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Opened 3 years ago

Last modified 3 years ago

#7325 closed defect

ChimeraX bug report submission — at Initial Version

Reported by:	chimerax-bug-report@…	Owned by:
Priority:	normal	Milestone:
Component:	Surface	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: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open
> C:\\\Users\\\jvarg\\\Documents\\\huji\\\fusolisin\\\fusolisin_figure_surface.cxs

registering illegal selector name "interface_res"  

registering illegal selector name "int_res"  

Log from Sun Jul 24 00:35:18 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open C:\Users\jvarg\Documents\huji\fusolisin\fusolisin_figure.cxs format
> session

registering illegal selector name "interface_res"  

registering illegal selector name "int_res"  

Log from Sat Jul 23 20:33:38 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open C:\Users\jvarg\Documents\huji\fusolisin\fusolisin_figure.cxs format
> session

registering illegal selector name "interface_res"  

registering illegal selector name "int_res"  

Log from Tue Jul 12 00:05:22 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open V:\\\projects\\\fusolisin\\\figures\\\fusolisin_figure_v2.cxs

registering illegal selector name "interface_res"  

registering illegal selector name "int_res"  

Log from Mon Jun 13 21:11:39 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open V:/projects/fusolisin/fusolisin_figure_v2.cxs

registering illegal selector name "interface_res"  

registering illegal selector name "int_res"  

Log from Tue Jun 7 11:23:29 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open fusolisin_figure.cxs

registering illegal selector name "interface_res"  

registering illegal selector name "int_res"  

Log from Mon Jun 6 17:29:07 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open fusolisin_figure.cxs

registering illegal selector name "interface_res"  

registering illegal selector name "int_res"  

Log from Mon Jun 6 16:08:31 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open C:\Users\jvarg\Documents\huji\fusolisin_figure.cxs format session

registering illegal selector name "interface_res"  

registering illegal selector name "int_res"  

Log from Sat Jun 4 20:15:09 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open C:\Users\jvarg\Documents\huji\fusolisin_figure.cxs format session

registering illegal selector name "interface_res"  

registering illegal selector name "int_res"  

Log from Thu Jun 2 10:16:36 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/jvarg/Documents/huji/fusolisin.pse

Unrecognized file suffix '.pse'  

> open
> C:/Users/jvarg/Documents/huji/relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb
> C:/Users/jvarg/Documents/huji/relax_short_fusolisin_SQAS_0001_0064_top1.pdb

Chain information for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb #1  
---  
Chain | Description  
D | No description available  
P | No description available  
  
Chain information for relax_short_fusolisin_SQAS_0001_0064_top1.pdb #2  
---  
Chain | Description  
D | No description available  
P | No description available  
  

> hide cartoons

> show cartoons

> color #1 white transparency 0

> select #1/D:77-414

2597 atoms, 2649 bonds, 338 residues, 1 model selected  

> select #1/P:74-79

41 atoms, 40 bonds, 6 residues, 1 model selected  

> style sel stick

Changed 41 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> color sel bychain

> select #2/D:77-414

2597 atoms, 2649 bonds, 338 residues, 1 model selected  

> color sel white

> select #2/P:76-79

27 atoms, 26 bonds, 4 residues, 1 model selected  

> color sel cornflower blue

> color sel medium blue

> color sel byelement

> select #1/P:74-79

41 atoms, 40 bonds, 6 residues, 1 model selected  

> color sel byhetero

> select clear

> color byhetero

> lighting flat

> lighting full

> lighting soft

> set bgColor white

Drag select of 2 atoms, 9 residues, 1 bonds  

> lighting simple

> lighting full

> select clear

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows false

> lighting shadows true

> lighting flat

[Repeated 1 time(s)]

> lighting full

No Surface models open  

> volume planes z style image imageMode "full region"

No volumes specified  

> transparency 50

> volume style surface

No volumes specified  

> select #1/D:77-414

2597 atoms, 2649 bonds, 338 residues, 1 model selected  

> volume style surface

No volumes specified  

> volume hide

No volumes specified  

> open
> C:/Users/jvarg/Documents/huji/relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb

Chain information for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb #3  
---  
Chain | Description  
D | No description available  
P | No description available  
  

> hide #3 models

> select #2/P:76-79

27 atoms, 26 bonds, 4 residues, 1 model selected  

> color sel light sea green

> color sel forest green

> color sel light sea green

> ui tool show "Color Actions"

> color sel teal

> color sel byhetero

> color sel steel blue

> color sel byhetero

Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 0 maps.  

> volume step 1

No volumes specified  

> volume planes z style image imageMode "full region"

No volumes specified  

> ui tool show "Volume Viewer"

> show sel surfaces

> undo

> hide sel surfaces

> select #1/D:77-414

2597 atoms, 2649 bonds, 338 residues, 1 model selected  

> show sel surfaces

> hide sel surfaces

> show sel surfaces

> transparency sel 50

> surface style #1 mesh

> surface style #1 solid

> hide #!2 models

> hide sel surfaces

> select clear

Alignment identifier is 1  
Alignment identifier is 2  
Alignment identifier is 2/P  

> lighting soft

> select #1/P:74-79

41 atoms, 40 bonds, 6 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel gold

> color sel byhetero

> color sel light salmon

> color sel turquoise

> color sel dark turquoise

> color sel byhetero

> color sel orchid

> color sel hot pink

> color sel light green

> color sel pale green

> color sel light green

> color sel light blue

> color sel byhetero

> color sel light sky blue

> color sel sky blue

> color sel byhetero

> select clear

Drag select of 8 residues  

> select clear

[Repeated 1 time(s)]

> select #1/P:77@CD

1 atom, 1 residue, 1 model selected  
Drag select of 4 atoms, 1 residues, 3 bonds  

> select clear

Drag select of 2 atoms, 2 residues, 2 bonds  

> select #1/D:239@CG

1 atom, 1 residue, 1 model selected  

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 2 models selected  

> style sel sphere

Changed 8 atom styles  

> style sel sphere

Changed 8 atom styles  

> style sel stick

Changed 8 atom styles  

> ui tool show "Color Actions"

> color sel gold

> color sel byhetero

> select #1/D:344@CB

1 atom, 1 residue, 1 model selected  

> select up

6 atoms, 5 bonds, 1 residue, 2 models selected  

> color sel gold

[Repeated 1 time(s)]

> color sel byhetero

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

10 atoms, 10 bonds, 1 residue, 2 models selected  

> color sel gold

> color sel byhetero

> select clear

> hbonds

3108 hydrogen bonds found  

> hide #4 models

> select chain D

Expected an objects specifier or a keyword  

> select D

Nothing selected  

> select chain_ID=D

Expected an objects specifier or a keyword  

> select chain_ID="D"

Expected an objects specifier or a keyword  

> select #1/D:77-414

2597 atoms, 2649 bonds, 339 pseudobonds, 338 residues, 2 models selected  

> select chain_ID="D"

Expected an objects specifier or a keyword  

> select :.A

Expected an objects specifier or a keyword  

> select :.D

Expected an objects specifier or a keyword  

> select :D

Nothing selected  

> select :.D

Expected an objects specifier or a keyword  

> select :.P

Expected an objects specifier or a keyword  

> select :.D

Expected an objects specifier or a keyword  

> log metadata #1

No models had metadata

> log chains #1

Chain information for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb #1  
---  
Chain | Description  
D | No description available  
P | No description available  
  

> select #1

2638 atoms, 2689 bonds, 353 pseudobonds, 344 residues, 2 models selected  

> select #2

2624 atoms, 2675 bonds, 350 pseudobonds, 342 residues, 2 models selected  

> select #3

2638 atoms, 2689 bonds, 353 pseudobonds, 344 residues, 2 models selected  

> select #4

3108 pseudobonds, 1 model selected  

> select #1

2638 atoms, 2689 bonds, 353 pseudobonds, 344 residues, 2 models selected  

> select #1:D

Nothing selected  

> select #1:.D

Expected an objects specifier or a keyword  

> hbonds #1

1732 hydrogen bonds found  

> show #4 models

> hide #4 models

> toolshed show

> ui tool show H-Bonds

> select #1/D

2597 atoms, 2649 bonds, 339 pseudobonds, 338 residues, 2 models selected  

> hbonds sel color #aaff7f restrict cross reveal true

1366 hydrogen bonds found  

> undo

Undo failed, probably because structures have been modified.  

> hide sel atoms

Drag select of 1 atoms, 2 residues  

> select #1/D:122

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

> style sel stick

Changed 10 atom styles  

> show sel atoms

> select #1/D:344

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

> select up

34 atoms, 34 bonds, 5 residues, 2 models selected  

> select up

2597 atoms, 2649 bonds, 338 residues, 2 models selected  

> select down

34 atoms, 34 bonds, 5 residues, 2 models selected  

> select down

6 atoms, 5 bonds, 1 residue, 2 models selected  

> show sel atoms

> select #1/D:239

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

> show sel atoms

> interfaces

15 buried areas: #3/D #2/D 7468, #2/D #1/D 7468, #3/D #1/D 7400, #3/D #3/P
538, #3/D #1/P 538, #1/D #3/P 538, #1/D #1/P 538, #2/D #3/P 529, #2/D #1/P
529, #3/P #1/P 436, #2/D #2/P 393, #3/D #2/P 391, #1/D #2/P 391, #3/P #2/P
300, #1/P #2/P 300  

> hbonds #1/D #1/P

1732 hydrogen bonds found  

> show #4 models

> hide #4 models

> interfaces select #1/D contacting #1/P

12 contacting residues  

> show sel atoms

> name

Missing or invalid "name" argument: Expected a text string  

> name interface_res sel

registering illegal selector name "interface_res"  

> name int_res interfaces select #1/D contacting #1/P

"interfaces select #1/D contacting #1/P": invalid atom specifier  

> select

7900 atoms, 8053 bonds, 1732 pseudobonds, 1030 residues, 4 models selected  

> interfaces select #1/D contacting #1/P

12 contacting residues  

> name frozen int_res

Missing or invalid "objects" argument: empty atom specifier  

> name frozen int_res sel

registering illegal selector name "int_res"  

> int_res

Unknown command: int_res  

> select int_res

Expected an objects specifier or a keyword  

> name frozen int_res sel

registering illegal selector name "int_res"  

> name frozen intres sel

> save C:/Users/jvarg/Documents/huji/fusolisin_figure.cxs

——— End of log from Thu Jun 2 10:16:36 2022 ———

opened ChimeraX session  

> name frozen intres sel

> ui tool show H-Bonds

> hbonds sel color #00aaff restrict both

0 hydrogen bonds found  

> select #1/D:211

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

> select intres

92 atoms, 89 bonds, 12 residues, 1 model selected  

> ui mousemode right select

> select #1/D:211@CG

1 atom, 1 residue, 1 model selected  

> select #1/D:211@CA

1 atom, 1 residue, 1 model selected  

> select #1/D:211

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

> select clear

> select #1/P:74

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

> select #1/P:76

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

> select #1/P:78

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

> select #1/P:74

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

> select up

41 atoms, 40 bonds, 6 residues, 1 model selected  

> select add #1/P:74@CA

1 atom, 1 bond, 1 residue, 1 model selected  

> select up

3 atoms, 1 bond, 2 residues, 1 model selected  

> select up

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select up

205 atoms, 204 bonds, 30 residues, 2 models selected  

> select down

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select add #1/P:76

22 atoms, 19 bonds, 3 residues, 2 models selected  

> select subtract #1/D:239

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select add #1/P:75

20 atoms, 17 bonds, 3 residues, 1 model selected  

> select add #1/P:78

25 atoms, 21 bonds, 4 residues, 1 model selected  

> select add #1/P:77

34 atoms, 29 bonds, 5 residues, 1 model selected  

> select add #1/P:79

41 atoms, 35 bonds, 6 residues, 1 model selected  

> select add #1/D:239@CG

42 atoms, 35 bonds, 7 residues, 1 model selected  

> select intres

92 atoms, 89 bonds, 12 residues, 1 model selected  

> select subtract #1/D:211

78 atoms, 74 bonds, 11 residues, 2 models selected  

> hbonds sel color #00aaff restrict cross

73 hydrogen bonds found  

> hbonds sel color #00aaff restrict cross

73 hydrogen bonds found  

> hbonds sel color #00aaff restrict cross

73 hydrogen bonds found  

> show #4 models

> select #1/D:211

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

> hide sel atoms

> select clear

> select #1/D:147

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

> select #1/P:74

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

> select up

41 atoms, 40 bonds, 6 residues, 1 model selected  

> color sel hot pink

> ui tool show "Color Actions"

