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#7602 closed defect (fixed)

Session reset/restore: 'Tasks' object has no attribute 'remove'

Reported by:	chimerax-bug-report@…	Owned by:	Zach Pearson
Priority:	normal	Milestone:	1.5
Component:	Sessions	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.19043
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open D:/科研文件/约克大学实验/P450实验/蛋白结构预测/JOBS/Sch11416_translation.pdb

Chain information for Sch11416_translation.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open D:/科研文件/约克大学实验/P450实验/蛋白结构预测/JOBS/Sch15640_translation.pdb

Chain information for Sch15640_translation.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open D:/科研文件/约克大学实验/P450实验/蛋白结构预测/JOBS/Sch28415_translation.pdb

Chain information for Sch28415_translation.pdb #3  
---  
Chain | Description  
A | No description available  
  

> hide #3 models

> hide #2 models

> open
> D:/科研文件/约克大学实验/P450实验/蛋白结构预测/1661950111791_CPDI_CYM_min_1661950173467_dock/rot-1661950111791_CPDI_CYM_min_1661950173467_docked_1_addH.pdb

Chain information for
rot-1661950111791_CPDI_CYM_min_1661950173467_docked_1_addH.pdb #4  
---  
Chain | Description  
A | No description available  
  

> hide #1 models

> ui windowfill toggle

[Repeated 1 time(s)]

> open
> D:/科研文件/约克大学实验/P450实验/蛋白结构预测/1661950111791_CPDI_CYM_min_1661950173467_dock/1661950111791_CPDI_CYM_min.pdb

Summary of feedback from opening
D:/科研文件/约克大学实验/P450实验/蛋白结构预测/1661950111791_CPDI_CYM_min_1661950173467_dock/1661950111791_CPDI_CYM_min.pdb  
---  
warnings | Ignored bad PDB record found on line 8230  
Grid_score -73  
  
Ignored bad PDB record found on line 8231  
Transform_accept_ratio 0.1735  
  
Ignored bad PDB record found on line 8232  
classic_grid_F -69  
  
Ignored bad PDB record found on line 8233  
dslf_fa13 0  
  
Ignored bad PDB record found on line 8234  
fa_atr -3017.56  
  
549 messages similar to the above omitted  
  
Chain information for 1661950111791_CPDI_CYM_min.pdb #5  
---  
Chain | Description  
A | No description available  
  

> hide #!4 models

> show #!4 models

> hide #!5 models

> color #4 cornflower blue

> select ligand

170 atoms, 178 bonds, 3 residues, 2 models selected  

> color (#!4 & sel) gray

> select clear

> select ligand

170 atoms, 178 bonds, 3 residues, 2 models selected  

> show (#!4 & sel) target ab

> ui tool show "Modeller Comparative"

> help help:user/tools/modeller.html

> ui tool show Matchmaker

> matchmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Sch11416_translation.pdb, chain A (#1) with
Sch28415_translation.pdb, chain A (#3), sequence alignment score = 1962.8  
RMSD between 425 pruned atom pairs is 0.736 angstroms; (across all 494 pairs:
8.064)  
  

> hide #!4 models

> ui tool show Matchmaker

> matchmaker #3 & sel to #1 & sel

No 'to' model specified  

> ui tool show Matchmaker

> matchmaker #3 & sel to #1 & sel

No 'to' model specified  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\ui\options\options.py", line 50, in <lambda>  
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\ui\options\options.py", line 311, in set_value  
self.widget.setChecked(value)  
RuntimeError: wrapped C/C++ object of type QCheckBox has been deleted  
  
Error processing trigger "setting changed":  
RuntimeError: wrapped C/C++ object of type QCheckBox has been deleted  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\ui\options\options.py", line 311, in set_value  
self.widget.setChecked(value)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\ui\options\options.py", line 50, in <lambda>  
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\ui\options\options.py", line 311, in set_value  
self.widget.setChecked(value)  
RuntimeError: wrapped C/C++ object of type QCheckBox has been deleted  
  
Error processing trigger "setting changed":  
RuntimeError: wrapped C/C++ object of type QCheckBox has been deleted  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\ui\options\options.py", line 311, in set_value  
self.widget.setChecked(value)  
  
See log for complete Python traceback.  
  

> matchmaker #3 & sel to #1 & sel

No 'to' model specified  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\ui\options\options.py", line 50, in <lambda>  
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\ui\options\options.py", line 341, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\ui\options\options.py", line 341, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> show #!4 models

> delete solvent

[Repeated 1 time(s)]

> preset "overall look" interactive

Using preset: Overall Look / Interactive  
Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f
    lighting depthCue t

  

> preset "overall look" interactive

Using preset: Overall Look / Interactive  
Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f
    lighting depthCue t

  

> interfaces select & #!4 & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> ui tool show Matchmaker

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\ui\options\options.py", line 50, in <lambda>  
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\ui\options\options.py", line 341, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\ui\options\options.py", line 341, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  

> matchmaker #2-3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Sch11416_translation.pdb, chain A (#1) with
Sch15640_translation.pdb, chain A (#2), sequence alignment score = 1750.5  
RMSD between 425 pruned atom pairs is 0.808 angstroms; (across all 493 pairs:
8.991)  
  
Matchmaker Sch11416_translation.pdb, chain A (#1) with
Sch28415_translation.pdb, chain A (#3), sequence alignment score = 1962.8  
RMSD between 425 pruned atom pairs is 0.736 angstroms; (across all 494 pairs:
8.064)  
  

> interfaces select & #!4 & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> hide #!4 models

> show #1 models

> hide #1 models

> show #!4 models

> ui tool show Matchmaker

> matchmaker #2-3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Sch11416_translation.pdb, chain A (#1) with
Sch15640_translation.pdb, chain A (#2), sequence alignment score = 1750.5  
RMSD between 425 pruned atom pairs is 0.808 angstroms; (across all 493 pairs:
8.991)  
  
Matchmaker Sch11416_translation.pdb, chain A (#1) with
Sch28415_translation.pdb, chain A (#3), sequence alignment score = 1962.8  
RMSD between 425 pruned atom pairs is 0.736 angstroms; (across all 494 pairs:
8.064)  
  

> matchmaker #2-3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Sch11416_translation.pdb, chain A (#1) with
Sch15640_translation.pdb, chain A (#2), sequence alignment score = 1750.5  
RMSD between 425 pruned atom pairs is 0.808 angstroms; (across all 493 pairs:
8.991)  
  
