7.6/A
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> hide sel atoms
> hide sel atoms
> hide sel atoms
> select clear
> hide #7.6 models
> show #7.6 models
> hide #7.6 models
> hide #7.5 models
> show #7.5 models
> hide #7.4 models
> show #7.4 models
> hide #!7.3 models
> show #!7.3 models
> hide #7.2 models
> show #7.2 models
> hide #!7.1 models
> show #!7.1 models
> select #7.1/A
Nothing selected
> hide #7.8 models
> hide #7.7 models
> hide #!7.3 models
> show #!7.3 models
> hide #7.2 models
> hide #!7.1 models
> show #!7.1 models
> hide #!7 models
> show #!7 models
> hide #7.5 models
> hide #7.4 models
> hide #!7.1,3 atoms
> show #7.2 models
> show #7.4 models
> show #7.5 models
> show #7.6 models
> show #7.7 models
> show #7.8 models
> hide #!7.1 models
> show #!7.1 models
> hide #7.2 models
> show #7.2 models
> hide #!7.3 models
> show #!7.3 models
> hide #7.2 models
> show #7.2 models
> hide #7.4 models
> show #7.4 models
> hide #!7.3 models
> show #!7.3 models
> hide #7.2 models
> show #7.2 models
> hide #7.5 models
> show #7.5 models
> hide #7.5 models
> show #7.5 models
> hide #7.6 models
> show #7.6 models
> hide #7.7 models
> show #7.7 models
> save /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/modeling.cxs
——— End of log from Thu Feb 24 10:30:24 2022 ———
opened ChimeraX session
> open
> /Users/amberms/Desktop/wynton/Rosetta/simplerefinement/NEC_022422_relax_0001.pdb
Summary of feedback from opening
/Users/amberms/Desktop/wynton/Rosetta/simplerefinement/NEC_022422_relax_0001.pdb
---
warnings | Ignored bad PDB record found on line 43604
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 43605
#BEGIN_POSE_ENERGIES_TABLE NEC_022422_relax_0001.pdb
Ignored bad PDB record found on line 43606
label fa_atr fa_rep fa_sol fa_intra_atr_xover4 fa_intra_rep_xover4
fa_intra_sol_xover4 lk_ball lk_ball_iso lk_ball_bridge lk_ball_bridge_uncpl
fa_elec fa_intra_elec hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13
omega fa_dun_dev fa_dun_rot fa_dun_semi p_aa_pp hxl_tors ref rama_prepro
cart_bonded gen_bonded elec_dens_fast total
Ignored bad PDB record found on line 43607
weights 1 0.55 1 1 0.55 1 0.92 -0.38 -0.33 -0.33 1 1 1 1 1 1 1.25 0.48 0.69
0.76 0.78 0.61 1 1 0.5 0.5 1 35 NA
Ignored bad PDB record found on line 43608
pose -18186.9 8318.39 13913.9 -1210.27 626.42 911.958 7143.99 -7407.41
-19.4343 -138.112 -5842.29 -739.947 -2006.86 -162.956 -331.571 -355.668 0
-4.32301 71.5825 1433.08 2452.51 -383.577 481.574 -437.954 455.788 1741.79 0
-65625.8 -65302.1
2633 messages similar to the above omitted
Chain information for NEC_022422_relax_0001.pdb #11
---
Chain | Description
A | No description available
B | No description available
D H | No description available
G | No description available
K | No description available
> hide #7.8 models
> hide #7.7 models
> hide #7.6 models
> hide #7.5 models
> hide #7.4 models
> hide #7.2 models
> hide #!7 models
> hide #!7.1 models
> hide #!7.3 models
> show #!8 models
> hide #!11 atoms
> show #!11 cartoons
> show #!11 cartoons
> volume #8 level 0.0207
> hide #!8 models
> show #!8 models
> show #!7 models
> show #!7.1 models
> show #7.2 models
> show #!7.3 models
> show #7.4 models
> show #7.6 models
> show #7.5 models
> show #7.7 models
> show #7.8 models
> hide #!8 models
> hide #!7 models
> show #!7 models
> hide #!11 models
> show #!8 models
> volume style surface
> transparency 0
> transparency 50
> hide #7.2 models
> hide #7.4 models
> hide #7.5 models
> hide #7.8 models
> hide #!7.3 models
> hide #!7.1 models
> hide #7.7 models
> hide #7.6 models
> show #7.7 models
> show #7.6 models
> hide #7.7 models
> hide #7.6 models
> open /Users/amberms/Desktop/wynton/refmodels/NEC_012722.pdb
> /Users/amberms/Desktop/wynton/refmodels/NEC_4PMI.pdb
Chain information for NEC_012722.pdb #12
---
Chain | Description
A C | No description available
B I | No description available
D H | No description available
G | No description available
J | No description available
K | No description available
Chain information for NEC_4PMI.pdb #13
---
Chain | Description
A C | No description available
B I | No description available
D H | No description available
G | No description available
J | No description available
K | No description available
> hide #!12-13 atoms
> show #!12-13 cartoons
> hide #!8 models
> hide #!12 models
> show #!11 models
> close #11
> show #!10 models
> hide #!13 models
> show #!13 models
> hide #!10 models
> close #10
> show #!12 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #!8 models
> hide #!8 models
> show #!7.1 models
> show #7.2 models
> show #!7.3 models
> show #7.4 models
> show #7.5 models
> show #7.6 models
> show #7.7 models
> show #7.8 models
> hide #!12 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!12 models
> hide #!12 models
> show #!12 models
> show #!13 models
> hide #!13 models
> hide #!7 models
> show #!8 models
> show #!13 models
> hide #!12 models
> show #!7 models