> color sel moccasin

> color sel dark gray

> color sel medium spring green

> color sel salmon

> color sel byhetero

> color sel cyan

> color sel deep sky blue

> color sel thistle

> color sel light goldenrod yellow

> color sel byhetero

> color sel orchid

> color sel byhetero

Drag select of 12 residues, 1 pseudobonds  

> select #1/P:74

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

> select up

41 atoms, 40 bonds, 6 residues, 1 model selected  

> ui mousemode right translate

> color sel indian red

> color sel yellow green

> color sel byhetero

> ui mousemode right rotate

> ui mousemode right translate

> color sel pale goldenrod

> color sel byhetero

> color sel azure

> color sel byhetero

> color sel mint cream

> color sel byhetero

> color sel light cyan

> color sel byhetero

> color sel gainsboro

> color sel lavender

> color sel dark turquoise

> color sel byhetero

> color sel cadet blue

> color sel byhetero

> color #4 white models transparency 0

> color #4 #aaff7f models transparency 0

> color #4 #ffaa00 models transparency 0

> color #4 #ff557f models transparency 0

> color #4 #ff55ff models transparency 0

> color #4 #55ffff models transparency 0

> color #4 magenta models transparency 0

> color #4 #aa0000 models transparency 0

> color #4 black models transparency 0

> color #4 #aaaaff models transparency 0

> color #4 white models transparency 0

> color #4 #cfcfcf models transparency 0

> color #4 #616161 models transparency 0

> color #4 #b8b8b8 models transparency 0

> color #1 #ffff7f transparency 0

> undo

> color #4 #aaaa7f models transparency 0

> color #4 #ffff7f models transparency 0

> color #4 #55ffff models transparency 0

> color #4 #ffff7f models transparency 0

> color #4 #d9d96c models transparency 0

> color #4 #ffff7f models transparency 0

> color #4 yellow models transparency 0

> color #4 #fdfd00 models transparency 0

> lighting soft

> lighting full

> lighting shadows false

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> lighting simple

> lighting soft

> graphics silhouettes false

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting soft

> lighting flat

[Repeated 1 time(s)]

> lighting soft

> lighting full

> lighting flat

[Repeated 2 time(s)]

> lighting soft

> lighting full

> lighting soft

> lighting full

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> view

> ui tool show "Side View"

> view sel

> ui mousemode right select

> select add #1/D:239

49 atoms, 47 bonds, 7 residues, 1 model selected  

> select add #1/D:344

55 atoms, 52 bonds, 8 residues, 2 models selected  

> select add #1/D:122

65 atoms, 62 bonds, 9 residues, 2 models selected  

> name frozen cattriad sel

> select #1/P:76

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

> select up

41 atoms, 40 bonds, 6 residues, 1 model selected  

> name frozen peptide sel

> lighting soft

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

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

> style sel stick

Changed 7 atom styles  

> show sel atoms

> select up

41 atoms, 40 bonds, 6 residues, 1 model selected  

> show sel atoms

> hide sel cartoons

> ui mousemode right translate

> ui mousemode right "rotate slab"

> ui mousemode right select

> select #1/P:77@CA

1 atom, 1 residue, 1 model selected  

> select #1/P:77@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

41 atoms, 40 bonds, 6 residues, 1 model selected  

> view sel

> save C:/Users/jvarg/Documents/huji/fusolisin_active_site.cxs

> save C:/Users/jvarg/Documents/huji/fusolisin_active_site.png width 1321
> height 785 supersample 4 transparentBackground true

> select clear

> save C:/Users/jvarg/Documents/huji/fusolisin_active_site.png width 1321
> height 785 supersample 3

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #!1 surfaces

> hide #!1.1 models

> show #!1.1 models

> hide #1.2 models

> mlp #!1

Map values for surface "relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface": minimum -30.77, mean -6.378, maximum 21.71  
Map values for surface "relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_P SES
surface": minimum -22.18, mean -8.438, maximum 18.02  
To also show corresponding color key, enter the above mlp command and add key
true  

> select #1/D

2597 atoms, 2649 bonds, 13 pseudobonds, 338 residues, 2 models selected  

> hide sel surfaces

> select

7900 atoms, 8053 bonds, 73 pseudobonds, 1030 residues, 6 models selected  

> hide sel & #!1 surfaces

> select #1/D

2597 atoms, 2649 bonds, 13 pseudobonds, 338 residues, 2 models selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -15.26, mean -1.22, maximum 13.83  
To also show corresponding color key, enter the above coulombic command and
add key true  

> lighting full

> lighting soft

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting flat

> lighting soft

> lighting simple

> mlp sel

Map values for surface "relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface": minimum -30.77, mean -6.378, maximum 21.71  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide sel surfaces

> show sel surfaces

> mlp sel

Map values for surface "relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface": minimum -30.77, mean -6.378, maximum 21.71  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide #!1.1 models

> hide #1.2 models

> show #!1.1 models

> hide sel surfaces

> show sel surfaces

> color #1.1 #ffffff80

> hide #!1.1 models

> select clear

> save C:/Users/jvarg/Documents/huji/fusolisin_figure.cxs

[Repeated 1 time(s)]

——— End of log from Sat Jun 4 20:15:09 2022 ———

opened ChimeraX session  

> lighting gentle

> lighting soft

> select #1/D

2597 atoms, 2649 bonds, 13 pseudobonds, 338 residues, 2 models selected  

> cartoon style (#!1 & sel) xsection oval modeHelix default

> select clear

> select #1/D

2597 atoms, 2649 bonds, 13 pseudobonds, 338 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel cornflower blue

> color sel sky blue

> select #1/P

41 atoms, 40 bonds, 6 residues, 1 model selected  

> color sel pink

> color sel peach puff

> color sel light salmon

> select #1/D

2597 atoms, 2649 bonds, 13 pseudobonds, 338 residues, 2 models selected  

> color sel cornflower blue

> graphics silhouettes true width 1

> lighting soft

> set bgColor white

> surface #1/D

> transparency 95 target s

> color byhetero target #1/P

Invalid "target" argument: Character '#' is not an allowed target, must be one
of acrsbmpfl  

> transparency 95 target a

> transparency 95 target s

> cartoon style (#!1 & sel & coil) xsection oval

> cartoon style (#!1 & sel) xsection barbell modeHelix default

> cartoon style (#!1 & sel) modeHelix tube sides 20

> select #1/P

41 atoms, 40 bonds, 6 residues, 1 model selected  

> transparency 0 target a

> color byhetero target a

> cartoon style (#!1 & sel) xsection oval modeHelix default

> lighting flat

[Repeated 1 time(s)]

> lighting shadows true intensity 0.5

> lighting full

> lighting soft

> lighting simple

> lighting soft

> graphics silhouettes false

> select #1/D

2597 atoms, 2649 bonds, 13 pseudobonds, 338 residues, 2 models selected  

> graphics selection color black

> graphics selection color white

> transparency 85 target s

> ui mousemode right clip

[Repeated 1 time(s)]

> transparency 95 target s

[Repeated 1 time(s)]

> transparency 100 target s

> transparency 99 target s

> transparency 95 target s

> delete #2

> delete #3

> hide #4 models

> show #4 models

> open
> V:/projects/fusolisin/modeling/flexpepbind_results/fpb_relax_long_cd16/input_files/relax_long_fusolisin_ISSQAS_0001_0078.pdb

Summary of feedback from opening
V:/projects/fusolisin/modeling/flexpepbind_results/fpb_relax_long_cd16/input_files/relax_long_fusolisin_ISSQAS_0001_0078.pdb  
---  
warnings | Ignored bad PDB record found on line 5229  
score -1048.85  
  
Ignored bad PDB record found on line 5230  
silent_score -1048.85  
  
Ignored bad PDB record found on line 5231  
time 1349  
  
Ignored bad PDB record found on line 5232  
  
Chain information for relax_long_fusolisin_ISSQAS_0001_0078.pdb #2  
---  
Chain | Description  
D | No description available  
P | No description available  
  

> align #2, #1

Missing or invalid "atoms" argument: only initial part "#2" of atom specifier
valid  

> align #2 #1

Missing required "to_atoms" argument  

> ui tool show Matchmaker

> matchmaker #2 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 relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb, chain D (#1) with
relax_long_fusolisin_ISSQAS_0001_0078.pdb, chain D (#2), sequence alignment
score = 1707.9  
RMSD between 338 pruned atom pairs is 0.000 angstroms; (across all 338 pairs:
0.000)  
  

> select #1

2638 atoms, 2689 bonds, 26 pseudobonds, 344 residues, 2 models selected  

> hide sel cartoons

> graphics silhouettes true

> ui mousemode right translate

> ui mousemode right clip

> ui mousemode right translate

> graphics silhouettes true black

Expected a keyword  

> lighting soft

> lighting gentle

> graphics silhouettes true width 1

> surface #1

> surface #1/D

> colory byhet target a

Unknown command: colory byhet target a  

> hide #2 models

> color bonds yellow

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> select chain #1/P

Expected an objects specifier or a keyword  

> select #1/P

41 atoms, 40 bonds, 6 residues, 1 model selected  

> surface hidePatches (#!1 & sel)

> select #1/D

2597 atoms, 2649 bonds, 13 pseudobonds, 338 residues, 2 models selected  

> show sel cartoons

> graphics silhouettes false

> lighting soft

> hide sel surfaces

> lighting soft

> lighting gentle

> graphics silhouettes true

> ui mousemode right select

> select clear

> select #1/D:163@CB

1 atom, 1 residue, 1 model selected  

> select up

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

> hide sel atoms

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> hide sel atoms

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

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

> hide sel atoms

> select sel

1 pseudobond, 1 model selected  

> hide sel

[Repeated 4 time(s)]

> save C:/Users/jvarg/Documents/huji/fusolisin_figure.cxs

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> select #1/P

41 atoms, 40 bonds, 6 residues, 1 model selected  

> graphics selection color black

> select clear

> graphics selection color black

> select #1/P

41 atoms, 40 bonds, 6 residues, 1 model selected  

> select #1/D

2597 atoms, 2649 bonds, 13 pseudobonds, 338 residues, 2 models selected  

> show sel surfaces

> select #1/P

41 atoms, 40 bonds, 6 residues, 1 model selected  

> cartoon round

Expected an atoms specifier or a keyword  

> cartoon rounded

Expected an atoms specifier or a keyword  

> cartoon style rounded

Expected an atoms specifier or a keyword  

> select #1/D

2597 atoms, 2649 bonds, 13 pseudobonds, 338 residues, 2 models selected  

> cartoon style (#!1 & sel) xsection oval modeHelix default

> select #1/P

41 atoms, 40 bonds, 6 residues, 1 model selected  

> ui tool show ViewDockX

No suitable models found for ViewDockX  

> toolshed show

> lighting soft

> lighting full

> lighting simple

> lighting gentle

> select add #1/D:239@CB

42 atoms, 40 bonds, 7 residues, 2 models selected  

> select subtract #1/D:239@CB

41 atoms, 40 bonds, 6 residues, 3 models selected  

> select add #1/D:239@ND2

42 atoms, 40 bonds, 7 residues, 2 models selected  

> select subtract #1/D:239@ND2

41 atoms, 40 bonds, 6 residues, 3 models selected  

> select #1/D:239@ND2

1 atom, 1 residue, 1 model selected  

> select #1/D:239@CB

1 atom, 1 residue, 1 model selected  

> select #1/D:239@CB

1 atom, 1 residue, 1 model selected  

> select #1/D:240@CG

1 atom, 1 residue, 1 model selected  

> select #1/D:239@CB

1 atom, 1 residue, 1 model selected  

> select #1/D:239@ND2

1 atom, 1 residue, 1 model selected  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> select up

41 atoms, 40 bonds, 6 residues, 2 models selected  

> ui mousemode right label

> label #1/D:245

[Repeated 1 time(s)]

> ui mousemode right pivot

> ui mousemode right label

> label #1/D:245

> ui mousemode right "move label"

> clip

> undo

> clip front 0

> clip front 1

> clip front 10

> clip front -10

> clip front -20

> clip front -15

> clip back -15

> clip front -10

> clip front 0

> clip front 1

> clip front -10

> clip front -20

> clip back 15

> clip back 10

> clip back 7.5

> clip back 10

> clip back 15

> ui mousemode right select

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> select up

41 atoms, 40 bonds, 6 residues, 2 models selected  

> select #1/D:288@CB

1 atom, 1 residue, 1 model selected  

> select up

7 atoms, 6 bonds, 1 residue, 2 models selected  

> hide sel atoms

[Repeated 1 time(s)]