Matchmaker Sch11416_translation.pdb, chain A (#1) with
Sch28415_translation.pdb, chain A (#3), sequence alignment score = 1962.8  
RMSD between 425 pruned atom pairs is 0.736 angstroms; (across all 494 pairs:
8.064)  
  

> ui windowfill toggle

[Repeated 1 time(s)]

> hide #!4 models

> ui tool show Matchmaker

> matchmaker #2-3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Sch11416_translation.pdb, chain A (#1) with
Sch15640_translation.pdb, chain A (#2), sequence alignment score = 1750.5  
RMSD between 425 pruned atom pairs is 0.808 angstroms; (across all 493 pairs:
8.991)  
  
Matchmaker Sch11416_translation.pdb, chain A (#1) with
Sch28415_translation.pdb, chain A (#3), sequence alignment score = 1962.8  
RMSD between 425 pruned atom pairs is 0.736 angstroms; (across all 494 pairs:
8.064)  
  

> matchmaker #2-3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Sch11416_translation.pdb, chain A (#1) with
Sch15640_translation.pdb, chain A (#2), sequence alignment score = 1750.5  
RMSD between 425 pruned atom pairs is 0.808 angstroms; (across all 493 pairs:
8.991)  
  
Matchmaker Sch11416_translation.pdb, chain A (#1) with
Sch28415_translation.pdb, chain A (#3), sequence alignment score = 1962.8  
RMSD between 425 pruned atom pairs is 0.736 angstroms; (across all 494 pairs:
8.064)  
  

> show #1 models

> show #2 models

> show #3 models

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> sequence chain #2/A

Alignment identifier is 2/A  

> sequence chain #3/A

Alignment identifier is 3/A  
Drag select of 95 residues  
Drag select of 651 residues  

> select clear

> select #1/A:11

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select clear

Drag select of 936 residues  

> select clear

> select #1/A:18

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select clear

Drag select of 21 residues  
Drag select of 30 residues  

> select clear

> select #1/A:32

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/A:31

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:32

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/A:31

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:32

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/A:31

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:30

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #1/A:29

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1/A:32

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/A:32

11 atoms, 10 bonds, 1 residue, 1 model selected  
Drag select of 10 residues  

> hide #1 models

> hide #2 models

> hide #3 models

> show #3 models

> show #2 models

> hide #2 models

> hide #3 models

> show #!4 models

> hide #!4 models

> show #!5 models

> open
> D:/科研文件/约克大学实验/P450实验/蛋白结构预测/1661950111791_CPDI_CYM_min_1661950173467_dock/1661950111791_CPDI_CYM_min.pdb

Summary of feedback from opening
D:/科研文件/约克大学实验/P450实验/蛋白结构预测/1661950111791_CPDI_CYM_min_1661950173467_dock/1661950111791_CPDI_CYM_min.pdb  
---  
warnings | Ignored bad PDB record found on line 8230  
Grid_score -73  
  
Ignored bad PDB record found on line 8231  
Transform_accept_ratio 0.1735  
  
Ignored bad PDB record found on line 8232  
classic_grid_F -69  
  
Ignored bad PDB record found on line 8233  
dslf_fa13 0  
  
Ignored bad PDB record found on line 8234  
fa_atr -3017.56  
  
549 messages similar to the above omitted  
  
Chain information for 1661950111791_CPDI_CYM_min.pdb #6  
---  
Chain | Description  
A | No description available  
  

> open D:/科研文件/约克大学实验/P450实验/蛋白结构预测/28415_C3/1661957325368_CPDI_CYM_min.pdb

Summary of feedback from opening
D:/科研文件/约克大学实验/P450实验/蛋白结构预测/28415_C3/1661957325368_CPDI_CYM_min.pdb  
---  
warnings | Ignored bad PDB record found on line 8126  
Grid_score -64  
  
Ignored bad PDB record found on line 8127  
Transform_accept_ratio 0.177  
  
Ignored bad PDB record found on line 8128  
classic_grid_F -72  
  
Ignored bad PDB record found on line 8129  
dslf_fa13 0  
  
Ignored bad PDB record found on line 8130  
fa_atr -3037.01  
  
547 messages similar to the above omitted  
  
Chain information for 1661957325368_CPDI_CYM_min.pdb #7  
---  
Chain | Description  
A | No description available  
  

> open D:/科研文件/约克大学实验/P450实验/蛋白结构预测/11416_C5/1661957501908_CPDI_CYM_min.pdb

Summary of feedback from opening
D:/科研文件/约克大学实验/P450实验/蛋白结构预测/11416_C5/1661957501908_CPDI_CYM_min.pdb  
---  
warnings | Ignored bad PDB record found on line 8171  
Grid_score -73  
  
Ignored bad PDB record found on line 8172  
Transform_accept_ratio 0.1625  
  
Ignored bad PDB record found on line 8173  
classic_grid_F -73  
  
Ignored bad PDB record found on line 8174  
dslf_fa13 -1.21552  
  
Ignored bad PDB record found on line 8175  
fa_atr -3015.76  
  
544 messages similar to the above omitted  
  
Chain information for 1661957501908_CPDI_CYM_min.pdb #8  
---  
Chain | Description  
A | No description available  
  

> hide #!5 models

> ~select

Nothing selected  

> rlad ligand

Unknown command: rlad ligand  

> rlab ligand

Unknown command: rlab ligand  

> show ligand

> select
> #1/A:2-32,47-50,55-66,85-94,106-111,113-115,124-137,140-163,171-193,196-210,215-218,223-228,230-255,266-275,285-316,318-331,340-345,347-359,391-396,409-412,432-434,439-456,462-464,467-469

4808 atoms, 4832 bonds, 290 residues, 1 model selected  

> select clear

> select #8/A:22

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select #8/A:26

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #7

8055 atoms, 8145 bonds, 6 pseudobonds, 500 residues, 3 models selected  

> select add #6

16192 atoms, 16382 bonds, 12 pseudobonds, 1001 residues, 5 models selected  

> select clear

> select #8/A:22

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select
> #1/A:2-32,47-50,55-66,85-94,106-111,113-115,124-137,140-163,171-193,196-210,215-218,223-228,230-255,266-275,285-316,318-331,340-345,347-359,391-396,409-412,432-434,439-456,462-464,467-469

4808 atoms, 4832 bonds, 290 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #!7-8 to #6

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1661950111791_CPDI_CYM_min.pdb, chain A (#6) with
1661957325368_CPDI_CYM_min.pdb, chain A (#7), sequence alignment score =
1756.1  
RMSD between 441 pruned atom pairs is 0.723 angstroms; (across all 493 pairs:
1.910)  
  