> hide #!7 models
> show #!12 models
> hide #!13 models
> hide #!12 models
> show #!12 models
> show #!7 models
> transparency 0
> hide #!12 models
> hide #!8 models
> show #!13 models
> hide #!13 models
> show #!8 models
> volume #8 level 0.02183
> volume #8 level 0.02
> volume #8 level 0.025
> volume #8 level 0.022
> volume #8 level 0.0218
> open /Users/amberms/Desktop/wynton/MaskCreate/job325/mask.mrc
Opened mask.mrc as #10, grid size 220,220,220, pixel 1.67, shown at level 1,
step 1, values float32
> volume #10 level 1
> volume flip #10
Opened mask.mrc z flip as #11, grid size 220,220,220, pixel 1.67, shown at
step 1, values float32
> transparency #8.1#11.1 50
> hide #!11 models
> transparency #8.1 0
> show #!11 models
> hide #!11 models
> volume #!8 showOutlineBox false
> hide #!8 models
> hide #!7 models
> show #!7 models
> show #!12 models
> hide #12.1 models
> hide #12.2 models
> hide #!12 models
> hide #13.1 models
> hide #13.2 models
> hide #!7 models
> show #!13 models
> show #!12 models
> show #!7 models
> hide #!7 models
> close #12
> save /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/modeling.cxs
> split #13 chains
Split NEC_4PMI.pdb (#13) into 11 models
Chain information for NEC_4PMI.pdb A #13.1
---
Chain | Description
A | No description available
Chain information for NEC_4PMI.pdb B #13.2
---
Chain | Description
B | No description available
Chain information for NEC_4PMI.pdb C #13.3
---
Chain | Description
C | No description available
Chain information for NEC_4PMI.pdb D #13.4
---
Chain | Description
D | No description available
Chain information for NEC_4PMI.pdb G #13.7
---
Chain | Description
G | No description available
Chain information for NEC_4PMI.pdb H #13.8
---
Chain | Description
H | No description available
Chain information for NEC_4PMI.pdb I #13.9
---
Chain | Description
I | No description available
Chain information for NEC_4PMI.pdb J #13.10
---
Chain | Description
J | No description available
Chain information for NEC_4PMI.pdb K #13.11
---
Chain | Description
K | No description available
> hide #!13 models
> show #!13 models
> hide #!13.3 models
> show #!13.3 models
> hide #!13.1 models
> show #!13.1 models
> hide #13.5 models
> show #13.5 models
> hide #13.5 models
> show #13.5 models
> hide #13.5 models
> hide #13.6 models
> show #13.6 models
> hide #13.6 models
> hide #!13 models
> show #!8 models
> transparency #8.1 50
> transparency #8.1 0
> transparency #8 80 surfaces
> modeldisplay #13.1
Unknown command: modeldisplay #13.1
> display #13.1
Unknown command: modeller display #13.1
> modeldisp #13.1
Unknown command: modeldisp #13.1
> show #13.1
> show #!13 models
> hide #13.2,7,9-11#!13.1,3-4,8 atoms
> hide #13.1
> hide #!13.1 models
> hide #!13.3 models
> hide #13.2 models
> hide #!13.4 models
> hide #13.7 models
> hide #!13.8 models
> hide #13.9 models
> hide #13.10 models
> hide #13.11 models
> show #13.1
> show #!13.1 models
> show #13.2 models
> show #!13.3 models
> show #!13.4 models
> show #13.5 models
> show #13.6 models
> show #13.7 models
> show #!13.8 models
> show #13.9 models
> show #13.10 models
> show #13.11 models
> hide #13.5 models
> hide #13.6 models
> hide #13.2,7,9-11#!13.1,3-4,8 atoms
> hide #!13 models
> show #13.1
> show #!13 models
> hide #13.2,7,9-11#!13.1,3-4,8 atoms
> hide #!13 models
> show #!13 models
> modeldisplay
Unknown command: modeldisplay
> toolshed show
> hide #13.1 cartoons
> hide #13.1-13.22 cartoons
> hide #13.1-13.11 cartoons
> hide #13 cartoons
> show #13.1,13.3 cartoons
> show #13.1 cartoons
> show #13.3 cartoons
> hide #13.3 cartoons
> hide #13.1 cartoons
> transparency #8.1 0
> transparency #8 80 surfaces
> show #13.1 cartoons, show #13.3 cartoons; turn y 1 360;
Missing or invalid "what" argument: Should be one of 'atoms', 'bonds',
'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces'
> transparency #8.1 0
> transparency #8 80 surfaces
> show #13.1 cartoons
> show #13.3 cartoons
> turn y 1 360
> hide #13.3 cartoons
> hide #13.1 cartoons
> transparency #8.1 0
> transparency #8 80 surfaces
> wait
wait requires a frame count argument unless motion is in progress
> show #13.1 cartoons
> show #13.3 cartoons
> turn y 1 360
> hide #13.2,7,9-11#!13.1,3-4,8 cartoons
> transparency #8.1 0
> transparency #8 80 surfaces
> show #13.1 cartoons
> show #13.3 cartoons
> turn y 1 180
> show #13.4 cartoons
> show #13.8 cartoons
> turn y 1 180
> show #13.2 cartoons
> show #13.9 cartoons
> turn y 1 180
> show #13.7 cartoons
> show #13.10 cartoons
> show #13.11 cartooons; turn y 1 180
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #13.2,7,9-11#!13.1,3-4,8 cartoons
> transparency #8.1 0
> transparency #8 80 surfaces
> wait
wait requires a frame count argument unless motion is in progress
> show #13.1 cartoons
> transparency #8.1 0
> hide #13.2,7,9-11#!13.1,3-4,8 cartoons
> transparency #8 80 surfaces
> wait 2
> show #13.1 cartoons
> hide #13.2,7,9-11#!13.1,3-4,8 cartoons