> select #1/D:288@CB

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #1/D:288@CB

1 atom, 1 residue, 1 model selected  

> select #1/D:288@CB

1 atom, 1 residue, 1 model selected  

> select #1/D:288@O

1 atom, 1 residue, 1 model selected  

> select #1/D:291@N

1 atom, 1 residue, 1 model selected  

> select #1/D:291@CB

1 atom, 1 residue, 1 model selected  

> select #1/D:288@N

1 atom, 1 residue, 1 model selected  

> select #1/D:288@C

1 atom, 1 residue, 1 model selected  

> select #1/D:288@N

1 atom, 1 residue, 1 model selected  

> select #1/D:287@CA

1 atom, 1 residue, 1 model selected  

> ui mousemode right translate

> ui mousemode right select

> select #1/D:295@CD1

1 atom, 1 residue, 1 model selected  

> select #1/D:295@CD1

1 atom, 1 residue, 1 model selected  

> select #1/D:295@CD1

1 atom, 1 residue, 1 model selected  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> hide sel atoms

> ui mousemode right translate

> ui mousemode right label

> label #1/D:211

[Repeated 1 time(s)]

> label #1/D:162

> label #1/P:74

> label #1/P:75

[Repeated 1 time(s)]

> label #1/D:160

> label #1/D:153

> label delete residues

[Repeated 1 time(s)]

> ui mousemode right translate

> ui mousemode right select

> select up

2 atoms, 1 bond, 2 residues, 1 model selected  

> select up

15 atoms, 14 bonds, 2 residues, 2 models selected  

> select up

41 atoms, 40 bonds, 6 residues, 2 models selected  

> ui mousemode right translate

> ui mousemode right select

> hide sel surfaces

> select clear

> hide #!1 surfaces

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

10 atoms, 10 bonds, 1 residue, 2 models selected  

> select up

12 atoms, 11 bonds, 2 residues, 2 models selected  

> select up

14 atoms, 12 bonds, 3 residues, 2 models selected  

> select up

24 atoms, 22 bonds, 3 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel medium spring green

> color sel medium aquamarine

> color sel yellow

> color sel gold

> color sel pale green

> color sel byhetero

> name frozen intres sel

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> select up

41 atoms, 40 bonds, 6 residues, 2 models selected  

> lightning deptCue true

Unknown command: lightning deptCue true  

> lighting depthCue true

> background solid white

Unknown command: background solid white  

> lighting depthCueColor white

> lighting depthCue true

> cartoon style (#!1 & sel) modeHelix tube sides 20

> cartoon style modeHelix tude sides 24

Invalid "modeHelix" argument: Should be one of 'default', 'tube', or 'wrap'  

> cartoon style modeHelix tube sides 24

> select #1/D:341@CG2

1 atom, 1 residue, 1 model selected  

> select add #1/D:341@CD1

2 atoms, 1 residue, 2 models selected  

> hide sel atoms

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> select up

41 atoms, 40 bonds, 6 residues, 2 models selected  
Alignment identifier is 1/P  

> select clear

Alignment identifier is 1  
Alignment identifier is 2  

> select #1/D:344

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

> select add #1/D:343

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select add #1/D:341

20 atoms, 17 bonds, 3 residues, 2 models selected  

> select add #1/D:342

24 atoms, 20 bonds, 4 residues, 2 models selected  

> save C:/Users/jvarg/Documents/huji/fusolisin_figure.cxs

——— End of log from Mon Jun 6 16:08:31 2022 ———

opened ChimeraX session  

failed to create compose table  

> info

7 models  
#1, relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb, shown  
2638 atoms, 2689 bonds, 344 residues, 2 chains (D,P)  
#1.1, relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES surface, shown,
274332 triangles  
#1.1.1, cap front, shown  
#1.1.2, cap back, shown  
#1.2, relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_P SES surface, shown,
9494 triangles  
#2, relax_long_fusolisin_ISSQAS_0001_0078.pdb, hidden  
5217 atoms, 5268 bonds, 344 residues, 2 chains (D,P)  
#4, hydrogen bonds, shown, 26 pseudobonds  

> info selection

atom id #1/D:341@N idatm_type Npl  
atom id #1/D:341@CA idatm_type C3  
atom id #1/D:341@C idatm_type C2  
atom id #1/D:341@O idatm_type O2  
atom id #1/D:341@CB idatm_type C3  
atom id #1/D:341@CG1 idatm_type C3  
atom id #1/D:341@CG2 idatm_type C3  
atom id #1/D:341@CD1 idatm_type C3  
atom id #1/D:342@N idatm_type Npl  
atom id #1/D:342@CA idatm_type C3  
atom id #1/D:342@C idatm_type C2  
atom id #1/D:342@O idatm_type O2  
atom id #1/D:343@N idatm_type Npl  
atom id #1/D:343@CA idatm_type C3  
atom id #1/D:343@C idatm_type C2  
atom id #1/D:343@O idatm_type O2  
atom id #1/D:343@CB idatm_type C3  
atom id #1/D:343@OG idatm_type O3  
atom id #1/D:344@N idatm_type Npl  
atom id #1/D:344@CA idatm_type C3  
atom id #1/D:344@C idatm_type C2  
atom id #1/D:344@O idatm_type O2  
atom id #1/D:344@CB idatm_type C3  
atom id #1/D:344@OG idatm_type O3  