Matchmaker 1661950111791_CPDI_CYM_min.pdb, chain A (#6) with
1661957501908_CPDI_CYM_min.pdb, chain A (#8), sequence alignment score =
1743.5  
RMSD between 425 pruned atom pairs is 0.811 angstroms; (across all 493 pairs:
8.993)  
  

> matchmaker #!7-8 to #6

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1661950111791_CPDI_CYM_min.pdb, chain A (#6) with
1661957325368_CPDI_CYM_min.pdb, chain A (#7), sequence alignment score =
1756.1  
RMSD between 441 pruned atom pairs is 0.723 angstroms; (across all 493 pairs:
1.910)  
  
Matchmaker 1661950111791_CPDI_CYM_min.pdb, chain A (#6) with
1661957501908_CPDI_CYM_min.pdb, chain A (#8), sequence alignment score =
1743.5  
RMSD between 425 pruned atom pairs is 0.811 angstroms; (across all 493 pairs:
8.993)  
  

> ui tool show "Modeller Comparative"

> ui tool show "Show Sequence Viewer"

[Repeated 1 time(s)]

> sequence chain #4/A #5/A #6/A

Alignment identifier is 1  

> sequence chain #7/A

Alignment identifier is 7/A  

> sequence chain #8/A

Alignment identifier is 8/A  

QWindowsWindow::setGeometry: Unable to set geometry 1920x1047+0+35 (frame:
1942x1103-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 470x698 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=727,
y=1103)))  

> hide #!6 models

> show #!6 models

> hide #!6 models

> ui tool show Matchmaker

> matchmaker #!6-8 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Sch11416_translation.pdb, chain A (#1) with
1661950111791_CPDI_CYM_min.pdb, chain A (#6), sequence alignment score =
1742.8  
RMSD between 425 pruned atom pairs is 0.810 angstroms; (across all 493 pairs:
8.993)  
  
Matchmaker Sch11416_translation.pdb, chain A (#1) with
1661957325368_CPDI_CYM_min.pdb, chain A (#7), sequence alignment score =
1938.3  
RMSD between 425 pruned atom pairs is 0.746 angstroms; (across all 494 pairs:
8.066)  
  
Matchmaker Sch11416_translation.pdb, chain A (#1) with
1661957501908_CPDI_CYM_min.pdb, chain A (#8), sequence alignment score =
2593.5  
RMSD between 495 pruned atom pairs is 0.054 angstroms; (across all 495 pairs:
0.054)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #6/A

Alignment identifier is 6/A  

> show #!6 models

Drag select of 18 residues  

> select clear

> select #6/A:367@CG1

1 atom, 1 residue, 1 model selected  

> select clear

> ui tool show "Modeller Comparative"

> modeller comparative 6/A:1 7/A:1 8/A:1 numModels 5 fast false multichain
> true hetPreserve false hydrogens false waterPreserve false

No Modeller license key provided. Get a license key by registering at the
Modeller web site.  

> modeller comparative 6/A:1 7/A:1 8/A:1 numModels 5 fast false multichain
> true hetPreserve false hydrogens false waterPreserve false

Webservices job id: QIP8GEFQYZZ8QDFM  
Modeller job ID QIP8GEFQYZZ8QDFM finished  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1661950111791_CPDI_CYM_min.pdb, chain A (#6) with target, chain A
(#), sequence alignment score = 2597.9  
RMSD between 487 pruned atom pairs is 0.259 angstroms; (across all 500 pairs:
1.275)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1661950111791_CPDI_CYM_min.pdb, chain A (#6) with target, chain A
(#), sequence alignment score = 2583.5  
RMSD between 493 pruned atom pairs is 0.287 angstroms; (across all 500 pairs:
0.956)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1661950111791_CPDI_CYM_min.pdb, chain A (#6) with target, chain A
(#), sequence alignment score = 2587.1  
RMSD between 483 pruned atom pairs is 0.212 angstroms; (across all 500 pairs:
1.380)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1661950111791_CPDI_CYM_min.pdb, chain A (#6) with target, chain A
(#), sequence alignment score = 2588.3  
RMSD between 483 pruned atom pairs is 0.214 angstroms; (across all 500 pairs:
1.263)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1661950111791_CPDI_CYM_min.pdb, chain A (#6) with target, chain A
(#), sequence alignment score = 2594.3  
RMSD between 480 pruned atom pairs is 0.291 angstroms; (across all 500 pairs:
2.783)  
  
Associated target chain A to chain A with 0 mismatches  
[Repeated 4 time(s)]Associated target chain A to chain A with 204 mismatches
and/or gaps  
[Repeated 4 time(s)]Associated target chain A to chain A with 203 mismatches
and/or gaps  
[Repeated 4 time(s)] Chain information for target  
---  
Chain | Description  
9.1/A 9.2/A 9.3/A 9.4/A 9.5/A | No description available  
  

> select #9.5/A:1-500

4001 atoms, 4099 bonds, 500 residues, 1 model selected  

> select #9.1/A:1-500

4001 atoms, 4099 bonds, 500 residues, 1 model selected  

> open
> D:/科研文件/约克大学实验/P450实验/蛋白结构预测/11416_C5/rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb

Chain information for
rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #10  
---  
Chain | Description  
A | No description available  
  

> select #10/A:1-495

8003 atoms, 7761 bonds, 495 residues, 1 model selected  

> hide #9.4 models

> hide #!9 models

> hide #!8 models

> hide #!7 models

> hide #!6 models

> show #9.3 models

> hide #9.3 models

> color #9.3 #00007f transparency 0

> color #9.2 #aa007f transparency 0

> show #9.1 models

> show #9.2 models

> hide #!10 models

> hide #9.2 models

> hide #!9 models

> hide #9.1 models

> show #!10 models

> select clear

> open
> D:/科研文件/约克大学实验/P450实验/蛋白结构预测/11416_C5/rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb

Chain information for
rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #11  
---  
Chain | Description  
A | No description available  
  

> hide #!10 models

> show #!10 models

> hide #!10 models

> hide #!11 models

> show #!10 models

> show #!6 models

> hide #!10 models

> show #!4 models

> show #!10 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #!10 models

> show #!4 models

> select #4/A:135@CG

1 atom, 1 residue, 1 model selected  

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain #4/A

Alignment identifier is 4/A  

> select #4/A:433

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select #4/A:433-439

111 atoms, 106 bonds, 7 residues, 1 model selected  

> open
> D:/科研文件/约克大学实验/P450实验/蛋白结构预测/11416_C5/rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb

Chain information for
rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12  
---  
Chain | Description  
A | No description available  
  

> hide #!6 models

> color #10 #ffff7f transparency 0

> color #12 #55ff7f transparency 0

> color #12 #ffaa7f transparency 0

> hide #!4 models

> show #!11 models

> show #!10 models

> hide #!12 models

> hide #!11 models

> hide #!10 models

> ui tool show "Show Sequence Viewer"

> sequence chain #10/A

Alignment identifier is 10/A  

> sequence chain #11/A

Alignment identifier is 11/A  

> sequence chain #12/A

Alignment identifier is 12/A  

> show #!10 models

> show #!11 models

> show #!12 models

> hide #!10 models

> show #!10 models

> hide #!11 models

> show #!11 models

> hide #!12 models

> show #!12 models

> hide #!11 models

> show #!11 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> select clear

> select #10/A:297@CB

1 atom, 1 residue, 1 model selected  

> open D:/科研文件/约克大学实验/P450实验/蛋白结构预测/11416_C5/1661957501908_CPDI_CYM_min.pdb

Summary of feedback from opening
D:/科研文件/约克大学实验/P450实验/蛋白结构预测/11416_C5/1661957501908_CPDI_CYM_min.pdb  
---  
warnings | Ignored bad PDB record found on line 8171  
Grid_score -73  
  
Ignored bad PDB record found on line 8172  
Transform_accept_ratio 0.1625  
  
Ignored bad PDB record found on line 8173  
classic_grid_F -73  
  
Ignored bad PDB record found on line 8174  
dslf_fa13 -1.21552  
  
Ignored bad PDB record found on line 8175  
fa_atr -3015.76  
  
544 messages similar to the above omitted  
  
Chain information for 1661957501908_CPDI_CYM_min.pdb #13  
---  
Chain | Description  
A | No description available  
  

> hide #!10 models

> hide #!11 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> show #!11 models

> show #!12 models

> hide #!13 models

> select clear

> hide #10-12 target a

> select ligand

752 atoms, 788 bonds, 13 residues, 9 models selected  

> show (#!10-12 & sel) target ab

> select ::name="HEM"

666 atoms, 684 bonds, 45 pseudobonds, 9 residues, 18 models selected  

> show (#!10-12 & sel) target ab

> select clear

> hide #!10 models

> hide #!11 models

> select add #12/A:301

15 atoms, 21 bonds, 1 residue, 1 model selected  

> select subtract #12/A:301

8 bonds, 1 model selected  

> select add #12/A:497@H3

1 atom, 12 bonds, 1 residue, 1 model selected  

> select add #12/A:497@C10

2 atoms, 14 bonds, 1 residue, 1 model selected  

> select add #12/A:497@C8

3 atoms, 16 bonds, 1 residue, 1 model selected  

> select add #12/A:497@H13

4 atoms, 22 bonds, 1 residue, 1 model selected  

> select add #12/A:497@H6

5 atoms, 23 bonds, 1 residue, 1 model selected  

> select add #12/A:497@H8

6 atoms, 23 bonds, 1 residue, 1 model selected  

> select add #12/A:497@H10

7 atoms, 23 bonds, 1 residue, 1 model selected  

> select add #12/A:497@H11

8 atoms, 23 bonds, 1 residue, 1 model selected  

> select add #12/A:497@H4

9 atoms, 23 bonds, 1 residue, 1 model selected  

> select add #12/A:497@H1

10 atoms, 24 bonds, 1 residue, 1 model selected  

> name frozen ligand sel

"ligand" is reserved and cannot be redefined  

> name frozen limonene sel

[Repeated 2 time(s)]

> select sel :< 5

1241 atoms, 1218 bonds, 20 pseudobonds, 58 residues, 8 models selected  

> show (#!12 & sel) target ab

> view sel

> select limonene

10 atoms, 24 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel reveal true

129 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners  

0 hydrogen bonds found  

> ui tool show H-Bonds

> hbonds sel reveal true

129 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners  

0 hydrogen bonds found  

> hbonds sel reveal true

129 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners  

0 hydrogen bonds found  

> ui tool show H-Bonds

> hbonds sel reveal true log true

129 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners  

    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 Sch11416_translation.pdb
    	2 Sch15640_translation.pdb
    	3 Sch28415_translation.pdb
    	4 rot-1661950111791_CPDI_CYM_min_1661950173467_docked_1_addH.pdb
    	5 1661950111791_CPDI_CYM_min.pdb
    	6 1661950111791_CPDI_CYM_min.pdb
    	7 1661957325368_CPDI_CYM_min.pdb
    	8 1661957501908_CPDI_CYM_min.pdb
    	9.1 target
    	9.2 target
    	9.3 target
    	9.4 target
    	9.5 target
    	10 rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb
    	11 rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb
    	12 rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb
    	13 1661957501908_CPDI_CYM_min.pdb
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  

> cartoon hide sel

[Repeated 1 time(s)]

> select limonene

10 atoms, 24 bonds, 1 residue, 1 model selected  

> hide sel target ab

> show sel target ab

> surface hidePatches sel

> cartoon hide sel

> hbonds sel reveal true

129 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners  

0 hydrogen bonds found  

> hide sel target ab

> show sel target ab

> select #12/A:177

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select clear

> hide #12,14 target a

> select limonene

10 atoms, 24 bonds, 1 residue, 1 model selected  

> select sel :< 5

1241 atoms, 1218 bonds, 20 pseudobonds, 58 residues, 8 models selected  

> select sel :< 5

6994 atoms, 6826 bonds, 24 pseudobonds, 431 residues, 8 models selected  

> select clear

> select limonene

10 atoms, 24 bonds, 1 residue, 1 model selected  

> show sel target ab

> select sel :< 5

1241 atoms, 1218 bonds, 20 pseudobonds, 58 residues, 8 models selected  

> show (#!12 & sel) target ab

> view sel

[Repeated 1 time(s)]

> select limonene

10 atoms, 24 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel reveal true log true

129 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners  

    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 Sch11416_translation.pdb
    	2 Sch15640_translation.pdb
    	3 Sch28415_translation.pdb
    	4 rot-1661950111791_CPDI_CYM_min_1661950173467_docked_1_addH.pdb
    	5 1661950111791_CPDI_CYM_min.pdb
    	6 1661950111791_CPDI_CYM_min.pdb
    	7 1661957325368_CPDI_CYM_min.pdb
    	8 1661957501908_CPDI_CYM_min.pdb
    	9.1 target
    	9.2 target
    	9.3 target
    	9.4 target
    	9.5 target
    	10 rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb
    	11 rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb
    	12 rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb
    	13 1661957501908_CPDI_CYM_min.pdb
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  