> transparency #8.1 0
> transparency #8 80 surfaces
> wait 5
> show #13.1 cartoons
> transparency #8.1 0
> hide #13.2,7,9-11#!13.1,3-4,8 cartoons
> transparency #8 80 surfaces
> wait 5
> show #13.1,13.3 cartoons
> transparency #8.1 0
> transparency #8 80 surfaces
> wait 5
> show #13.1, 13.3 cartoons
> transparency #8.1 0
> transparency #8 80 surfaces
> wait 5
> show #13.1 & 13.3 cartoons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> transparency #8.1 0
> transparency #8 80 surfaces
> wait 5
> show #13.1-13.3 cartoons
> transparency #8.1 0
> transparency #8 80 surfaces
> wait 5
> show #13.1 cartoons
> show #13.3 cartoons
> transparency #8.1 0
> hide #13.2,7,9-11#!13.1,3-4,8 cartoons
> transparency #8 80 surfaces
> wait 5
> show #13.1 cartoons
> show #13.3 cartoons
> wait 5
> turn y 1 180
> show #13.4 cartoons
> show #13.8 cartoons
> wait 5
> turn y 1 180
> show #13.2 cartoons
> show #13.9 cartoons
> wait 5
> turn y 1 180
> show #13.7 cartoons
> show #13.10 cartoons
> show #13.11 cartoons
> turn y 1 180
> hide #13.2,7,9-11#!13.1,3-4,8 cartoons
> transparency #8.1 0
> transparency #8 80 surfaces
> wait 5
> show #13.1 cartoons
> show #13.3 cartoons
> wait 10
> turn y 1 180
> show #13.4 cartoons
> show #13.8 cartoons
> wait 10
> turn y 1 180
> show #13.2 cartoons
> show #13.9 cartoons
> wait 10
> turn y 1 180
> show #13.7 cartoons
> show #13.10 cartoons
> show #13.11 cartoons
> turn y 1 180
> transparency #8.1 0
> hide #13.2,7,9-11#!13.1,3-4,8 cartoons
> transparency #8 80 surfaces
> wait 5
> show #13.1 cartoons
> show #13.3 cartoons
> wait 10
> show #13.4 cartoons
> show #13.8 cartoons
> wait 10
> show #13.2 cartoons
> show #13.9 cartoons
> wait 10
> show #13.7 cartoons
> show #13.10 cartoons
> show #13.11 cartoons
> turn y 1 180
> hide #13.2,7,9-11#!13.1,3-4,8 cartoons
> transparency #8.1 0
> transparency #8 80 surfaces
> wait 15
> show #13.1 cartoons
> show #13.3 cartoons
> wait 15
> show #13.4 cartoons
> show #13.8 cartoons
> wait 15
> show #13.2 cartoons
> show #13.9 cartoons
> wait 15
> show #13.7 cartoons
> turn y 1 360
> transparency #8.1 0
> hide #13.2,7,9-11#!13.1,3-4,8 cartoons
> transparency #8 80 surfaces
> wait 15
> show #13.1 cartoons
> show #13.3 cartoons
> wait 30
> show #13.4 cartoons
> show #13.8 cartoons
> wait 30
> show #13.7 cartoons
> turn y 1 360
> hide #13.2,7,9-11#!13.1,3-4,8 cartoons
> volume #!8 style surface
> transparency #8.1 0
> movie record
> transparency #8 80 surfaces
> wait 15
> show #13.1 cartoons
> show #13.3 cartoons
> wait 30
> show #13.4 cartoons
> show #13.8 cartoons
> wait 30
> show #13.7 cartoons
> turn y 1 360
> movie encode
Movie saved to /Users/amberms/Desktop/movie.mp4
> transparency #8.1 0
> hide #13.2,7,9-11#!13.1,3-4,8 cartoons
> movie record
> wait 30
> transparency #8 80 surfaces
> wait 15
> show #13.1 cartoons
> show #13.3 cartoons
> wait 30
> show #13.4 cartoons
> show #13.8 cartoons
> wait 30
> show #13.7 cartoons
> turn y 1 360
> movie encode
Movie saved to /Users/amberms/Desktop/movie.mp4
> hide #13.2,7,9-11#!13.1,3-4,8 cartoons
> transparency #8.1 0
> movie record
> wait 30
> transparency #8 80 surfaces
> wait 15
> show #13.1 cartoons
> show #13.3 cartoons
> wait 30
> show #13.4 cartoons
> show #13.8 cartoons
> wait 30
> show #13.7 cartoons
> turn y 1 360
> wait 30
> movie encode
Movie saved to /Users/amberms/Desktop/movie.mp4
> transparency #8.1 0
> hide #13.2,7,9-11#!13.1,3-4,8 cartoons
> movie record
> wait 30
> transparency #8 80 surfaces
> wait 15
> show #13.1 cartoons
> show #13.3 cartoons
> wait 30
> show #13.4 cartoons
> show #13.8 cartoons
> wait 30
> show #13.7 cartoons
> turn y 1 360
> wait 30
> stop
> movie encode
Movie saved to /Users/amberms/Desktop/movie.mp4
> hide #13.2,7,9-11#!13.1,3-4,8 cartoons
> transparency #8.1 0
> movie record
> wait 20
> transparency #8 80 surfaces
> wait 10
> show #13.1 cartoons
> show #13.3 cartoons
> wait 20
> show #13.4 cartoons
> show #13.8 cartoons
> wait 30
> show #13.7 cartoons
> turn y 1 360
> wait 10
> stop
> movie encode
Movie saved to /Users/amberms/Desktop/movie.mp4
> open http://www.cgl.ucsf.edu/chimera/data/wcpcw-mar2017/moviemaking.html
Opened http://www.cgl.ucsf.edu/chimera/data/wcpcw-mar2017/moviemaking.html
> transparency #8.1 0
> hide #13.2,7,9-11#!13.1,3-4,8 cartoons
> open /Users/amberms/Desktop/movie.cxc
No such file/path: /Users/amberms/Desktop/movie.cxc
> open /Users/amberms/Desktop/movie.cxc
> movie record supersample 3
> wait 20
> transparency #8 80 surfaces
> wait 20
> show #13.1 cartoons
> show #13.3 cartoons
> wait 20
> show #13.4 cartoons
> show #13.8 cartoons
> wait 30
> show #13.7 cartoons
> turn y 1 360
> wait 30
> movie encode
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/movie_022422.mp4
> quality high
Movie saved to /Users/amberms/.../groupmtg_March2022/movie_022422.mp4
executed movie.cxc
> transparency #8.1 0
> hide #13.2,7,9-11#!13.1,3-4,8 cartoons
> open /Users/amberms/Desktop/movie.cxc
> movie record supersample 3