> info selection residue

Expected a keyword  

> info selection r

Expected a keyword  

> info selection res

Expected a keyword  

> info selection residue

Expected a keyword  

> info selection level=residue

Expected a keyword  

> info selection atom

Expected a keyword  

> info atoms

atom id #1/D:77@N idatm_type N3+  
atom id #1/D:77@CA idatm_type C3  
atom id #1/D:77@C idatm_type C2  
atom id #1/D:77@O idatm_type O2  
atom id #1/D:77@CB idatm_type C3  
atom id #1/D:77@CG idatm_type Car  
atom id #1/D:77@CD1 idatm_type Car  
atom id #1/D:77@CD2 idatm_type Car  
atom id #1/D:77@CE1 idatm_type Car  
atom id #1/D:77@CE2 idatm_type Car  
atom id #1/D:77@CZ idatm_type Car  
atom id #1/D:77@OH idatm_type O3  
atom id #1/D:78@N idatm_type Npl  
atom id #1/D:78@CA idatm_type C3  
atom id #1/D:78@C idatm_type C2  
atom id #1/D:78@O idatm_type O2  
atom id #1/D:78@CB idatm_type C3  
atom id #1/D:78@CG idatm_type C2  
atom id #1/D:78@ND2 idatm_type Npl  
atom id #1/D:78@OD1 idatm_type O2  
atom id #1/D:79@N idatm_type Npl  
atom id #1/D:79@CA idatm_type C3  
atom id #1/D:79@C idatm_type C2  
atom id #1/D:79@O idatm_type O2  
atom id #1/D:80@N idatm_type Npl  
atom id #1/D:80@CA idatm_type C3  
atom id #1/D:80@C idatm_type C2  
atom id #1/D:80@O idatm_type O2  
atom id #1/D:80@CB idatm_type C3  
atom id #1/D:80@OG idatm_type O3  
atom id #1/D:81@N idatm_type Npl  
atom id #1/D:81@CA idatm_type C3  
atom id #1/D:81@C idatm_type C2  
atom id #1/D:81@O idatm_type O2  
atom id #1/D:81@CB idatm_type C3  
atom id #1/D:81@CG2 idatm_type C3  
atom id #1/D:81@OG1 idatm_type O3  
atom id #1/D:82@N idatm_type Npl  
atom id #1/D:82@CA idatm_type C3  
atom id #1/D:82@C idatm_type C2  
atom id #1/D:82@O idatm_type O2  
atom id #1/D:82@CB idatm_type C3  
atom id #1/D:82@CG1 idatm_type C3  
atom id #1/D:82@CG2 idatm_type C3  
atom id #1/D:83@N idatm_type Npl  
atom id #1/D:83@CA idatm_type C3  
atom id #1/D:83@C idatm_type C2  
atom id #1/D:83@O idatm_type O2  
atom id #1/D:83@CB idatm_type C3  
atom id #1/D:83@CG idatm_type C3  
atom id #1/D:83@CD idatm_type C3  
atom id #1/D:83@CE idatm_type C3  
atom id #1/D:83@NZ idatm_type N3+  
atom id #1/D:84@N idatm_type Npl  
atom id #1/D:84@CA idatm_type C3  
atom id #1/D:84@C idatm_type C2  
atom id #1/D:84@O idatm_type O2  
atom id #1/D:84@CB idatm_type C3  
atom id #1/D:84@CG1 idatm_type C3  
atom id #1/D:84@CG2 idatm_type C3  
atom id #1/D:84@CD1 idatm_type C3  
atom id #1/D:85@N idatm_type Npl  
atom id #1/D:85@CA idatm_type C3  
atom id #1/D:85@C idatm_type C2  
atom id #1/D:85@O idatm_type O2  
atom id #1/D:86@N idatm_type Npl  
atom id #1/D:86@CA idatm_type C3  
atom id #1/D:86@C idatm_type C2  
atom id #1/D:86@O idatm_type O2  
atom id #1/D:86@CB idatm_type C3  
atom id #1/D:86@CG1 idatm_type C3  
atom id #1/D:86@CG2 idatm_type C3  
atom id #1/D:86@CD1 idatm_type C3  
atom id #1/D:87@N idatm_type Npl  
atom id #1/D:87@CA idatm_type C3  
atom id #1/D:87@C idatm_type C2  
atom id #1/D:87@O idatm_type O2  
atom id #1/D:87@CB idatm_type C3  
atom id #1/D:87@CG idatm_type C3  
atom id #1/D:87@CD1 idatm_type C3  
atom id #1/D:87@CD2 idatm_type C3  
atom id #1/D:88@N idatm_type Npl  
atom id #1/D:88@CA idatm_type C3  
atom id #1/D:88@C idatm_type C2  
atom id #1/D:88@O idatm_type O2  
atom id #1/D:88@CB idatm_type C3  
atom id #1/D:88@CG idatm_type Cac  
atom id #1/D:88@OD1 idatm_type O2-  
atom id #1/D:88@OD2 idatm_type O2-  
atom id #1/D:89@N idatm_type Npl  
atom id #1/D:89@CA idatm_type C3  
atom id #1/D:89@C idatm_type C2  
atom id #1/D:89@O idatm_type O2  
atom id #1/D:89@CB idatm_type C3  
atom id #1/D:89@OG idatm_type O3  
atom id #1/D:90@N idatm_type Npl  
atom id #1/D:90@CA idatm_type C3  
atom id #1/D:90@C idatm_type C2  
atom id #1/D:90@O idatm_type O2  
atom id #1/D:90@CB idatm_type C3  
atom id #1/D:90@CG idatm_type Cac  
atom id #1/D:90@OD1 idatm_type O2-  
atom id #1/D:90@OD2 idatm_type O2-  
atom id #1/D:91@N idatm_type Npl  
atom id #1/D:91@CA idatm_type C3  
atom id #1/D:91@C idatm_type C2  
atom id #1/D:91@O idatm_type O2  
atom id #1/D:91@CB idatm_type C3  
atom id #1/D:91@CG idatm_type Car  
atom id #1/D:91@CD1 idatm_type Car  
atom id #1/D:91@CD2 idatm_type Car  
atom id #1/D:91@CE1 idatm_type Car  
atom id #1/D:91@CE2 idatm_type Car  
atom id #1/D:91@CZ idatm_type Car  
atom id #1/D:92@N idatm_type Npl  
atom id #1/D:92@CA idatm_type C3  
atom id #1/D:92@C idatm_type C2  
atom id #1/D:92@O idatm_type O2  
atom id #1/D:92@CB idatm_type C3  
atom id #1/D:92@CG2 idatm_type C3  
atom id #1/D:92@OG1 idatm_type O3  
atom id #1/D:93@N idatm_type Npl  
atom id #1/D:93@CA idatm_type C3  
atom id #1/D:93@C idatm_type C2  
atom id #1/D:93@O idatm_type O2  
atom id #1/D:93@CB idatm_type C3  
atom id #1/D:93@CG idatm_type Cac  
atom id #1/D:93@OD1 idatm_type O2-  
atom id #1/D:93@OD2 idatm_type O2-  
atom id #1/D:94@N idatm_type Npl  
atom id #1/D:94@CA idatm_type C3  
atom id #1/D:94@C idatm_type C2  
atom id #1/D:94@O idatm_type O2  
atom id #1/D:94@CB idatm_type C3  
atom id #1/D:94@CG idatm_type C3  
atom id #1/D:94@CD idatm_type C3  
atom id #1/D:95@N idatm_type Npl  
atom id #1/D:95@CA idatm_type C3  
atom id #1/D:95@C idatm_type C2  
atom id #1/D:95@O idatm_type O2  
atom id #1/D:95@CB idatm_type C3  
atom id #1/D:95@CG1 idatm_type C3  
atom id #1/D:95@CG2 idatm_type C3  
atom id #1/D:96@N idatm_type Npl  
atom id #1/D:96@CA idatm_type C3  
atom id #1/D:96@C idatm_type C2  
atom id #1/D:96@O idatm_type O2  
atom id #1/D:96@CB idatm_type C3  
atom id #1/D:96@CG idatm_type C3  
atom id #1/D:96@CD idatm_type C3  
atom id #1/D:96@NE idatm_type Ng+  
atom id #1/D:96@CZ idatm_type C2  
atom id #1/D:96@NH1 idatm_type Ng+  
atom id #1/D:96@NH2 idatm_type Ng+  
atom id #1/D:97@N idatm_type Npl  
atom id #1/D:97@CA idatm_type C3  
atom id #1/D:97@C idatm_type C2  
atom id #1/D:97@O idatm_type O2  
atom id #1/D:97@CB idatm_type C3  
atom id #1/D:97@CG idatm_type C3  
atom id #1/D:97@CD idatm_type C3  
atom id #1/D:97@CE idatm_type C3  
atom id #1/D:97@NZ idatm_type N3+  
atom id #1/D:98@N idatm_type Npl  
atom id #1/D:98@CA idatm_type C3  
atom id #1/D:98@C idatm_type C2  
atom id #1/D:98@O idatm_type O2  
atom id #1/D:98@CB idatm_type C3  
atom id #1/D:99@N idatm_type Npl  
atom id #1/D:99@CA idatm_type C3  
atom id #1/D:99@C idatm_type C2  
atom id #1/D:99@O idatm_type O2  
atom id #1/D:99@CB idatm_type C3  
atom id #1/D:99@CG idatm_type C3  
atom id #1/D:99@CD idatm_type C2  
atom id #1/D:99@NE2 idatm_type Npl  
atom id #1/D:99@OE1 idatm_type O2  
atom id #1/D:100@N idatm_type Npl  
atom id #1/D:100@CA idatm_type C3  
atom id #1/D:100@C idatm_type C2  
atom id #1/D:100@O idatm_type O2  
atom id #1/D:100@CB idatm_type C3  
atom id #1/D:100@CG idatm_type C3  
atom id #1/D:100@CD1 idatm_type C3  
atom id #1/D:100@CD2 idatm_type C3  
atom id #1/D:101@N idatm_type Npl  
atom id #1/D:101@CA idatm_type C3  
atom id #1/D:101@C idatm_type C2  
atom id #1/D:101@O idatm_type O2  
atom id #1/D:101@CB idatm_type C3  
atom id #1/D:101@OG idatm_type O3  
atom id #1/D:102@N idatm_type Npl  
atom id #1/D:102@CA idatm_type C3  
atom id #1/D:102@C idatm_type C2  
atom id #1/D:102@O idatm_type O2  
atom id #1/D:102@CB idatm_type C3  
atom id #1/D:103@N idatm_type Npl  
atom id #1/D:103@CA idatm_type C3  
atom id #1/D:103@C idatm_type C2  
atom id #1/D:103@O idatm_type O2  
atom id #1/D:103@CB idatm_type C3  
atom id #1/D:103@CG idatm_type C3  
atom id #1/D:103@CD idatm_type C3  
atom id #1/D:103@NE idatm_type Ng+  
atom id #1/D:103@CZ idatm_type C2  
atom id #1/D:103@NH1 idatm_type Ng+  
atom id #1/D:103@NH2 idatm_type Ng+  
atom id #1/D:104@N idatm_type Npl  
atom id #1/D:104@CA idatm_type C3  
atom id #1/D:104@C idatm_type C2  
atom id #1/D:104@O idatm_type O2  
atom id #1/D:104@CB idatm_type C3  
atom id #1/D:104@CG idatm_type Car  
atom id #1/D:104@CD1 idatm_type Car  
atom id #1/D:104@CD2 idatm_type Car  
atom id #1/D:104@CE1 idatm_type Car  
atom id #1/D:104@CE2 idatm_type Car  
atom id #1/D:104@CZ idatm_type Car  
atom id #1/D:104@OH idatm_type O3  
atom id #1/D:105@N idatm_type Npl  
atom id #1/D:105@CA idatm_type C3  
atom id #1/D:105@C idatm_type C2  
atom id #1/D:105@O idatm_type O2  
atom id #1/D:105@CB idatm_type C3  
atom id #1/D:105@CG idatm_type C3  
atom id #1/D:105@CD idatm_type C3  
atom id #1/D:106@N idatm_type Npl  
atom id #1/D:106@CA idatm_type C3  
atom id #1/D:106@C idatm_type C2  
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atom id #1/D:209@CE1 idatm_type Car  
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atom id #1/D:209@CZ idatm_type Car  
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atom id #1/D:210@N idatm_type Npl  
atom id #1/D:210@CA idatm_type C3  
atom id #1/D:210@C idatm_type C2  
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atom id #1/D:210@CB idatm_type C3  
atom id #1/D:210@CG1 idatm_type C3  
atom id #1/D:210@CG2 idatm_type C3  
atom id #1/D:211@N idatm_type Npl  
atom id #1/D:211@CA idatm_type C3  
atom id #1/D:211@C idatm_type C2  
atom id #1/D:211@O idatm_type O2  
atom id #1/D:211@CB idatm_type C3  
atom id #1/D:211@CG idatm_type Car  
atom id #1/D:211@CD1 idatm_type Car  
atom id #1/D:211@CD2 idatm_type Car  
atom id #1/D:211@CE2 idatm_type Car  
atom id #1/D:211@CE3 idatm_type Car  
atom id #1/D:211@NE1 idatm_type Npl  
atom id #1/D:211@CZ2 idatm_type Car  
atom id #1/D:211@CZ3 idatm_type Car  
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atom id #1/D:212@N idatm_type Npl  
atom id #1/D:212@CA idatm_type C3  
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atom id #1/D:212@O idatm_type O2  
atom id #1/D:212@CB idatm_type C3  
atom id #1/D:213@N idatm_type Npl  
atom id #1/D:213@CA idatm_type C3  
atom id #1/D:213@C idatm_type C2  
atom id #1/D:213@O idatm_type O2  
atom id #1/D:214@N idatm_type Npl  
atom id #1/D:214@CA idatm_type C3  
atom id #1/D:214@C idatm_type C2  
atom id #1/D:214@O idatm_type O2  
atom id #1/D:214@CB idatm_type C3  
atom id #1/D:214@CG idatm_type Cac  
atom id #1/D:214@OD1 idatm_type O2-  
atom id #1/D:214@OD2 idatm_type O2-  
atom id #1/D:215@N idatm_type Npl  
atom id #1/D:215@CA idatm_type C3  
atom id #1/D:215@C idatm_type C2  
atom id #1/D:215@O idatm_type O2  
atom id #1/D:215@CB idatm_type C3  
atom id #1/D:215@OG idatm_type O3  
atom id #1/D:216@N idatm_type Npl  
atom id #1/D:216@CA idatm_type C3  
atom id #1/D:216@C idatm_type C2  
atom id #1/D:216@O idatm_type O2  
atom id #1/D:216@CB idatm_type C3  
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atom id #1/D:216@CD idatm_type C3  
atom id #1/D:216@CE idatm_type C3  
atom id #1/D:216@NZ idatm_type N3+  
atom id #1/D:217@N idatm_type Npl  
atom id #1/D:217@CA idatm_type C3  
atom id #1/D:217@C idatm_type C2  
atom id #1/D:217@O idatm_type O2  
atom id #1/D:217@CB idatm_type C3  
atom id #1/D:217@CG idatm_type C3  
atom id #1/D:217@CD idatm_type C3  
atom id #1/D:218@N idatm_type Npl  
atom id #1/D:218@CA idatm_type C3  
atom id #1/D:218@C idatm_type C2  
atom id #1/D:218@O idatm_type O2  
atom id #1/D:218@CB idatm_type C3  
atom id #1/D:218@CG idatm_type Car  
atom id #1/D:218@CD1 idatm_type Car  
atom id #1/D:218@CD2 idatm_type Car  
atom id #1/D:218@CE1 idatm_type Car  
atom id #1/D:218@CE2 idatm_type Car  
atom id #1/D:218@CZ idatm_type Car  
atom id #1/D:219@N idatm_type Npl  
atom id #1/D:219@CA idatm_type C3  
atom id #1/D:219@C idatm_type C2  
atom id #1/D:219@O idatm_type O2  
atom id #1/D:219@CB idatm_type C3  
atom id #1/D:220@N idatm_type Npl  
atom id #1/D:220@CA idatm_type C3  