> hide #14 models

> select subtract #14

10 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #14

10 atoms, 24 bonds, 1 residue, 1 model selected  

> show #14 models

> select #12/A:69-74,77-82,365-369,374-376,379-381,386-390,457-460,489-492

624 atoms, 604 bonds, 36 residues, 1 model selected  

> select clear

> select #12/A:69-74,77-82,365-369,374-376,379-381,386-390,457-460,489-492

624 atoms, 604 bonds, 36 residues, 1 model selected  

> cartoon hide sel

> undo

> select clear

> cartoon hide #12,14

> select limonene

10 atoms, 24 bonds, 1 residue, 1 model selected  

> color sel red

> select clear

[Repeated 1 time(s)]

> select add #12/A:112@HH2

1 atom, 6 bonds, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select #12/A:112@HZ2

1 atom, 1 residue, 1 model selected  

> select clear

[Repeated 3 time(s)]

> select
> #12/A:2-32,47-50,55-66,85-94,106-111,113-115,124-137,140-163,171-193,196-210,215-218,223-228,230-255,266-275,285-316,318-331,340-345,347-359,391-396,409-412,432-434,439-456,462-464,467-469

4808 atoms, 4630 bonds, 290 residues, 1 model selected  

> show #!11 models

> hide #!11 models

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> select clear

> interfaces #!12 & ~solvent

1 buried areas: A F 642  

> set bgColor #ffffff00

> save D:/科研文件/约克大学实验/P450实验/蛋白结构预测/11416_C5/11416_C5_edit0915.cxs

> close #1

> close #2

> close #3

> close #4

> close #5-9,13

> cartoon #12,14

> hide #12,14 target a

> select limonene

10 atoms, 24 bonds, 1 residue, 1 model selected  

> show sel target ab

> color sel black

> color sel dim gray

> cartoon hide sel

> select clear

> cartoon hide #12,14

> cartoon #12,14

> select limonene

10 atoms, 24 bonds, 1 residue, 1 model selected  

> show sel target ab

> ui tool show H-Bonds

> hbonds sel reveal true log true

90 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners  

    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	10 rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb
    	11 rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb
    	12 rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  

> show sel target ab

> select sel :< 5

906 atoms, 891 bonds, 15 pseudobonds, 42 residues, 6 models selected  

> show (#!12 & sel) target ab

> select clear

> cartoon hide #12,14

> select limonene

10 atoms, 24 bonds, 1 residue, 1 model selected  

> color sel magenta

> select clear

> select
> #12/A:2-32,47-50,55-66,85-94,106-111,113-115,124-137,140-163,171-193,196-210,215-218,223-228,230-255,266-275,285-316,318-331,340-345,347-359,391-396,409-412,432-434,439-456,462-464,467-469

4808 atoms, 4630 bonds, 290 residues, 1 model selected  

> select #12/A:363@HE1

1 atom, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select #12/A:102@NH2

1 atom, 1 residue, 1 model selected  

> select #12/A:102@1HH2

1 atom, 1 residue, 1 model selected  

> select clear

Drag select of 210 atoms, 209 bonds  
Drag select of 151 atoms, 144 bonds  

> select clear

Drag select of 101 atoms, 100 bonds  
Drag select of 128 atoms, 127 bonds  

> select clear

Drag select of 302 atoms, 5 pseudobonds, 297 bonds  

> label (#!12 & sel) attribute name

> label height 0.7

> label (#!12 & sel) text "{0.name} {0.number}{0.insertion_code}"

> save D:/科研文件/约克大学实验/P450实验/蛋白结构预测/11416_C5/11416_C5_edit0915.cxs

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!11 models

> select limonene

10 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #11

8113 atoms, 7887 bonds, 6 pseudobonds, 498 residues, 3 models selected  

> select subtract #11

10 atoms, 24 bonds, 1 residue, 1 model selected  

> show target m

> view clip false

> hide #!12 models

> hide #!10 models

> hide #14 models

> select subtract #14

10 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #11

8113 atoms, 7887 bonds, 6 pseudobonds, 498 residues, 3 models selected  

> log metadata #11

No models had metadata

> log chains #11

Chain information for
rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #11  
---  
Chain | Description  
A | No description available  
  

> show #!11 target m

> color #11 #cccccc transparency 0

[Repeated 1 time(s)]

> color #11 #f0f0f0 transparency 0

> color #11 #55aaff transparency 0

> color #11 #ffaaff transparency 0

> color #11 #55ffff transparency 0

> color #11 white transparency 0

> color #11 #aaff7f transparency 0

> color #11 cyan transparency 0

> color #11 #ffaa00 transparency 0

> color #11 #00aaff transparency 0

> color #11 #00557f transparency 0

> color #11 #00007f transparency 0

> color #11 #5500ff transparency 0

> color #11 magenta transparency 0

> color #11 #f0f0f0 transparency 0

> color #11 #55557f transparency 0

> color #11 #ff557f transparency 0

> color #11 #aaff7f transparency 0

> color #11 #aaffff transparency 0

> color #11 #aaaaff transparency 0

> show #!11 target m

> view #11 clip false

> show #!12 models

> hide #!11 models

> close #10-11

> open
> D:/科研文件/约克大学实验/P450实验/蛋白结构预测/11416_C5/rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb
> D:/科研文件/约克大学实验/P450实验/蛋白结构预测/11416_C5/rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb

Chain information for
rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for
rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2  
---  
Chain | Description  
A | No description available  
  

> hide #!1 models

> hide #!2 models

> hide #!12 models

> show #!2 models

> hide #2 target ab

> select ligand

294 atoms, 306 bonds, 6 residues, 3 models selected  

> select limonene

10 atoms, 24 bonds, 1 residue, 1 model selected  

> show #2 target ab

> hide #2 target ab

> select ligand

294 atoms, 306 bonds, 6 residues, 3 models selected  

> show (#!2 & sel) target ab

> color (#!2 & sel) red

> color (#!2 & sel) orange

> select clear

[Repeated 1 time(s)]