> wait 20
> transparency #8 80 surfaces
> wait 20
> show #13.1 cartoons
> show #13.3 cartoons
> wait 20
> show #13.4 cartoons
> show #13.8 cartoons
> wait 30
> show #13.7 cartoons
> turn y 1 360
> wait 75
> movie encode
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/movie_022422.mp4
> quality high
Movie saved to /Users/amberms/.../groupmtg_March2022/movie_022422.mp4
executed movie.cxc
> volume #!8 style surface
> volume #!8 style surface
> transparency #8.1 0
> hide #13.2,7,9-11#!13.1,3-4,8 cartoons
> open /Users/amberms/Desktop/movie.cxc
> movie record supersample 3
> wait 20
> transparency #8 80 surfaces
> wait 20
> show #13.1 cartoons
> show #13.3 cartoons
> wait 20
> show #13.4 cartoons
> show #13.8 cartoons
> wait 30
> show #13.7 cartoons
> turn y 1 360
> wait 150
> movie encode
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/movie_022422.mp4
> quality high
Movie saved to /Users/amberms/.../groupmtg_March2022/movie_022422.mp4
executed movie.cxc
> hide #13.2,7,9-11#!13.1,3-4,8 cartoons
> transparency #8.1 0
> open /Users/amberms/Desktop/movie.cxc
> movie record supersample 3
> wait 20
> transparency #8 80 surfaces
> wait 20
> show #13.1 cartoons
> show #13.3 cartoons
> wait 20
> show #13.4 cartoons
> show #13.8 cartoons
> wait 30
> show #13.7 cartoons
> turn y 1 360
> wait 250
> movie encode
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/movie_022422.mp4
> quality high
Movie saved to /Users/amberms/.../groupmtg_March2022/movie_022422.mp4
executed movie.cxc
> open /Users/amberms/Desktop/movie.cxc
> movie record supersample 3
> wait 20
> transparency #8 80 surfaces
> wait 20
> show #13.1 cartoons
> show #13.3 cartoons
> wait 20
> show #13.4 cartoons
> show #13.8 cartoons
> wait 30
> show #13.7 cartoons
> turn y 1 360
> wait 250
> movie encode
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/movie_022422_2.mp4
> quality high
Movie saved to /Users/amberms/.../groupmtg_March2022/movie_022422_2.mp4
executed movie.cxc
> transparency #8.1 0
> hide #13.2,7,9-11#!13.1,3-4,8 cartoons
> open /Users/amberms/Desktop/movie.cxc
> movie record supersample 3
> wait 20
> transparency #8 80 surfaces
> wait 20
> show #13.1 cartoons
> show #13.3 cartoons
> wait 20
> show #13.4 cartoons
> show #13.8 cartoons
> wait 30
> show #13.7 cartoons
> turn y 1 360
> wait 350
> movie encode
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/movie_022422_3.mp4
> quality high
Movie saved to /Users/amberms/.../groupmtg_March2022/movie_022422_3.mp4
executed movie.cxc
> transparency #8.1 0
> volume #!8 style mesh
> volume #!8 step 2
> volume #!8 step 1
> volume #!8 step 2
> volume #!8 step 4
> volume #!8 step 1
> volume #!8 step 2
> volume #!8 step 1
> toolshed show
> volume #!8 style mesh
> float spacing = 0.37, thickness = 0.01
Unknown command: float spacing = 0.37, thickness = 0.01
> volume #!8 style mesh
> volume #!8 style surface
> save /Users/amberms/Desktop/image7.png supersample 3
> volume #8 level 0.008411
> save /Users/amberms/Desktop/image8.png supersample 3
> save /Users/amberms/Desktop/image9.png supersample 3
> save /Users/amberms/Desktop/image10.png supersample 3
> turn x 1 180
> save /Users/amberms/Desktop/image11.png supersample 3
> volume #!8 style mesh
> volume #!8 style surface
> https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-
> sites.html#esp
Unknown command:
https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#esp
> open https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-
> sites.html#esp
Opened https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-
sites.html#esp
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2149, in <lambda>
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 626, in close_request
tool_instance.delete()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 512, in delete
ToolInstance.delete(self)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 154, in delete
self.session.ui.remove_tool(self)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 345, in remove_tool
self.main_window.remove_tool(tool_instance)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 725, in remove_tool
tw._destroy()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2049, in _destroy
self.__toolkit.destroy()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2189, in destroy
sbar.destroy()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 51, in destroy
v.delete()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 438, in delete
self.make_current()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current
return self._opengl_context.make_current()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 99, in make_current
qc = self._initialize_context()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)
RuntimeError: wrapped C/C++ object of type QScreen has been deleted
RuntimeError: wrapped C/C++ object of type QScreen has been deleted
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)