atom id #1/D:220@C idatm_type C2  
atom id #1/D:220@O idatm_type O2  
atom id #1/D:220@CB idatm_type C3  
atom id #1/D:220@CG2 idatm_type C3  
atom id #1/D:220@OG1 idatm_type O3  
atom id #1/D:221@N idatm_type Npl  
atom id #1/D:221@CA idatm_type C3  
atom id #1/D:221@C idatm_type C2  
atom id #1/D:221@O idatm_type O2  
atom id #1/D:221@CB idatm_type C3  
atom id #1/D:221@CG idatm_type Car  
atom id #1/D:221@CD1 idatm_type Car  
atom id #1/D:221@CD2 idatm_type Car  
atom id #1/D:221@CE1 idatm_type Car  
atom id #1/D:221@CE2 idatm_type Car  
atom id #1/D:221@CZ idatm_type Car  
atom id #1/D:221@OH idatm_type O3  
atom id #1/D:222@N idatm_type Npl  
atom id #1/D:222@CA idatm_type C3  
atom id #1/D:222@C idatm_type C2  
atom id #1/D:222@O idatm_type O2  
atom id #1/D:222@CB idatm_type C3  
atom id #1/D:222@CG idatm_type Car  
atom id #1/D:222@CD1 idatm_type Car  
atom id #1/D:222@CD2 idatm_type Car  
atom id #1/D:222@CE1 idatm_type Car  
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atom id #1/D:222@CZ idatm_type Car  
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atom id #1/D:223@CA idatm_type C3  
atom id #1/D:223@C idatm_type C2  
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atom id #1/D:223@CB idatm_type C3  
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atom id #1/D:223@OE1 idatm_type O2-  
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atom id #1/D:224@N idatm_type Npl  
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atom id #1/D:224@C idatm_type C2  
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atom id #1/D:224@CB idatm_type C3  
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atom id #1/D:224@CD idatm_type Cac  
atom id #1/D:224@OE1 idatm_type O2-  
atom id #1/D:224@OE2 idatm_type O2-  
atom id #1/D:225@N idatm_type Npl  
atom id #1/D:225@CA idatm_type C3  
atom id #1/D:225@C idatm_type C2  
atom id #1/D:225@O idatm_type O2  
atom id #1/D:225@CB idatm_type C3  
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atom id #1/D:225@CD idatm_type C3  
atom id #1/D:225@CE idatm_type C3  
atom id #1/D:225@NZ idatm_type N3+  
atom id #1/D:226@N idatm_type Npl  
atom id #1/D:226@CA idatm_type C3  
atom id #1/D:226@C idatm_type C2  
atom id #1/D:226@O idatm_type O2  
atom id #1/D:226@CB idatm_type C3  
atom id #1/D:226@CG1 idatm_type C3  
atom id #1/D:226@CG2 idatm_type C3  
atom id #1/D:227@N idatm_type Npl  
atom id #1/D:227@CA idatm_type C3  
atom id #1/D:227@C idatm_type C2  
atom id #1/D:227@O idatm_type O2  
atom id #1/D:227@CB idatm_type C3  
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atom id #1/D:227@ND2 idatm_type Npl  
atom id #1/D:227@OD1 idatm_type O2  
atom id #1/D:228@N idatm_type Npl  
atom id #1/D:228@CA idatm_type C3  
atom id #1/D:228@C idatm_type C2  
atom id #1/D:228@O idatm_type O2  
atom id #1/D:228@CB idatm_type C3  
atom id #1/D:228@CG idatm_type C2  
atom id #1/D:228@ND2 idatm_type Npl  
atom id #1/D:228@OD1 idatm_type O2  
atom id #1/D:229@N idatm_type Npl  
atom id #1/D:229@CA idatm_type C3  
atom id #1/D:229@C idatm_type C2  
atom id #1/D:229@O idatm_type O2  
atom id #1/D:229@CB idatm_type C3  
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atom id #1/D:229@OD1 idatm_type O2-  
atom id #1/D:229@OD2 idatm_type O2-  
atom id #1/D:230@N idatm_type Npl  
atom id #1/D:230@CA idatm_type C3  
atom id #1/D:230@C idatm_type C2  
atom id #1/D:230@O idatm_type O2  
atom id #1/D:231@N idatm_type Npl  
atom id #1/D:231@CA idatm_type C3  
atom id #1/D:231@C idatm_type C2  
atom id #1/D:231@O idatm_type O2  
atom id #1/D:232@N idatm_type Npl  
atom id #1/D:232@CA idatm_type C3  
atom id #1/D:232@C idatm_type C2  
atom id #1/D:232@O idatm_type O2  
atom id #1/D:232@CB idatm_type C3  
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atom id #1/D:232@CD1 idatm_type C3  
atom id #1/D:232@CD2 idatm_type C3  
atom id #1/D:233@N idatm_type Npl  
atom id #1/D:233@CA idatm_type C3  
atom id #1/D:233@C idatm_type C2  
atom id #1/D:233@O idatm_type O2  
atom id #1/D:233@CB idatm_type C3  
atom id #1/D:233@CG idatm_type Car  
atom id #1/D:233@CD1 idatm_type Car  
atom id #1/D:233@CD2 idatm_type Car  
atom id #1/D:233@CE1 idatm_type Car  
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atom id #1/D:233@CZ idatm_type Car  
atom id #1/D:234@N idatm_type Npl  
atom id #1/D:234@CA idatm_type C3  
atom id #1/D:234@C idatm_type C2  
atom id #1/D:234@O idatm_type O2  
atom id #1/D:234@CB idatm_type C3  
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atom id #1/D:234@CG2 idatm_type C3  
atom id #1/D:235@N idatm_type Npl  
atom id #1/D:235@CA idatm_type C3  
atom id #1/D:235@C idatm_type C2  
atom id #1/D:235@O idatm_type O2  
atom id #1/D:235@CB idatm_type C3  
atom id #1/D:235@CG idatm_type Car  
atom id #1/D:235@CD1 idatm_type Car  
atom id #1/D:235@CD2 idatm_type Car  
atom id #1/D:235@CE2 idatm_type Car  
atom id #1/D:235@CE3 idatm_type Car  
atom id #1/D:235@NE1 idatm_type Npl  
atom id #1/D:235@CZ2 idatm_type Car  
atom id #1/D:235@CZ3 idatm_type Car  
atom id #1/D:235@CH2 idatm_type Car  
atom id #1/D:236@N idatm_type Npl  
atom id #1/D:236@CA idatm_type C3  
atom id #1/D:236@C idatm_type C2  
atom id #1/D:236@O idatm_type O2  
atom id #1/D:236@CB idatm_type C3  
atom id #1/D:237@N idatm_type Npl  
atom id #1/D:237@CA idatm_type C3  
atom id #1/D:237@C idatm_type C2  
atom id #1/D:237@O idatm_type O2  
atom id #1/D:237@CB idatm_type C3  
atom id #1/D:238@N idatm_type Npl  
atom id #1/D:238@CA idatm_type C3  
atom id #1/D:238@C idatm_type C2  
atom id #1/D:238@O idatm_type O2  
atom id #1/D:239@N idatm_type Npl  
atom id #1/D:239@CA idatm_type C3  
atom id #1/D:239@C idatm_type C2  
atom id #1/D:239@O idatm_type O2  
atom id #1/D:239@CB idatm_type C3  
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atom id #1/D:239@OD1 idatm_type O2  
atom id #1/D:240@N idatm_type Npl  
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atom id #1/D:240@O idatm_type O2  
atom id #1/D:240@CB idatm_type C3  
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atom id #1/D:240@CD idatm_type C3  
atom id #1/D:240@NE idatm_type Ng+  
atom id #1/D:240@CZ idatm_type C2  
atom id #1/D:240@NH1 idatm_type Ng+  
atom id #1/D:240@NH2 idatm_type Ng+  
atom id #1/D:241@N idatm_type Npl  
atom id #1/D:241@CA idatm_type C3  
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atom id #1/D:241@CB idatm_type C3  
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atom id #1/D:241@NZ idatm_type N3+  
atom id #1/D:242@N idatm_type Npl  
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atom id #1/D:243@N idatm_type Npl  
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atom id #1/D:244@C idatm_type C2  
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atom id #1/D:245@CB idatm_type C3  
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atom id #1/D:248@N idatm_type Npl  
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atom id #1/D:248@CB idatm_type C3  
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atom id #1/D:320@N idatm_type Npl  
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atom id #1/D:322@NZ idatm_type N3+  
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atom id #1/D:338@NE idatm_type Ng+  
atom id #1/D:338@CZ idatm_type C2  
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atom id #1/D:349@NE idatm_type Ng+  
atom id #1/D:349@CZ idatm_type C2  
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atom id #1/D:349@NH2 idatm_type Ng+  
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atom id #1/D:352@CZ idatm_type C2  
atom id #1/D:352@NH1 idatm_type Ng+  
atom id #1/D:352@NH2 idatm_type Ng+  
atom id #1/D:353@N idatm_type Npl  
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atom id #1/D:370@NE idatm_type Ng+  
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atom id #2/D:209@HH idatm_type H  
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atom id #2/D:213@N idatm_type Npl  
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atom id #2/D:214@N idatm_type Npl  
atom id #2/D:214@CA idatm_type C3  
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atom id #2/D:214@OD1 idatm_type O2-  
atom id #2/D:214@OD2 idatm_type O2-  
atom id #2/D:214@H idatm_type H  
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atom id #2/D:215@N idatm_type Npl  
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atom id #2/D:216@NZ idatm_type N3+  
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atom id #2/D:216@1HZ idatm_type H  
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atom id #2/D:217@CA idatm_type C3  
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atom id #2/D:217@CB idatm_type C3  
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atom id #2/D:217@1HD idatm_type HC  
atom id #2/D:217@2HD idatm_type HC  
atom id #2/D:218@N idatm_type Npl  
atom id #2/D:218@CA idatm_type C3  
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atom id #2/D:218@CB idatm_type C3  
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atom id #2/D:218@CE1 idatm_type Car  
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atom id #2/D:218@HE1 idatm_type HC  
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atom id #2/D:218@HZ idatm_type HC  
atom id #2/D:219@N idatm_type Npl  
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atom id #2/D:219@3HB idatm_type HC  
atom id #2/D:220@N idatm_type Npl  
atom id #2/D:220@CA idatm_type C3  
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atom id #2/D:221@CB idatm_type C3  
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atom id #2/D:221@HH idatm_type H  
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atom id #2/D:222@HZ idatm_type HC  
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atom id #2/D:223@CD idatm_type Cac  
atom id #2/D:223@OE1 idatm_type O2-  
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atom id #2/D:224@OE1 idatm_type O2-  
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atom id #2/D:225@NZ idatm_type N3+  
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atom id #2/D:229@OD1 idatm_type O2-  
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atom id #2/D:322@NZ idatm_type N3+  
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atom id #2/D:329@OD1 idatm_type O2-  
atom id #2/D:329@OD2 idatm_type O2-  
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atom id #2/D:330@OD1 idatm_type O2-  
atom id #2/D:330@OD2 idatm_type O2-  
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atom id #2/D:398@1HG1 idatm_type HC  
atom id #2/D:398@2HG1 idatm_type HC  
atom id #2/D:398@3HG1 idatm_type HC  
atom id #2/D:398@1HG2 idatm_type HC  
atom id #2/D:398@2HG2 idatm_type HC  
atom id #2/D:398@3HG2 idatm_type HC  
atom id #2/D:399@N idatm_type Npl  
atom id #2/D:399@CA idatm_type C3  
atom id #2/D:399@C idatm_type C2  
atom id #2/D:399@O idatm_type O2  
atom id #2/D:399@CB idatm_type C3  
atom id #2/D:399@CG idatm_type C3  
atom id #2/D:399@CD idatm_type C3  
atom id #2/D:399@CE idatm_type C3  
atom id #2/D:399@NZ idatm_type N3+  
atom id #2/D:399@H idatm_type H  
atom id #2/D:399@HA idatm_type HC  
atom id #2/D:399@1HB idatm_type HC  
atom id #2/D:399@2HB idatm_type HC  
atom id #2/D:399@1HG idatm_type HC  
atom id #2/D:399@2HG idatm_type HC  
atom id #2/D:399@1HD idatm_type HC  
atom id #2/D:399@2HD idatm_type HC  
atom id #2/D:399@1HE idatm_type HC  
atom id #2/D:399@2HE idatm_type HC  
atom id #2/D:399@1HZ idatm_type H  
atom id #2/D:399@2HZ idatm_type H  