> select add #2/A:497@H13

1 atom, 6 bonds, 1 residue, 1 model selected  

> select add #2/A:497@H1

2 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #2/A:497@C3

3 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #2/A:497@H6

4 atoms, 14 bonds, 1 residue, 1 model selected  

> select add #2/A:497@H3

5 atoms, 19 bonds, 1 residue, 1 model selected  

> select add #2/A:497@H9

6 atoms, 19 bonds, 1 residue, 1 model selected  

> select add #2/A:497@C2

7 atoms, 20 bonds, 1 residue, 1 model selected  

> name frozen limonene sel

> select limonene

7 atoms, 23 bonds, 1 residue, 1 model selected  

> select ligand

294 atoms, 306 bonds, 6 residues, 3 models selected  

> show (#!2 & sel) target ab

> select ::name="HEM"

222 atoms, 228 bonds, 15 pseudobonds, 3 residues, 6 models selected  

> select clear

> select ::name="HEM"

222 atoms, 228 bonds, 15 pseudobonds, 3 residues, 6 models selected  

> select clear

> show #2 target ab

> select clear

> hide #2 target a

> select limonene

7 atoms, 23 bonds, 1 residue, 1 model selected  

> select ligand

294 atoms, 306 bonds, 6 residues, 3 models selected  

> show (#!2 & sel) target ab

> select clear

> name frozen limonene sel

nothing is selected by specifier  

> name frozen limonene1 sel

nothing is selected by specifier  

> select add #2/A:497@H7

1 atom, 13 bonds, 1 residue, 1 model selected  

> select add #2/A:497@H4

2 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #2/A:497@H16

3 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #2/A:497@H15

4 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #2/A:497@H8

5 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #2/A:497@H9

6 atoms, 21 bonds, 1 residue, 1 model selected  

> select subtract #2/A:497@H7

5 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #2/A:497@H7

6 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #2/A:497@H2

7 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #2/A:497@H13

8 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #2/A:497@H1

9 atoms, 22 bonds, 1 residue, 1 model selected  

> select subtract #2/A:497@H13

8 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #2/A:497@H13

9 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #2/A:497@H14

10 atoms, 22 bonds, 1 residue, 1 model selected  

> select subtract #2/A:497@H2

9 atoms, 22 bonds, 1 residue, 1 model selected  

> select add #2/A:497@H6

10 atoms, 21 bonds, 1 residue, 1 model selected  

> set bgColor transparent

> name frozen limonene1 sel

> select sel :< 5

984 atoms, 969 bonds, 15 pseudobonds, 45 residues, 6 models selected  

> ui tool show H-Bonds

> hbonds sel reveal true log true

90 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners  

    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	12 rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb
    	1 rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb
    	2 rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb
    