See log for complete Python traceback.
> 8
Unknown command: 8
> volume #8 level 0.02051
> transparency #8.1 50
> save /Users/amberms/Desktop/image12.png supersample 3
> volume #8 level 0.0405
> volume #8 level 0.0105
> save /Users/amberms/Desktop/image13.png supersample 3
> turn x 1 180
> turn x 1 90
> save /Users/amberms/Desktop/image14.png supersample 3
> turn x 1 180
> save /Users/amberms/Desktop/image15.png supersample 3
> volume #8 level 0.0218
> transparency #8.1 0
> volume #!8 style image
> volume #!8 style image
> volume #!8 style surface
> transparency #8.1 50
> transparency #8 80 surfaces
> hide #!13.1 models
> hide #13.2 models
> hide #!13.3 models
> hide #!13.4 models
> hide #13.7 models
> hide #!13.8 models
> hide #13.9 models
> hide #13.10 models
> hide #13.11 models
> show #13.6 models
> hide #13.6 models
> show #!13.4 models
> show #!13.8 models
> show #!1 models
> show #!3 models
> hide #!13.4 models
> hide #!13.8 models
> show #!13.8 models
> show #!13.4 models
> hide #!3 models
> hide #!1 models
> show #!13.1 models
> show #!13.3 models
> volume #8 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.5 tiltedSlabSpacing 1.668 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #10 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.7 tiltedSlabSpacing 1.67 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #11 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.7 tiltedSlabSpacing 1.67 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #8 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.5 tiltedSlabSpacing 1.668 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #10 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.7 tiltedSlabSpacing 1.67 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #11 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.7 tiltedSlabSpacing 1.67 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #8 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.5 tiltedSlabSpacing 1.668 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #10 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.7 tiltedSlabSpacing 1.67 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #11 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.7 tiltedSlabSpacing 1.67 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #8 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.5 tiltedSlabSpacing 1.668 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #10 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.7 tiltedSlabSpacing 1.67 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #11 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.7 tiltedSlabSpacing 1.67 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #8 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.5 tiltedSlabSpacing 1.668 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #10 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.7 tiltedSlabSpacing 1.67 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #11 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.7 tiltedSlabSpacing 1.67 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #!8 planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #8 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.5 tiltedSlabSpacing 1.668 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #10 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.7 tiltedSlabSpacing 1.67 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #11 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.7 tiltedSlabSpacing 1.67 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #!8 planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #8 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.5 tiltedSlabSpacing 1.668 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #10 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.7 tiltedSlabSpacing 1.67 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #11 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 183.7 tiltedSlabSpacing 1.67 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #8 orthoplanes xyz positionPlanes 110,110,110 style image region all
> mousemode rightMode "move planes"
> volume #10 orthoplanes xyz positionPlanes 110,110,110 style image region all
> mousemode rightMode "move planes"
> volume #11 orthoplanes xyz positionPlanes 110,110,110 style image region all
> mousemode rightMode "move planes"
> volume #8 orthoplanes xyz positionPlanes 110,110,110 style image region all
> mousemode rightMode "move planes"
> volume #10 orthoplanes xyz positionPlanes 110,110,110 style image region all
> mousemode rightMode "move planes"
> volume #11 orthoplanes xyz positionPlanes 110,110,110 style image region all
> mousemode rightMode "move planes"
> volume #!8 region all imageMode "full region"
> volume unzone #!8
> mousemode rightMode "crop volume"
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 12
atomic models, 1 maps.