atom id #2/D:399@3HZ idatm_type H  
atom id #2/D:400@N idatm_type Npl  
atom id #2/D:400@CA idatm_type C3  
atom id #2/D:400@C idatm_type C2  
atom id #2/D:400@O idatm_type O2  
atom id #2/D:400@CB idatm_type C3  
atom id #2/D:400@OG1 idatm_type O3  
atom id #2/D:400@CG2 idatm_type C3  
atom id #2/D:400@H idatm_type H  
atom id #2/D:400@HA idatm_type HC  
atom id #2/D:400@HB idatm_type HC  
atom id #2/D:400@HG1 idatm_type H  
atom id #2/D:400@1HG2 idatm_type HC  
atom id #2/D:400@2HG2 idatm_type HC  
atom id #2/D:400@3HG2 idatm_type HC  
atom id #2/D:401@N idatm_type Npl  
atom id #2/D:401@CA idatm_type C3  
atom id #2/D:401@C idatm_type C2  
atom id #2/D:401@O idatm_type O2  
atom id #2/D:401@CB idatm_type C3  
atom id #2/D:401@OG idatm_type O3  
atom id #2/D:401@H idatm_type H  
atom id #2/D:401@HA idatm_type HC  
atom id #2/D:401@1HB idatm_type HC  
atom id #2/D:401@2HB idatm_type HC  
atom id #2/D:401@HG idatm_type H  
atom id #2/D:402@N idatm_type Npl  
atom id #2/D:402@CA idatm_type C3  
atom id #2/D:402@C idatm_type C2  
atom id #2/D:402@O idatm_type O2  
atom id #2/D:402@CB idatm_type C3  
atom id #2/D:402@CG idatm_type C3  
atom id #2/D:402@CD idatm_type C3  
atom id #2/D:402@HA idatm_type HC  
atom id #2/D:402@1HB idatm_type HC  
atom id #2/D:402@2HB idatm_type HC  
atom id #2/D:402@1HG idatm_type HC  
atom id #2/D:402@2HG idatm_type HC  
atom id #2/D:402@1HD idatm_type HC  
atom id #2/D:402@2HD idatm_type HC  
atom id #2/D:403@N idatm_type Npl  
atom id #2/D:403@CA idatm_type C3  
atom id #2/D:403@C idatm_type C2  
atom id #2/D:403@O idatm_type O2  
atom id #2/D:403@CB idatm_type C3  
atom id #2/D:403@CG idatm_type Cac  
atom id #2/D:403@OD1 idatm_type O2-  
atom id #2/D:403@OD2 idatm_type O2-  
atom id #2/D:403@H idatm_type H  
atom id #2/D:403@HA idatm_type HC  
atom id #2/D:403@1HB idatm_type HC  
atom id #2/D:403@2HB idatm_type HC  
atom id #2/D:404@N idatm_type Npl  
atom id #2/D:404@CA idatm_type C3  
atom id #2/D:404@C idatm_type C2  
atom id #2/D:404@O idatm_type O2  
atom id #2/D:404@CB idatm_type C3  
atom id #2/D:404@CG idatm_type Car  
atom id #2/D:404@CD1 idatm_type Car  
atom id #2/D:404@CD2 idatm_type Car  
atom id #2/D:404@CE1 idatm_type Car  
atom id #2/D:404@CE2 idatm_type Car  
atom id #2/D:404@CZ idatm_type Car  
atom id #2/D:404@OH idatm_type O3  
atom id #2/D:404@H idatm_type H  
atom id #2/D:404@HA idatm_type HC  
atom id #2/D:404@1HB idatm_type HC  
atom id #2/D:404@2HB idatm_type HC  
atom id #2/D:404@HD1 idatm_type HC  
atom id #2/D:404@HD2 idatm_type HC  
atom id #2/D:404@HE1 idatm_type HC  
atom id #2/D:404@HE2 idatm_type HC  
atom id #2/D:404@HH idatm_type H  
atom id #2/D:405@N idatm_type Npl  
atom id #2/D:405@CA idatm_type C3  
atom id #2/D:405@C idatm_type C2  
atom id #2/D:405@O idatm_type O2  
atom id #2/D:405@CB idatm_type C3  
atom id #2/D:405@CG idatm_type C3  
atom id #2/D:405@CD idatm_type C3  
atom id #2/D:405@CE idatm_type C3  
atom id #2/D:405@NZ idatm_type N3+  
atom id #2/D:405@H idatm_type H  
atom id #2/D:405@HA idatm_type HC  
atom id #2/D:405@1HB idatm_type HC  
atom id #2/D:405@2HB idatm_type HC  
atom id #2/D:405@1HG idatm_type HC  
atom id #2/D:405@2HG idatm_type HC  
atom id #2/D:405@1HD idatm_type HC  
atom id #2/D:405@2HD idatm_type HC  
atom id #2/D:405@1HE idatm_type HC  
atom id #2/D:405@2HE idatm_type HC  
atom id #2/D:405@1HZ idatm_type H  
atom id #2/D:405@2HZ idatm_type H  
atom id #2/D:405@3HZ idatm_type H  
atom id #2/D:406@N idatm_type Npl  
atom id #2/D:406@CA idatm_type C3  
atom id #2/D:406@C idatm_type C2  
atom id #2/D:406@O idatm_type O2  
atom id #2/D:406@CB idatm_type C3  
atom id #2/D:406@CG idatm_type Car  
atom id #2/D:406@CD1 idatm_type Car  
atom id #2/D:406@CD2 idatm_type Car  
atom id #2/D:406@CE1 idatm_type Car  
atom id #2/D:406@CE2 idatm_type Car  
atom id #2/D:406@CZ idatm_type Car  
atom id #2/D:406@OH idatm_type O3  
atom id #2/D:406@H idatm_type H  
atom id #2/D:406@HA idatm_type HC  
atom id #2/D:406@1HB idatm_type HC  
atom id #2/D:406@2HB idatm_type HC  
atom id #2/D:406@HD1 idatm_type HC  
atom id #2/D:406@HD2 idatm_type HC  
atom id #2/D:406@HE1 idatm_type HC  
atom id #2/D:406@HE2 idatm_type HC  
atom id #2/D:406@HH idatm_type H  
atom id #2/D:407@N idatm_type Npl  
atom id #2/D:407@CA idatm_type C3  
atom id #2/D:407@C idatm_type C2  
atom id #2/D:407@O idatm_type O2  
atom id #2/D:407@H idatm_type H  
atom id #2/D:407@1HA idatm_type HC  
atom id #2/D:407@2HA idatm_type HC  
atom id #2/D:408@N idatm_type Npl  
atom id #2/D:408@CA idatm_type C3  
atom id #2/D:408@C idatm_type C2  
atom id #2/D:408@O idatm_type O2  
atom id #2/D:408@CB idatm_type C3  
atom id #2/D:408@CG idatm_type Car  
atom id #2/D:408@CD1 idatm_type Car  
atom id #2/D:408@CD2 idatm_type Car  
atom id #2/D:408@NE1 idatm_type Npl  
atom id #2/D:408@CE2 idatm_type Car  
atom id #2/D:408@CE3 idatm_type Car  
atom id #2/D:408@CZ2 idatm_type Car  
atom id #2/D:408@CZ3 idatm_type Car  
atom id #2/D:408@CH2 idatm_type Car  
atom id #2/D:408@H idatm_type H  
atom id #2/D:408@HA idatm_type HC  
atom id #2/D:408@1HB idatm_type HC  
atom id #2/D:408@2HB idatm_type HC  
atom id #2/D:408@HD1 idatm_type HC  
atom id #2/D:408@HE1 idatm_type H  
atom id #2/D:408@HE3 idatm_type HC  
atom id #2/D:408@HZ2 idatm_type HC  
atom id #2/D:408@HZ3 idatm_type HC  
atom id #2/D:408@HH2 idatm_type HC  
atom id #2/D:409@N idatm_type Npl  
atom id #2/D:409@CA idatm_type C3  
atom id #2/D:409@C idatm_type C2  
atom id #2/D:409@O idatm_type O2  
atom id #2/D:409@H idatm_type H  
atom id #2/D:409@1HA idatm_type HC  
atom id #2/D:409@2HA idatm_type HC  
atom id #2/D:410@N idatm_type Npl  
atom id #2/D:410@CA idatm_type C3  
atom id #2/D:410@C idatm_type C2  
atom id #2/D:410@O idatm_type O2  
atom id #2/D:410@CB idatm_type C3  
atom id #2/D:410@CG idatm_type C3  
atom id #2/D:410@SD idatm_type S3  
atom id #2/D:410@CE idatm_type C3  
atom id #2/D:410@H idatm_type H  
atom id #2/D:410@HA idatm_type HC  
atom id #2/D:410@1HB idatm_type HC  
atom id #2/D:410@2HB idatm_type HC  
atom id #2/D:410@1HG idatm_type HC  
atom id #2/D:410@2HG idatm_type HC  
atom id #2/D:410@1HE idatm_type HC  
atom id #2/D:410@2HE idatm_type HC  
atom id #2/D:410@3HE idatm_type HC  
atom id #2/D:411@N idatm_type Npl  
atom id #2/D:411@CA idatm_type C3  
atom id #2/D:411@C idatm_type C2  
atom id #2/D:411@O idatm_type O2  
atom id #2/D:411@CB idatm_type C3  
atom id #2/D:411@CG idatm_type C3  
atom id #2/D:411@CD1 idatm_type C3  
atom id #2/D:411@CD2 idatm_type C3  
atom id #2/D:411@H idatm_type H  
atom id #2/D:411@HA idatm_type HC  
atom id #2/D:411@1HB idatm_type HC  
atom id #2/D:411@2HB idatm_type HC  
atom id #2/D:411@HG idatm_type HC  
atom id #2/D:411@1HD1 idatm_type HC  
atom id #2/D:411@2HD1 idatm_type HC  
atom id #2/D:411@3HD1 idatm_type HC  
atom id #2/D:411@1HD2 idatm_type HC  
atom id #2/D:411@2HD2 idatm_type HC  
atom id #2/D:411@3HD2 idatm_type HC  
atom id #2/D:412@N idatm_type Npl  
atom id #2/D:412@CA idatm_type C3  
atom id #2/D:412@C idatm_type C2  
atom id #2/D:412@O idatm_type O2  
atom id #2/D:412@CB idatm_type C3  
atom id #2/D:412@CG idatm_type C2  
atom id #2/D:412@OD1 idatm_type O2  
atom id #2/D:412@ND2 idatm_type Npl  
atom id #2/D:412@H idatm_type H  
atom id #2/D:412@HA idatm_type HC  
atom id #2/D:412@1HB idatm_type HC  
atom id #2/D:412@2HB idatm_type HC  
atom id #2/D:412@1HD2 idatm_type H  
atom id #2/D:412@2HD2 idatm_type H  
atom id #2/D:413@N idatm_type Npl  
atom id #2/D:413@CA idatm_type C3  
atom id #2/D:413@C idatm_type C2  
atom id #2/D:413@O idatm_type O2  
atom id #2/D:413@CB idatm_type C3  
atom id #2/D:413@CG idatm_type C3  
atom id #2/D:413@CD idatm_type C2  
atom id #2/D:413@OE1 idatm_type O2  
atom id #2/D:413@NE2 idatm_type Npl  
atom id #2/D:413@H idatm_type H  
atom id #2/D:413@HA idatm_type HC  
atom id #2/D:413@1HB idatm_type HC  
atom id #2/D:413@2HB idatm_type HC  
atom id #2/D:413@1HG idatm_type HC  
atom id #2/D:413@2HG idatm_type HC  
atom id #2/D:413@1HE2 idatm_type H  
atom id #2/D:413@2HE2 idatm_type H  
atom id #2/D:414@N idatm_type Npl  
atom id #2/D:414@CA idatm_type C3  
atom id #2/D:414@C idatm_type Cac  
atom id #2/D:414@O idatm_type O2-  
atom id #2/D:414@OXT idatm_type O2-  
atom id #2/D:414@CB idatm_type C3  
atom id #2/D:414@CG idatm_type C3  
atom id #2/D:414@CD idatm_type Cac  
atom id #2/D:414@OE1 idatm_type O2-  
atom id #2/D:414@OE2 idatm_type O2-  
atom id #2/D:414@H idatm_type H  
atom id #2/D:414@HA idatm_type HC  
atom id #2/D:414@1HB idatm_type HC  
atom id #2/D:414@2HB idatm_type HC  
atom id #2/D:414@1HG idatm_type HC  
atom id #2/D:414@2HG idatm_type HC  
atom id #2/P:74@N idatm_type N3+  
atom id #2/P:74@CA idatm_type C3  
atom id #2/P:74@C idatm_type C2  
atom id #2/P:74@O idatm_type O2  
atom id #2/P:74@CB idatm_type C3  
atom id #2/P:74@CG1 idatm_type C3  
atom id #2/P:74@CG2 idatm_type C3  
atom id #2/P:74@CD1 idatm_type C3  
atom id #2/P:74@1H idatm_type H  
atom id #2/P:74@2H idatm_type H  
atom id #2/P:74@3H idatm_type H  
atom id #2/P:74@HA idatm_type HC  
atom id #2/P:74@HB idatm_type HC  
atom id #2/P:74@1HG1 idatm_type HC  
atom id #2/P:74@2HG1 idatm_type HC  
atom id #2/P:74@1HG2 idatm_type HC  
atom id #2/P:74@2HG2 idatm_type HC  
atom id #2/P:74@3HG2 idatm_type HC  
atom id #2/P:74@1HD1 idatm_type HC  
atom id #2/P:74@2HD1 idatm_type HC  
atom id #2/P:74@3HD1 idatm_type HC  
atom id #2/P:75@N idatm_type Npl  
atom id #2/P:75@CA idatm_type C3  
atom id #2/P:75@C idatm_type C2  
atom id #2/P:75@O idatm_type O2  
atom id #2/P:75@CB idatm_type C3  
atom id #2/P:75@OG idatm_type O3  
atom id #2/P:75@H idatm_type H  
atom id #2/P:75@HA idatm_type HC  
atom id #2/P:75@1HB idatm_type HC  
atom id #2/P:75@2HB idatm_type HC  
atom id #2/P:75@HG idatm_type H  
atom id #2/P:76@N idatm_type Npl  
atom id #2/P:76@CA idatm_type C3  
atom id #2/P:76@C idatm_type C2  
atom id #2/P:76@O idatm_type O2  
atom id #2/P:76@CB idatm_type C3  
atom id #2/P:76@OG idatm_type O3  
atom id #2/P:76@H idatm_type H  
atom id #2/P:76@HA idatm_type HC  
atom id #2/P:76@1HB idatm_type HC  
atom id #2/P:76@2HB idatm_type HC  
atom id #2/P:76@HG idatm_type H  
atom id #2/P:77@N idatm_type Npl  
atom id #2/P:77@CA idatm_type C3  
atom id #2/P:77@C idatm_type C2  
atom id #2/P:77@O idatm_type O2  
atom id #2/P:77@CB idatm_type C3  
atom id #2/P:77@CG idatm_type C3  
atom id #2/P:77@CD idatm_type C2  
atom id #2/P:77@OE1 idatm_type O2  
atom id #2/P:77@NE2 idatm_type Npl  
atom id #2/P:77@H idatm_type H  
atom id #2/P:77@HA idatm_type HC  
atom id #2/P:77@1HB idatm_type HC  
atom id #2/P:77@2HB idatm_type HC  
atom id #2/P:77@1HG idatm_type HC  
atom id #2/P:77@2HG idatm_type HC  
atom id #2/P:77@1HE2 idatm_type H  
atom id #2/P:77@2HE2 idatm_type H  
atom id #2/P:78@N idatm_type Npl  
atom id #2/P:78@CA idatm_type C3  
atom id #2/P:78@C idatm_type C2  
atom id #2/P:78@O idatm_type O2  
atom id #2/P:78@CB idatm_type C3  
atom id #2/P:78@H idatm_type H  
atom id #2/P:78@HA idatm_type HC  
atom id #2/P:78@1HB idatm_type HC  
atom id #2/P:78@2HB idatm_type HC  
atom id #2/P:78@3HB idatm_type HC  
atom id #2/P:79@N idatm_type Npl  
atom id #2/P:79@CA idatm_type C3  
atom id #2/P:79@C idatm_type Cac  
atom id #2/P:79@O idatm_type O2-  
atom id #2/P:79@OXT idatm_type O2-  
atom id #2/P:79@CB idatm_type C3  
atom id #2/P:79@OG idatm_type O3  
atom id #2/P:79@H idatm_type H  
atom id #2/P:79@HA idatm_type HC  
atom id #2/P:79@1HB idatm_type HC  
atom id #2/P:79@2HB idatm_type HC  
atom id #2/P:79@HG idatm_type H  