    162 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A TRP 112 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A SER 108 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A TRP 112 H      2.864  1.909
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A TRP 112 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A SER 108 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A TRP 112 H      2.864  1.909
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A TRP 112 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A SER 108 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A TRP 112 H      2.864  1.909
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A TRP 112 NE1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ASP 294 OD1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A TRP 112 HE1    2.952  1.998
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A TRP 112 NE1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ASP 294 OD1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A TRP 112 HE1    2.952  1.998
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A TRP 112 NE1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ASP 294 OD1  rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A TRP 112 HE1    2.952  1.998
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A LYS 115 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A TRP 112 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A LYS 115 H      2.804  1.947
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A LYS 115 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A TRP 112 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A LYS 115 H      2.804  1.947
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A LYS 115 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A TRP 112 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A LYS 115 H      2.804  1.947
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A PHE 119 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ASP 117 OD1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A PHE 119 H      2.853  1.858
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A PHE 119 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ASP 117 OD1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A PHE 119 H      2.853  1.858
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A PHE 119 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ASP 117 OD1  rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A PHE 119 H      2.853  1.858
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A VAL 203 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A LEU 199 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A VAL 203 H      2.936  2.035
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A VAL 203 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A LEU 199 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A VAL 203 H      2.936  2.035
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A VAL 203 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A LEU 199 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A VAL 203 H      2.936  2.035
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A LEU 207 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A VAL 203 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A LEU 207 H      2.795  1.795
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A LEU 207 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A VAL 203 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A LEU 207 H      2.795  1.795
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A LEU 207 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A VAL 203 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A LEU 207 H      2.795  1.795
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 210 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A LEU 207 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 210 H      3.389  2.576
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 210 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A LEU 207 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 210 H      3.389  2.576
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 210 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A LEU 207 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 210 H      3.389  2.576
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A PHE 293 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ASN 289 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A PHE 293 H      2.942  1.941
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A PHE 293 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ASN 289 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A PHE 293 H      2.942  1.941
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A PHE 293 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ASN 289 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A PHE 293 H      2.942  1.941
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ASP 294 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A GLY 290 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ASP 294 H      2.861  1.863
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ASP 294 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A GLY 290 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ASP 294 H      2.861  1.863
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ASP 294 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A GLY 290 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ASP 294 H      2.861  1.863
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 295 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A PHE 291 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 295 H      2.901  1.922
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 295 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A PHE 291 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 295 H      2.901  1.922
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 295 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A PHE 291 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 295 H      2.901  1.922
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 295 OG1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A PHE 291 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 295 HG1    2.755  1.826
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 295 OG1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A PHE 291 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 295 HG1    2.755  1.826
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 295 OG1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A PHE 291 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 295 HG1    2.755  1.826
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A SER 297 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A PHE 293 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A SER 297 H      2.964  1.985
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A SER 297 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A PHE 293 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A SER 297 H      2.964  1.985
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A SER 297 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A PHE 293 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A SER 297 H      2.964  1.985
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ALA 298 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ASP 294 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ALA 298 H      2.851  1.842
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ALA 298 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ASP 294 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ALA 298 H      2.851  1.842
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ALA 298 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ASP 294 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ALA 298 H      2.851  1.842
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A GLY 299 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 295 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A GLY 299 H      2.964  1.994
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A GLY 299 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 295 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A GLY 299 H      2.964  1.994
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A GLY 299 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 295 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A GLY 299 H      2.964  1.994
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 300 OG1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A SER 297 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 300 HG1    3.375  2.815
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 300 OG1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A SER 297 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 300 HG1    3.375  2.815
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 300 OG1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A SER 297 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 300 HG1    3.375  2.815
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 302 OG1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ALA 298 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 302 HG1    2.681  1.722
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 302 OG1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ALA 298 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 302 HG1    2.681  1.722
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 302 OG1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ALA 298 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 302 HG1    2.681  1.722
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ARG 434 NH1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ILE 118 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ARG 434 2HH1   3.566  2.870
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ARG 434 NH1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ILE 118 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ARG 434 2HH1   3.566  2.870
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ARG 434 NH1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ILE 118 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ARG 434 2HH1   3.566  2.870
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A CYM 436 SG    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/F HEM 496 NC    no hydrogen                                                                        3.160  N/A
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A CYM 436 SG    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/F HEM 496 NC    no hydrogen                                                                        3.160  N/A
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A CYM 436 SG    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/F HEM 496 NC   no hydrogen                                                                        3.160  N/A
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A TRP 112 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A SER 108 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A TRP 112 H      2.864  1.909
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A TRP 112 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A SER 108 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A TRP 112 H      2.864  1.909
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A TRP 112 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A SER 108 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A TRP 112 H      2.864  1.909
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A TRP 112 NE1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ASP 294 OD1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A TRP 112 HE1    2.952  1.998
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A TRP 112 NE1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ASP 294 OD1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A TRP 112 HE1    2.952  1.998
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A TRP 112 NE1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ASP 294 OD1  rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A TRP 112 HE1    2.952  1.998
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A LYS 115 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A TRP 112 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A LYS 115 H      2.804  1.947
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A LYS 115 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A TRP 112 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A LYS 115 H      2.804  1.947
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A LYS 115 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A TRP 112 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A LYS 115 H      2.804  1.947
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A PHE 119 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ASP 117 OD1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A PHE 119 H      2.853  1.858
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A PHE 119 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ASP 117 OD1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A PHE 119 H      2.853  1.858
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A PHE 119 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ASP 117 OD1  rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A PHE 119 H      2.853  1.858
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A VAL 203 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A LEU 199 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A VAL 203 H      2.936  2.035
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A VAL 203 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A LEU 199 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A VAL 203 H      2.936  2.035
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A VAL 203 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A LEU 199 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A VAL 203 H      2.936  2.035
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A LEU 207 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A VAL 203 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A LEU 207 H      2.795  1.795
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A LEU 207 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A VAL 203 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A LEU 207 H      2.795  1.795
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A LEU 207 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A VAL 203 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A LEU 207 H      2.795  1.795
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 210 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A LEU 207 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 210 H      3.389  2.576
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 210 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A LEU 207 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 210 H      3.389  2.576
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 210 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A LEU 207 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 210 H      3.389  2.576
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A PHE 293 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ASN 289 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A PHE 293 H      2.942  1.941
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A PHE 293 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ASN 289 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A PHE 293 H      2.942  1.941
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A PHE 293 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ASN 289 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A PHE 293 H      2.942  1.941
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ASP 294 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A GLY 290 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ASP 294 H      2.861  1.863
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ASP 294 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A GLY 290 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ASP 294 H      2.861  1.863
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ASP 294 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A GLY 290 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ASP 294 H      2.861  1.863
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 295 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A PHE 291 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 295 H      2.901  1.922
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 295 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A PHE 291 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 295 H      2.901  1.922
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 295 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A PHE 291 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 295 H      2.901  1.922
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 295 OG1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A PHE 291 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 295 HG1    2.755  1.826
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 295 OG1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A PHE 291 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 295 HG1    2.755  1.826
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 295 OG1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A PHE 291 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 295 HG1    2.755  1.826
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A SER 297 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A PHE 293 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A SER 297 H      2.964  1.985
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A SER 297 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A PHE 293 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A SER 297 H      2.964  1.985
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A SER 297 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A PHE 293 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A SER 297 H      2.964  1.985
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ALA 298 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ASP 294 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ALA 298 H      2.851  1.842
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ALA 298 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ASP 294 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ALA 298 H      2.851  1.842
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ALA 298 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ASP 294 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ALA 298 H      2.851  1.842
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A GLY 299 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 295 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A GLY 299 H      2.964  1.994
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A GLY 299 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 295 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A GLY 299 H      2.964  1.994
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A GLY 299 N     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 295 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A GLY 299 H      2.964  1.994
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 300 OG1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A SER 297 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 300 HG1    3.375  2.815
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 300 OG1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A SER 297 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 300 HG1    3.375  2.815
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 300 OG1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A SER 297 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 300 HG1    3.375  2.815
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 302 OG1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ALA 298 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 302 HG1    2.681  1.722
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 302 OG1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ALA 298 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 302 HG1    2.681  1.722
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 302 OG1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ALA 298 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 302 HG1    2.681  1.722
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ARG 434 NH1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ILE 118 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ARG 434 2HH1   3.566  2.870
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ARG 434 NH1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ILE 118 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ARG 434 2HH1   3.566  2.870
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ARG 434 NH1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ILE 118 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ARG 434 2HH1   3.566  2.870
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A CYM 436 SG    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/F HEM 496 NC    no hydrogen                                                                        3.160  N/A
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A CYM 436 SG    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/F HEM 496 NC    no hydrogen                                                                        3.160  N/A
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A CYM 436 SG    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/F HEM 496 NC   no hydrogen                                                                        3.160  N/A
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A TRP 112 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A SER 108 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A TRP 112 H     2.864  1.909
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A TRP 112 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A SER 108 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A TRP 112 H     2.864  1.909
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A TRP 112 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A SER 108 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A TRP 112 H     2.864  1.909
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A TRP 112 NE1  rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ASP 294 OD1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A TRP 112 HE1   2.952  1.998
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A TRP 112 NE1  rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ASP 294 OD1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A TRP 112 HE1   2.952  1.998
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A TRP 112 NE1  rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ASP 294 OD1  rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A TRP 112 HE1   2.952  1.998
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A LYS 115 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A TRP 112 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A LYS 115 H     2.804  1.947
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A LYS 115 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A TRP 112 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A LYS 115 H     2.804  1.947
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A LYS 115 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A TRP 112 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A LYS 115 H     2.804  1.947
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A PHE 119 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ASP 117 OD1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A PHE 119 H     2.853  1.858
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A PHE 119 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ASP 117 OD1   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A PHE 119 H     2.853  1.858
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A PHE 119 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ASP 117 OD1  rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A PHE 119 H     2.853  1.858
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A VAL 203 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A LEU 199 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A VAL 203 H     2.936  2.035
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A VAL 203 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A LEU 199 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A VAL 203 H     2.936  2.035
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A VAL 203 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A LEU 199 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A VAL 203 H     2.936  2.035
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A LEU 207 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A VAL 203 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A LEU 207 H     2.795  1.795
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A LEU 207 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A VAL 203 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A LEU 207 H     2.795  1.795
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A LEU 207 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A VAL 203 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A LEU 207 H     2.795  1.795
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 210 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A LEU 207 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 210 H     3.389  2.576
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 210 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A LEU 207 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 210 H     3.389  2.576
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 210 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A LEU 207 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 210 H     3.389  2.576
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A PHE 293 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ASN 289 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A PHE 293 H     2.942  1.941
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A PHE 293 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ASN 289 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A PHE 293 H     2.942  1.941
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A PHE 293 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ASN 289 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A PHE 293 H     2.942  1.941
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ASP 294 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A GLY 290 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ASP 294 H     2.861  1.863
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ASP 294 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A GLY 290 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ASP 294 H     2.861  1.863
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ASP 294 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A GLY 290 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ASP 294 H     2.861  1.863
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 295 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A PHE 291 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 295 H     2.901  1.922
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 295 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A PHE 291 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 295 H     2.901  1.922
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 295 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A PHE 291 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 295 H     2.901  1.922
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 295 OG1  rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A PHE 291 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 295 HG1   2.755  1.826
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 295 OG1  rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A PHE 291 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 295 HG1   2.755  1.826
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 295 OG1  rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A PHE 291 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 295 HG1   2.755  1.826
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A SER 297 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A PHE 293 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A SER 297 H     2.964  1.985
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A SER 297 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A PHE 293 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A SER 297 H     2.964  1.985
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A SER 297 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A PHE 293 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A SER 297 H     2.964  1.985
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ALA 298 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ASP 294 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ALA 298 H     2.851  1.842
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ALA 298 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ASP 294 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ALA 298 H     2.851  1.842
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ALA 298 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ASP 294 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ALA 298 H     2.851  1.842
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A GLY 299 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A THR 295 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A GLY 299 H     2.964  1.994
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A GLY 299 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A THR 295 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A GLY 299 H     2.964  1.994
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A GLY 299 N    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 295 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A GLY 299 H     2.964  1.994
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 300 OG1  rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A SER 297 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 300 HG1   3.375  2.815
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 300 OG1  rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A SER 297 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 300 HG1   3.375  2.815
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 300 OG1  rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A SER 297 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 300 HG1   3.375  2.815
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 302 OG1  rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ALA 298 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 302 HG1   2.681  1.722
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 302 OG1  rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ALA 298 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 302 HG1   2.681  1.722
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 302 OG1  rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ALA 298 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A THR 302 HG1   2.681  1.722
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ARG 434 NH1  rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/A ILE 118 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ARG 434 2HH1  3.566  2.870
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ARG 434 NH1  rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/A ILE 118 O     rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ARG 434 2HH1  3.566  2.870
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ARG 434 NH1  rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ILE 118 O    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A ARG 434 2HH1  3.566  2.870
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A CYM 436 SG   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_5_addH.pdb #1/F HEM 496 NC    no hydrogen                                                                        3.160  N/A
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A CYM 436 SG   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_6_addH.pdb #2/F HEM 496 NC    no hydrogen                                                                        3.160  N/A
    rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/A CYM 436 SG   rot-1661957501908_CPDI_CYM_min_1661957511828_docked_8_addH.pdb #12/F HEM 496 NC   no hydrogen                                                                        3.160  N/A
    