> volume #!8 style surface
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right "clip rotate"
> ui mousemode right clip
> volume #!8 showOutlineBox false
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right "move planes"
> volume #8 region 0,0,0,219,219,219
> volume #8 region 0,0,0,219,219,219
> volume #8 region 0,0,0,219,219,219
> volume #8 region 0,0,0,219,219,219
> volume #8 region 0,0,0,219,219,219
> volume #8 region 0,0,0,219,219,219
> volume #8 region 0,0,0,219,219,219
> volume #8 region 0,0,0,219,219,219
> volume #8 region 0,0,0,219,219,219
> open https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-
> sites.html#esp
Opened https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-
sites.html#esp
> coulombic protein
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
RanQ69L180_1.pdb #1/H MET 179
RevHIV1NS2Val_2.pdb #2/K LYS 14
RevHIV1NS2Val_2.pdb #2/K GLU 32
RevHIV1NS2Val_2.pdb #2/K ARG 35
RevHIV1NS2Val_2.pdb #2/K LEU 64
RanQ69L180_2.pdb #3/D MET 179
NES_2.pdb #4/B ILE 13
RevNS2Val_1.pdb #5/J LEU 13
RevNS2Val_1.pdb #5/J LYS 14
RevNS2Val_1.pdb #5/J ARG 17
RevNS2Val_1.pdb #5/J LYS 20
RevNS2Val_1.pdb #5/J GLN 24
RevNS2Val_1.pdb #5/J ARG 42
RevNS2Val_1.pdb #5/J ARG 46
RevNS2Val_1.pdb #5/J TYR 63
NEC_022422.pdb #7.1/H MET 179
NEC_022422.pdb #7.2/K LYS 14
NEC_022422.pdb #7.2/K GLU 32
NEC_022422.pdb #7.2/K ARG 35
NEC_022422.pdb #7.2/K LEU 64
NEC_022422.pdb #7.3/D MET 179
NEC_4PMI.pdb D #13.4/D MET 179
NEC_4PMI.pdb H #13.8/H MET 179
NEC_4PMI.pdb J #13.10/J LEU 13
NEC_4PMI.pdb J #13.10/J LYS 14
NEC_4PMI.pdb J #13.10/J ARG 17
NEC_4PMI.pdb J #13.10/J LYS 20
NEC_4PMI.pdb J #13.10/J GLN 24
NEC_4PMI.pdb J #13.10/J ARG 42
NEC_4PMI.pdb J #13.10/J ARG 46
NEC_4PMI.pdb J #13.10/J TYR 63
NEC_4PMI.pdb K #13.11/K LYS 14
NEC_4PMI.pdb K #13.11/K GLU 32
NEC_4PMI.pdb K #13.11/K ARG 35
NEC_4PMI.pdb K #13.11/K LEU 64
Using Amber 20 recommended default charges and atom types for standard
residues
Using Amber 20 recommended default charges and atom types for standard
residues
Using Amber 20 recommended default charges and atom types for standard
residues
Using Amber 20 recommended default charges and atom types for standard
residues
Using Amber 20 recommended default charges and atom types for standard
residues
Using Amber 20 recommended default charges and atom types for standard
residues
Using Amber 20 recommended default charges and atom types for standard
residues
Using Amber 20 recommended default charges and atom types for standard
residues
Using Amber 20 recommended default charges and atom types for standard
residues
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of RanQ69L180_2.pdb #/D MET 179 H bonded to atom that should not
have hydrogens (copy of RanQ69L180_2.pdb #/D MET 179 C)
> show #!11 models
> hide #!11 models
> show #!11 models
> volume #8 region 0,0,0,219,219,219
> volume #8 region 0,0,0,219,219,219
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> volume #10 level 0,0 level 0.1,0.8 level 1,1
> ui mousemode right "move planes"
> ui mousemode right "move planes"
> ui mousemode right "contour level"
> ui mousemode right "pick blobs"
> hide #!10 models
> hide #!8 models
> hide #!13.8 models
> show #!13.8 models
> show #!11 models
> hide #!11 models
> show #!8 models
> coulombic #!13.1,3-4,8
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
NEC_4PMI.pdb H #13.8/H MET 179 O
NEC_4PMI.pdb D #13.4/D MET 179 O
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of NEC_4PMI.pdb H #/H MET 179 H bonded to atom that should not
have hydrogens (copy of NEC_4PMI.pdb H #/H MET 179 C)
> hide #!8 models
> coulombic #!13.1,3-4,8
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
NEC_4PMI.pdb H #13.8/H MET 179 O
NEC_4PMI.pdb D #13.4/D MET 179 O
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of NEC_4PMI.pdb H #/H MET 179 H bonded to atom that should not
have hydrogens (copy of NEC_4PMI.pdb H #/H MET 179 C)
> show #!8 models
> volume #!8 style surface
> transparency #8.1 0
> hide #!13 models
> show #!13 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!13.1,3-4,8 surfaces
> hide #!13.1,3-4,8 surfaces
> show #!13.1,3-4,8 surfaces
> coulombic #!13.1,3-4,8
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
NEC_4PMI.pdb H #13.8/H MET 179 O
NEC_4PMI.pdb D #13.4/D MET 179 O
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of NEC_4PMI.pdb H #/H MET 179 H bonded to atom that should not
have hydrogens (copy of NEC_4PMI.pdb H #/H MET 179 C)
> show #!13.1,3-4,8 surfaces
> style #!13.1,3-4,8 sphere
Changed 19634 atom styles
> coulombic #!13.1,3-4,8
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
NEC_4PMI.pdb H #13.8/H MET 179 O
NEC_4PMI.pdb D #13.4/D MET 179 O
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of NEC_4PMI.pdb H #/H MET 179 H bonded to atom that should not
have hydrogens (copy of NEC_4PMI.pdb H #/H MET 179 C)
> hide #!13.1,3-4,8 atoms
> hide #!13.1,3-4,8 atoms
> hide #!13.1,3-4,8 surfaces
> show #!13.1,3-4,8 surfaces
> color #13.1,3-4,8#!13 light gray
> color :LYS/ARG, blue
> color :GLU,ASP red
> color :LYS,ARG blue
> lighting soft
> coulombic #!13.1,3-4,8
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