> info selection atom

Expected a keyword  

> info selection, atom

Expected a models specifier or a keyword  

> info selection, residue

Expected a models specifier or a keyword  

> info selection, residue

Expected a models specifier or a keyword  

> info selection, residue residue

Expected a models specifier or a keyword  

> info selection residue residue

Expected a keyword  

> info selection residue atom

Expected a keyword  

> info selection level residue

residue id #1/D:341 name ILE index 264  
residue id #1/D:342 name GLY index 265  
residue id #1/D:343 name SER index 266  
residue id #1/D:344 name SER index 267  

> ui mousemode right select

> select #1/D:163

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

> select add #1/D:162

13 atoms, 11 bonds, 2 residues, 2 models selected  

> select add #1/D:161

22 atoms, 19 bonds, 3 residues, 2 models selected  

> select add #1/D:160

30 atoms, 26 bonds, 4 residues, 2 models selected  

> select add #1/D:159

37 atoms, 32 bonds, 5 residues, 2 models selected  

> select add #1/D:158

46 atoms, 40 bonds, 6 residues, 2 models selected  

> info selection level residue

residue id #1/D:158 name GLU index 81  
residue id #1/D:159 name THR index 82  
residue id #1/D:160 name ASN index 83  
residue id #1/D:161 name LYS index 84  
residue id #1/D:162 name SER index 85  
residue id #1/D:163 name VAL index 86  

> select #1/D:240

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

> select add #1/D:239

19 atoms, 17 bonds, 2 residues, 2 models selected  

> select add #1/D:238

23 atoms, 20 bonds, 3 residues, 2 models selected  

> select #1/D:192

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

> select add #1/D:191

9 atoms, 7 bonds, 2 residues, 2 models selected  

> select add #1/D:190

20 atoms, 18 bonds, 3 residues, 2 models selected  

> select #1/D:343

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

> select #1/D:122

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

> select #1/D:238

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

> select add #1/D:239

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select add #1/D:240

23 atoms, 20 bonds, 3 residues, 2 models selected  

> select #1/D341-344,158-163,238-240,190-192,122

Nothing selected  

> select #1/D:341-344,158-163,238-240,190-192,122

123 atoms, 120 bonds, 4 pseudobonds, 17 residues, 2 models selected  

> select #1/D:340

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

> select #1/D:340-344,158-163,238-240,190-192,122

127 atoms, 124 bonds, 4 pseudobonds, 18 residues, 2 models selected  

> select #1/D:340-344,158-163,238-240,190-192,122 & 1#/P

Expected a keyword  

> select #1/D:340-344,158-163,238-240,190-192,122 | 1#/P

Expected a keyword  

> select (#1/D:340-344,158-163,238-240,190-192,122 | 1#/P)

Expected an objects specifier or a keyword  

> select #1/P,D:340-344,158-163,238-240,190-192,122

127 atoms, 124 bonds, 4 pseudobonds, 18 residues, 2 models selected  

> name frozen bindsite sel

> invert bindsite

Unknown command: invert bindsite  

> ~bindsite

Unknown command: ~bindsite  

> select ~bindsite

7728 atoms, 7833 bonds, 22 pseudobonds, 670 residues, 5 models selected  

> hide

> show

> hide

> show bindsite

> show #1/P

> bindsite

Unknown command: bindsite  

> select bindsite

2597 atoms, 124 bonds, 4 pseudobonds, 338 residues, 2 models selected  

> select up

2599 atoms, 2650 bonds, 4 pseudobonds, 340 residues, 3 models selected  

> select up

2612 atoms, 2663 bonds, 4 pseudobonds, 340 residues, 4 models selected  

> select up

2638 atoms, 2689 bonds, 4 pseudobonds, 344 residues, 4 models selected  

> name frozen bindsite sel

[Repeated 1 time(s)]

> select ~bindsite

5217 atoms, 5268 bonds, 344 residues, 3 models selected  

> hide

> show bindsite

> select ~bindsite

5217 atoms, 5268 bonds, 344 residues, 3 models selected  

> hide #!1 atoms

> select bindste

Expected an objects specifier or a keyword  

> select bindsite

2638 atoms, 2689 bonds, 26 pseudobonds, 344 residues, 2 models selected  

> info bindsite level residue

Expected a keyword  

> info selection level residue

residue id #1/D:77 name TYR index 0  
residue id #1/D:78 name ASN index 1  
residue id #1/D:79 name GLY index 2  
residue id #1/D:80 name SER index 3  
residue id #1/D:81 name THR index 4  
residue id #1/D:82 name VAL index 5  
residue id #1/D:83 name LYS index 6  
residue id #1/D:84 name ILE index 7  
residue id #1/D:85 name GLY index 8  
residue id #1/D:86 name ILE index 9  
residue id #1/D:87 name LEU index 10  
residue id #1/D:88 name ASP index 11  
residue id #1/D:89 name SER index 12  
residue id #1/D:90 name ASP index 13  
residue id #1/D:91 name PHE index 14  
residue id #1/D:92 name THR index 15  
residue id #1/D:93 name ASP index 16  
residue id #1/D:94 name PRO index 17  
residue id #1/D:95 name VAL index 18  
residue id #1/D:96 name ARG index 19  
residue id #1/D:97 name LYS index 20  
residue id #1/D:98 name ALA index 21  
residue id #1/D:99 name GLN index 22  
residue id #1/D:100 name LEU index 23  
residue id #1/D:101 name SER index 24  
residue id #1/D:102 name ALA index 25  
residue id #1/D:103 name ARG index 26  
residue id #1/D:104 name TYR index 27  
residue id #1/D:105 name PRO index 28  
residue id #1/D:106 name GLY index 29  
residue id #1/D:107 name ILE index 30  
residue id #1/D:108 name GLU index 31  
residue id #1/D:109 name PHE index 32  
residue id #1/D:110 name ILE index 33  
residue id #1/D:111 name PRO index 34  
residue id #1/D:112 name ARG index 35  
residue id #1/D:113 name VAL index 36  
residue id #1/D:114 name ASN index 37  
residue id #1/D:115 name SER index 38  
residue id #1/D:116 name ASP index 39  
residue id #1/D:117 name THR index 40  
residue id #1/D:118 name SER index 41  
residue id #1/D:119 name THR index 42  
residue id #1/D:120 name SER index 43  
residue id #1/D:121 name SER index 44  
residue id #1/D:122 name HIS index 45  
residue id #1/D:123 name GLY index 46  
residue id #1/D:124 name VAL index 47  
residue id #1/D:125 name GLN index 48  
residue id #1/D:126 name VAL index 49  
residue id #1/D:127 name LEU index 50  
residue id #1/D:128 name GLU index 51  
residue id #1/D:129 name VAL index 52  
residue id #1/D:130 name MET index 53  
residue id #1/D:131 name MET index 54  
residue id #1/D:132 name ASP index 55  
residue id #1/D:133 name THR index 56  
residue id #1/D:134 name LEU index 57  
residue id #1/D:135 name GLU index 58  
residue id #1/D:136 name ASP index 59  
residue id #1/D:137 name ARG index 60  
residue id #1/D:138 name THR index 61  
residue id #1/D:139 name LYS index 62  
residue id #1/D:140 name GLY index 63  
residue id #1/D:141 name LYS index 64  
residue id #1/D:142 name ALA index 65  
residue id #1/D:143 name LYS index 66  
residue id #1/D:144 name PHE index 67  
residue id #1/D:145 name LYS index 68  
residue id #1/D:146 name ALA index 69  
residue id #1/D:147 name ILE index 70  
residue id #1/D:148 name ALA index 71  
residue id #1/D:149 name ALA index 72  
residue id #1/D:150 name SER index 73  
residue id #1/D:151 name ILE index 74  
residue id #1/D:152 name GLY index 75  
residue id #1/D:153 name ASN index 76  
residue id #1/D:154 name GLY index 77  
residue id #1/D:155 name GLY index 78  
residue id #1/D:156 name ALA index 79  
residue id #1/D:157 name SER index 80  
residue id #1/D:158 name GLU index 81  
residue id #1/D:159 name THR index 82  
residue id #1/D:160 name ASN index 83  
residue id #1/D:161 name LYS index 84  
residue id #1/D:162 name SER index 85  
residue id #1/D:163 name VAL index 86  
residue id #1/D:164 name ASN index 87  
residue id #1/D:165 name PRO index 88  
residue id #1/D:166 name ASN index 89  
residue id #1/D:167 name VAL index 90  
residue id #1/D:168 name LYS index 91  
residue id #1/D:169 name THR index 92  
residue id #1/D:170 name TYR index 93  
residue id #1/D:171 name GLU index 94  
residue id #1/D:172 name LYS index 95  
residue id #1/D:173 name VAL index 96  
residue id #1/D:174 name PHE index 97  
residue id #1/D:175 name GLU index 98  
residue id #1/D:176 name ARG index 99  
residue id #1/D:177 name PHE index 100  
residue id #1/D:178 name ASN index 101  
residue id #1/D:179 name PHE index 102  
residue id #1/D:180 name ASN index 103  
residue id #1/D:181 name GLN index 104  
residue id #1/D:182 name LYS index 105  
residue id #1/D:183 name VAL index 106  
residue id #1/D:184 name LYS index 107  
residue id #1/D:185 name VAL index 108  
residue id #1/D:186 name VAL index 109  
residue id #1/D:187 name ASN index 110  
residue id #1/D:188 name GLN index 111  
residue id #1/D:189 name SER index 112  
residue id #1/D:190 name PHE index 113  
residue id #1/D:191 name GLY index 114  
residue id #1/D:192 name ALA index 115  
residue id #1/D:193 name ASP index 116  
residue id #1/D:194 name ILE index 117  
residue id #1/D:195 name THR index 118  
residue id #1/D:196 name ILE index 119  
residue id #1/D:197 name GLU index 120  
residue id #1/D:198 name GLU index 121  
residue id #1/D:199 name ALA index 122  
residue id #1/D:200 name PRO index 123  
residue id #1/D:201 name TYR index 124  
residue id #1/D:202 name THR index 125  
residue id #1/D:203 name LYS index 126  
residue id #1/D:204 name ASN index 127  
residue id #1/D:205 name ASN index 128  
residue id #1/D:206 name ILE index 129  
residue id #1/D:207 name ARG index 130  
residue id #1/D:208 name ASN index 131  
residue id #1/D:209 name TYR index 132  
residue id #1/D:210 name VAL index 133  
residue id #1/D:211 name TRP index 134  
residue id #1/D:212 name ALA index 135  
residue id #1/D:213 name GLY index 136  
residue id #1/D:214 name ASP index 137  
residue id #1/D:215 name SER index 138  
residue id #1/D:216 name LYS index 139  
residue id #1/D:217 name PRO index 140  
residue id #1/D:218 name PHE index 141  
residue id #1/D:219 name ALA index 142  
residue id #1/D:220 name THR index 143  
residue id #1/D:221 name TYR index 144  
residue id #1/D:222 name PHE index 145  
residue id #1/D:223 name GLU index 146  
residue id #1/D:224 name GLU index 147  
residue id #1/D:225 name LYS index 148  
residue id #1/D:226 name VAL index 149  
residue id #1/D:227 name ASN index 150  
residue id #1/D:228 name ASN index 151  
residue id #1/D:229 name ASP index 152  
residue id #1/D:230 name GLY index 153  
residue id #1/D:231 name GLY index 154  
residue id #1/D:232 name LEU index 155  
residue id #1/D:233 name PHE index 156  
residue id #1/D:234 name VAL index 157  
residue id #1/D:235 name TRP index 158  
residue id #1/D:236 name ALA index 159  
residue id #1/D:237 name ALA index 160  
residue id #1/D:238 name GLY index 161  
residue id #1/D:239 name ASN index 162  
residue id #1/D:240 name ARG index 163  
residue id #1/D:241 name LYS index 164  
residue id #1/D:242 name GLY index 165  
residue id #1/D:243 name ALA index 166  
residue id #1/D:244 name THR index 167  
residue id #1/D:245 name GLU index 168  
residue id #1/D:246 name THR index 169  
residue id #1/D:247 name ASN index 170  
residue id #1/D:248 name PRO index 171  
residue id #1/D:249 name GLY index 172  
residue id #1/D:250 name GLN index 173  
residue id #1/D:251 name ASP index 174  
residue id #1/D:252 name MET index 175  
residue id #1/D:253 name ASP index 176  
residue id #1/D:254 name SER index 177  
residue id #1/D:255 name VAL index 178  
residue id #1/D:256 name GLY index 179  
residue id #1/D:257 name MET index 180  
residue id #1/D:258 name GLU index 181  
residue id #1/D:259 name ALA index 182  
residue id #1/D:260 name GLY index 183  
residue id #1/D:261 name LEU index 184  
residue id #1/D:262 name PRO index 185  
residue id #1/D:263 name TYR index 186  
residue id #1/D:264 name LEU index 187  
residue id #1/D:265 name VAL index 188  
residue id #1/D:266 name ASN index 189  
residue id #1/D:267 name ASP index 190  
residue id #1/D:268 name LEU index 191  
residue id #1/D:269 name GLU index 192  
residue id #1/D:270 name LYS index 193  
residue id #1/D:271 name GLY index 194  
residue id #1/D:272 name TRP index 195  
residue id #1/D:273 name ILE index 196  
residue id #1/D:274 name ALA index 197  
residue id #1/D:275 name VAL index 198  
residue id #1/D:276 name VAL index 199  
residue id #1/D:277 name GLY index 200  
residue id #1/D:278 name ILE index 201  
residue id #1/D:279 name GLN index 202  
residue id #1/D:280 name PRO index 203  
residue id #1/D:281 name LYS index 204  
residue id #1/D:282 name GLU index 205  
residue id #1/D:283 name THR index 206  
residue id #1/D:284 name VAL index 207  
residue id #1/D:285 name ARG index 208  
residue id #1/D:286 name VAL index 209  
residue id #1/D:287 name GLY index 210  
residue id #1/D:288 name THR index 211  
residue id #1/D:289 name ALA index 212  
residue id #1/D:290 name PRO index 213  
residue id #1/D:291 name ASP index 214  
residue id #1/D:292 name GLY index 215  
residue id #1/D:293 name THR index 216  
residue id #1/D:294 name PRO index 217  
residue id #1/D:295 name ILE index 218  
residue id #1/D:296 name VAL index 219  
residue id #1/D:297 name ASN index 220  
residue id #1/D:298 name ILE index 221  
residue id #1/D:299 name LYS index 222  
residue id #1/D:300 name PRO index 223  
residue id #1/D:301 name ASN index 224  
residue id #1/D:302 name GLY index 225  
residue id #1/D:303 name LYS index 226  
residue id #1/D:304 name LEU index 227  
residue id #1/D:305 name ASN index 228  
residue id #1/D:306 name ILE index 229  
residue id #1/D:307 name HIS index 230  
residue id #1/D:308 name ARG index 231  
residue id #1/D:309 name THR index 232  
residue id #1/D:310 name GLY index 233  
residue id #1/D:311 name THR index 234  
residue id #1/D:312 name ASP index 235  
residue id #1/D:313 name ARG index 236  
residue id #1/D:314 name LEU index 237  
residue id #1/D:315 name ALA index 238  
residue id #1/D:316 name TYR index 239  
residue id #1/D:317 name ALA index 240  
residue id #1/D:318 name GLY index 241  
residue id #1/D:319 name ASP index 242  
residue id #1/D:320 name ASN index 243  
residue id #1/D:321 name ALA index 244  
residue id #1/D:322 name LYS index 245  
residue id #1/D:323 name TYR index 246  
residue id #1/D:324 name TRP index 247  
residue id #1/D:325 name SER index 248  
residue id #1/D:326 name ILE index 249  
residue id #1/D:327 name SER index 250  
residue id #1/D:328 name ALA index 251  
residue id #1/D:329 name ASP index 252  
residue id #1/D:330 name ASP index 253  
residue id #1/D:331 name SER index 254  
residue id #1/D:332 name ALA index 255  
residue id #1/D:333 name ILE index 256  
residue id #1/D:334 name PRO index 257  
residue id #1/D:335 name THR index 258  
residue id #1/D:336 name ALA index 259  
residue id #1/D:337 name GLY index 260  
residue id #1/D:338 name ARG index 261  
residue id #1/D:339 name ALA index 262  
residue id #1/D:340 name GLY index 263  
residue id #1/D:341 name ILE index 264  
residue id #1/D:342 name GLY index 265  
residue id #1/D:343 name SER index 266  
residue id #1/D:344 name SER index 267  
residue id #1/D:345 name TYR index 268  
residue id #1/D:346 name ALA index 269  
residue id #1/D:347 name ALA index 270  
residue id #1/D:348 name PRO index 271  
residue id #1/D:349 name ARG index 272  
residue id #1/D:350 name VAL index 273  
residue id #1/D:351 name SER index 274  
residue id #1/D:352 name ARG index 275  
residue id #1/D:353 name ALA index 276  
residue id #1/D:354 name ALA index 277  
residue id #1/D:355 name ALA index 278  
residue id #1/D:356 name LEU index 279  
residue id #1/D:357 name VAL index 280  
residue id #1/D:358 name ALA index 281  
residue id #1/D:359 name GLU index 282  
residue id #1/D:360 name LYS index 283  
residue id #1/D:361 name PHE index 284  
residue id #1/D:362 name ASP index 285  
residue id #1/D:363 name TRP index 286  
residue id #1/D:364 name MET index 287  
residue id #1/D:365 name THR index 288  
residue id #1/D:366 name ALA index 289  
residue id #1/D:367 name ASP index 290  
residue id #1/D:368 name GLN index 291  
residue id #1/D:369 name VAL index 292  
residue id #1/D:370 name ARG index 293  
residue id #1/D:371 name GLN index 294  
residue id #1/D:372 name THR index 295  
residue id #1/D:373 name LEU index 296  
residue id #1/D:374 name PHE index 297  
residue id #1/D:375 name THR index 298  
residue id #1/D:376 name THR index 299  
residue id #1/D:377 name THR index 300  
residue id #1/D:378 name ASP index 301  
residue id #1/D:379 name ASP index 302  
residue id #1/D:380 name THR index 303  
residue id #1/D:381 name GLU index 304  
residue id #1/D:382 name LEU index 305  
residue id #1/D:383 name ASP index 306  
residue id #1/D:384 name ALA index 307  
residue id #1/D:385 name SER index 308  
residue id #1/D:386 name LEU index 309  
residue id #1/D:387 name ALA index 310  
residue id #1/D:388 name GLY index 311  
residue id #1/D:389 name ASN index 312  
residue id #1/D:390 name ALA index 313  
residue id #1/D:391 name ASN index 314  
residue id #1/D:392 name ALA index 315  
residue id #1/D:393 name GLU index 316  
residue id #1/D:394 name LYS index 317  
residue id #1/D:395 name ARG index 318  
residue id #1/D:396 name ARG index 319  
residue id #1/D:397 name ARG index 320  
residue id #1/D:398 name VAL index 321  
residue id #1/D:399 name LYS index 322  
residue id #1/D:400 name THR index 323  
residue id #1/D:401 name SER index 324  
residue id #1/D:402 name PRO index 325  
residue id #1/D:403 name ASP index 326  
residue id #1/D:404 name TYR index 327  
residue id #1/D:405 name LYS index 328  
residue id #1/D:406 name TYR index 329  
residue id #1/D:407 name GLY index 330  
residue id #1/D:408 name TRP index 331  
residue id #1/D:409 name GLY index 332  
residue id #1/D:410 name MET index 333  
residue id #1/D:411 name LEU index 334  
residue id #1/D:412 name ASN index 335  
residue id #1/D:413 name GLN index 336  
residue id #1/D:414 name GLU index 337  
residue id #1/P:74 name ILE index 0  
residue id #1/P:75 name SER index 1  
residue id #1/P:76 name SER index 2  
residue id #1/P:77 name GLN index 3  
residue id #1/P:78 name ALA index 4  
residue id #1/P:79 name SER index 5  