  
162 hydrogen bonds found  

> cartoon hide (#!2 & sel)

> select clear

> cartoon hide #2

Drag select of 294 atoms, 282 bonds  

> select add #2

8103 atoms, 7863 bonds, 24 pseudobonds, 497 residues, 3 models selected  

> select subtract #2

Nothing selected  

> select add #2

8103 atoms, 7863 bonds, 24 pseudobonds, 497 residues, 3 models selected  

> view sel

[Repeated 1 time(s)]

> show #!12 models

> hide #!2 models

Drag select of 418 atoms, 6 pseudobonds, 400 bonds  

> select clear

> select add #12

8103 atoms, 7863 bonds, 24 pseudobonds, 497 residues, 4 models selected  

> select subtract #12

Nothing selected  

> show #14 models

> open D:/科研文件/约克大学实验/P450实验/蛋白结构预测/11416_C5/11416_C5_edit0915.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 697, in restore  
self.reset()  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\tasks.py", line 547, in reset_state  
task.terminate()  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\tasks.py", line 155, in terminate  
self.session.tasks.remove(self)  
AttributeError: 'Tasks' object has no attribute 'remove'  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 697, in restore  
self.reset()  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\tasks.py", line 547, in reset_state  
task.terminate()  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\tasks.py", line 155, in terminate  
self.session.tasks.remove(self)  
AttributeError: 'Tasks' object has no attribute 'remove'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 458, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 1001, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 739, in restore  
self.reset()  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\tasks.py", line 547, in reset_state  
task.terminate()  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\tasks.py", line 155, in terminate  
self.session.tasks.remove(self)  
AttributeError: 'Tasks' object has no attribute 'remove'  
  
AttributeError: 'Tasks' object has no attribute 'remove'  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\tasks.py", line 155, in terminate  
self.session.tasks.remove(self)  
  
See log for complete Python traceback.  
  

> hide #!12 models

> hide #14 models

> open D:/科研文件/约克大学实验/P450实验/蛋白结构预测/11416_C5/11416_C5_edit0915.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 697, in restore  
self.reset()  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\tasks.py", line 547, in reset_state  
task.terminate()  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\tasks.py", line 155, in terminate  
self.session.tasks.remove(self)  
AttributeError: 'Tasks' object has no attribute 'remove'  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 697, in restore  
self.reset()  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\tasks.py", line 547, in reset_state  
task.terminate()  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\tasks.py", line 155, in terminate  
self.session.tasks.remove(self)  
AttributeError: 'Tasks' object has no attribute 'remove'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 458, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 1001, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 739, in restore  
self.reset()  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\tasks.py", line 547, in reset_state  
task.terminate()  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\tasks.py", line 155, in terminate  
self.session.tasks.remove(self)  
AttributeError: 'Tasks' object has no attribute 'remove'  
  
AttributeError: 'Tasks' object has no attribute 'remove'  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\tasks.py", line 155, in terminate  
self.session.tasks.remove(self)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 512.92
OpenGL renderer: NVIDIA GeForce MX330/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: LENOVO
Model: 20S0A0JXCD
OS: Microsoft Windows 10 专业版 (Build 19043)
Memory: 34,098,466,816
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-10510U CPU @ 1.80GHz
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pywin32: 303
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 3 years ago

Component:	Unassigned → Sessions
Milestone:	→ 1.5
Owner:	set to Zach Pearson
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Session reset/restore: 'Tasks' object has no attribute 'remove'

comment:2 by Zach Pearson, 3 years ago

Resolution:	→ fixed
Status:	assigned → closed

Should be fixed by this commit.

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