NEC_4PMI.pdb H #13.8/H MET 179 O
NEC_4PMI.pdb D #13.4/D MET 179 O
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of NEC_4PMI.pdb H #/H MET 179 H bonded to atom that should not
have hydrogens (copy of NEC_4PMI.pdb H #/H MET 179 C)
> coulombic#13.1,3-4,8
Unknown command: coulombic#13.1,3-4,8
> coulombic #13.1,3-4,8
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
NEC_4PMI.pdb H #13.8/H MET 179 O
NEC_4PMI.pdb D #13.4/D MET 179 O
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of NEC_4PMI.pdb H #/H MET 179 H bonded to atom that should not
have hydrogens (copy of NEC_4PMI.pdb H #/H MET 179 C)
> color #13.1,3-4,8#!13 light gray
> coulombic #13.1,3-4,8
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
NEC_4PMI.pdb H #13.8/H MET 179 O
NEC_4PMI.pdb D #13.4/D MET 179 O
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of NEC_4PMI.pdb H #/H MET 179 H bonded to atom that should not
have hydrogens (copy of NEC_4PMI.pdb H #/H MET 179 C)
> coulombic #!13.1,3-4,8
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
NEC_4PMI.pdb H #13.8/H MET 179 O
NEC_4PMI.pdb D #13.4/D MET 179 O
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of NEC_4PMI.pdb H #/H MET 179 H bonded to atom that should not
have hydrogens (copy of NEC_4PMI.pdb H #/H MET 179 C)
> show #!20 models
> hide #!20 models
> coulombic #!13.1,3-4,8 key true
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
NEC_4PMI.pdb H #13.8/H MET 179 O
NEC_4PMI.pdb D #13.4/D MET 179 O
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of NEC_4PMI.pdb H #/H MET 179 H bonded to atom that should not
have hydrogens (copy of NEC_4PMI.pdb H #/H MET 179 C)
> hide #!13 models
> show #!13 models
> toolshed show
> color #13.1,3-4,8#!13 byhetero
> ui tool show "Surface Color"
> color electrostatic #13.1.2 map #8 palette -10,#ff0000:0,#ffffff:10,#0000ff
Map values for surface "NEC_4PMI.pdb A_A SES surface": minimum -0.01278, mean
0.01469, maximum 0.06756
> color electrostatic #13.3.2 map #8 palette -10,#ff0000:0,#ffffff:10,#0000ff
Map values for surface "NEC_4PMI.pdb C_C SES surface": minimum -0.01174, mean
0.01489, maximum 0.06606
> color electrostatic #13.4.2 map #8 palette -10,#ff0000:0,#ffffff:10,#0000ff
Map values for surface "NEC_4PMI.pdb D_D SES surface": minimum -0.00499, mean
0.01731, maximum 0.07628
> color electrostatic #13.8.2 map #8 palette -10,#ff0000:0,#ffffff:10,#0000ff
Map values for surface "NEC_4PMI.pdb H_H SES surface": minimum -0.008427, mean
0.01622, maximum 0.07553
> ui tool show "Surface Color"
> coulombic #!13.1,3-4,8
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
NEC_4PMI.pdb H #13.8/H MET 179 O
NEC_4PMI.pdb D #13.4/D MET 179 O
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of NEC_4PMI.pdb H #/H MET 179 H bonded to atom that should not
have hydrogens (copy of NEC_4PMI.pdb H #/H MET 179 C)
> color electrostatic #13.8.2 map #8 palette -10,#ff0000:0,#ffffff:10,#0000ff
Map values for surface "NEC_4PMI.pdb H_H SES surface": minimum -0.008427, mean
0.01622, maximum 0.07553
> hide #!13.1,3-4,8 surfaces
> hide #!13.1 models
> show #!13.1 models
> hide #!13.1 models
> show #!13.1 models
> show #13.2 models
> show #13.2#!13.1,3-4,8 cartoons
> show #13.2#!13.1,3-4,8 surfaces
> hide #!13.1-4,8 surfaces
> hide #!13.2 models
> show #!13.2 models
> color #13.1-4,8#!13 yellow
> hide #!13.3 models
> show #!13.3 models
> hide #!13.4 models
> show #!13.4 models
> show #!11 models
> hide #!11 models
> show #!8 models
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/amberms/Desktop/movie2.mp4
Movie saved to /Users/amberms/Desktop/movie2.mp4
> hide #!13 models
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/amberms/Desktop/movie3.mp4
Movie saved to /Users/amberms/Desktop/movie3.mp4
> save /Users/amberms/Desktop/image16.png supersample 3
> turn y 1 180
> save /Users/amberms/Desktop/image17.png supersample 3
> open /Users/amberms/Desktop/movie.cxc
> movie record supersample 3
> wait 20
> transparency #8 80 surfaces
> wait 20
> show #13.1 cartoons
> show #13.3 cartoons
> wait 20
> show #13.4 cartoons
> show #13.8 cartoons
> wait 30
> show #13.7 cartoons
> turn y 1 360
> wait 350
> movie encode
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/movie_022422_4.mp4
> quality high
Movie saved to /Users/amberms/.../groupmtg_March2022/movie_022422_4.mp4
executed movie.cxc
> transparency #8.1 0
> hide #!8 models
> show #!13 models
> show #!8 models
> hide #!13.1-4,8 cartoons
> open /Users/amberms/Desktop/movie.cxc
> movie record supersample 3
> wait 20
> transparency #8 80 surfaces
> wait 20
> show #13.1 cartoons
> show #13.3 cartoons
> wait 20
> show #13.4 cartoons
> show #13.8 cartoons
> wait 30
> show #13.7 cartoons
> turn y 1 360
> wait 350
> movie encode
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/movie_022422_4.mp4
> quality high
Movie saved to /Users/amberms/.../groupmtg_March2022/movie_022422_4.mp4
executed movie.cxc
> show #13.7 models
> hide #13.7#!13.1-4,8 cartoons
> transparency #8.1#13.1.2#13.2.1#13.3.2#13.4.2#13.8.2 0
> open /Users/amberms/Desktop/movie.cxc
> movie record supersample 3
> wait 20
> transparency #8 80 surfaces
> wait 20
> show #13.1 cartoons
> show #13.3 cartoons
> wait 20
> show #13.4 cartoons
> show #13.8 cartoons
> wait 30
> show #13.7 cartoons
> turn y 1 360
> wait 350
> movie encode
> /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/movie_022422_4.mp4
> quality high
Movie saved to /Users/amberms/.../groupmtg_March2022/movie_022422_4.mp4
executed movie.cxc
> open /Users/amberms/Desktop/wynton/refmodels/Crm1dimer.pdb
Chain information for Crm1dimer.pdb #12
---
Chain | Description
A C | No description available
> hide #!13 models
> close #12
> show #!13 models
> transparency #8.1#13.1.2#13.2.1#13.3.2#13.4.2#13.8.2 0
> transparency #8.1#13.1.2#13.2.1#13.3.2#13.4.2#13.8.2 50
> hide #!8 models
> ui mousemode right clip
> show #!8 models
> ui mousemode right clip
> save /Users/amberms/Desktop/image18.png supersample 3
> turn x 1 180
> turn x 1 180
> turn y 1 180
> save /Users/amberms/Desktop/image19.png supersample 3
> save /Users/amberms/Desktop/image20.png supersample 3
> turn y 1 180
> save /Users/amberms/Desktop/image21.png supersample 3
> save /Users/amberms/Desktop/image22.png supersample 3
> save /Users/amberms/Desktop/image23.png supersample 3
> hide #!13 models
> show #!1 models
> show #!3 models
> show #23 models
> show #26 models
> hide #!8 models
> show #23,26#!1,3 surfaces
> show #!1,3,23,26 surfaces
> show #!1,3,23,26 surfaces
> hide #!1,3,23,26 surfaces
> ui tool show "Color Actions"
> color #1,3,23,26 light gray
> show #!8 models
> show #!6 models
> hide #!6 models
> show #!13 models
> hide #!13.1 models
> hide #!13.3 models
> hide #!13.4 models
> hide #!13.8 models
> save /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/modeling.cxs
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown
return self.__toolkit.shown
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fe9dfe78c10> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fe9d16a4910>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fe9dfe78c10> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fe9d16a4910>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fe9dfe78c10> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fe9d16a4910>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown
return self.__toolkit.shown
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fe9dfe78c10> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fe9d16a4910>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fe9dfe78c10> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fe9d16a4910>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fe9dfe78c10> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fe9d16a4910>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save /Users/amberms/Desktop/wynton/figures/groupmtg_March2022/modeling.cxs
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown
return self.__toolkit.shown
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fe9dfe78c10> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fe9d16a4910>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fe9dfe78c10> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fe9d16a4910>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fe9dfe78c10> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fe9d16a4910>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown
return self.__toolkit.shown
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fe9dfe78c10> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fe9d16a4910>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fe9dfe78c10> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fe9d16a4910>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fe9dfe78c10> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fe9d16a4910>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-16.5.4
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro12,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.9 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 3 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 428.40.10.0.0
SMC Version (system): 2.28f7
Software:
System Software Overview:
System Version: macOS 11.6.1 (20G224)
Kernel Version: Darwin 20.6.0
Time since boot: 8 days 19:00
Graphics/Displays:
Intel Iris Graphics 6100:
Chipset Model: Intel Iris Graphics 6100
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x162b
Revision ID: 0x0009
Metal Family: Supported, Metal GPUFamily macOS 1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2416D:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 59.00Hz
Framebuffer Depth: 24-Bit Color (ARGB8888)
Display Serial Number: TN5PP6CO174S
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Connection Type: Thunderbolt/DisplayPort
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-Clipper: 0.16.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.2.2
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
matplotlib-inline: 0.1.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → wrapped C/C++ object of type QScreen has been deleted |
comment:2 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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