> select ~bindsite

5217 atoms, 5268 bonds, 344 residues, 3 models selected  

> delete relax_long_fusolisin_ISSQAS_0001_0078.pdb

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete #2

> select ~bindsite

2 models selected  

> select bindsite

2638 atoms, 2689 bonds, 26 pseudobonds, 344 residues, 2 models selected  

> show sel atoms

> select ~bindsite

2 models selected  

> hide atoms

> select peptide

41 atoms, 40 bonds, 6 residues, 1 model selected  

> show sel atoms

> select cattriad

2638 atoms, 62 bonds, 5 pseudobonds, 344 residues, 2 models selected  

> select #1/D:340-344,158-163,238-240,190-192,122

127 atoms, 124 bonds, 4 pseudobonds, 18 residues, 2 models selected  

> select #1/P,D:340-344,158-163,238-240,190-192,122

127 atoms, 124 bonds, 4 pseudobonds, 18 residues, 2 models selected  

> select #1/P,D:340-344,158-163,238-240,190-192,122

127 atoms, 124 bonds, 4 pseudobonds, 18 residues, 2 models selected  

> show sel atoms

> name frozen bindsite sel

[Repeated 1 time(s)]

> select ~bindsite

2511 atoms, 2565 bonds, 22 pseudobonds, 326 residues, 4 models selected  

> select subtract /P:78@C

2510 atoms, 2565 bonds, 22 pseudobonds, 326 residues, 6 models selected  

> select subtract /P:79@CA

2509 atoms, 2565 bonds, 22 pseudobonds, 326 residues, 6 models selected  

> select subtract /P:79@OG

2508 atoms, 2564 bonds, 22 pseudobonds, 326 residues, 6 models selected  

> select down

2508 atoms, 2564 bonds, 22 pseudobonds, 326 residues, 6 models selected  

> select down

2508 atoms, 2564 bonds, 22 pseudobonds, 326 residues, 6 models selected  

> select subtract /P:79@O

2507 atoms, 2560 bonds, 22 pseudobonds, 326 residues, 6 models selected  

> select subtract /P:79@N

2506 atoms, 2559 bonds, 22 pseudobonds, 326 residues, 6 models selected  

> select bindsite

2597 atoms, 124 bonds, 4 pseudobonds, 338 residues, 2 models selected  
Drag select of 1 residues  

> select bindsite

2597 atoms, 124 bonds, 4 pseudobonds, 338 residues, 2 models selected  

> select clear

> select bindsite

2597 atoms, 124 bonds, 4 pseudobonds, 338 residues, 2 models selected  

> select bindsite

2597 atoms, 124 bonds, 4 pseudobonds, 338 residues, 2 models selected  

> select intres

2597 atoms, 22 bonds, 338 residues, 1 model selected  

> select up

2638 atoms, 2689 bonds, 344 residues, 2 models selected  

> select clear

> select cattriad

2638 atoms, 62 bonds, 5 pseudobonds, 344 residues, 2 models selected  

> select clear

> select /D:344

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

> select /D:239@CB

1 atom, 1 residue, 1 model selected  

> select add /D:344

7 atoms, 6 bonds, 2 residues, 2 models selected  

> select up

8 atoms, 6 bonds, 2 residues, 2 models selected  

> select up

9 atoms, 7 bonds, 2 residues, 2 models selected  

> select /D:239@OD1

1 atom, 1 residue, 1 model selected  

> select add /D:239@ND2

2 atoms, 2 bonds, 1 residue, 2 models selected  

> select subtract /D:239@OD1

1 atom, 3 bonds, 1 residue, 2 models selected  

> select add /D:239@CB

2 atoms, 3 bonds, 1 residue, 2 models selected  

> select add /D:239@OD1

3 atoms, 3 bonds, 1 residue, 2 models selected  

> select add /D:344

9 atoms, 9 bonds, 2 residues, 2 models selected  

> select add /D:122

19 atoms, 19 bonds, 3 residues, 2 models selected  

> name frozen cattriad sel

> select clear

> select #1/P,D:340-344,158-163,238-240,190-192,122

127 atoms, 124 bonds, 4 pseudobonds, 18 residues, 2 models selected  

> name frozen bindsite sel

> select clear

> select ~bindsite

2511 atoms, 2565 bonds, 22 pseudobonds, 326 residues, 4 models selected  

> select clear

> select bindsite

2597 atoms, 124 bonds, 4 pseudobonds, 338 residues, 2 models selected  

> select up

2599 atoms, 2650 bonds, 4 pseudobonds, 339 residues, 3 models selected  

> select up

2606 atoms, 2657 bonds, 4 pseudobonds, 339 residues, 4 models selected  

> select up

2638 atoms, 2689 bonds, 4 pseudobonds, 344 residues, 4 models selected  

> select clear

> select #1/P,D:340-344,158-163,238-240,190-192,122

127 atoms, 124 bonds, 4 pseudobonds, 18 residues, 2 models selected  

> select add /P:77@CD

128 atoms, 124 bonds, 4 pseudobonds, 19 residues, 3 models selected  

> select up

129 atoms, 125 bonds, 4 pseudobonds, 19 residues, 4 models selected  

> select up

136 atoms, 132 bonds, 4 pseudobonds, 19 residues, 4 models selected  

> select up

629 atoms, 631 bonds, 4 pseudobonds, 90 residues, 4 models selected  

> select down

136 atoms, 132 bonds, 4 pseudobonds, 19 residues, 4 models selected  

> select up

138 atoms, 134 bonds, 4 pseudobonds, 20 residues, 4 models selected  

> select up

142 atoms, 138 bonds, 4 pseudobonds, 20 residues, 4 models selected  

> select up

629 atoms, 631 bonds, 4 pseudobonds, 90 residues, 4 models selected  

> select down

142 atoms, 138 bonds, 4 pseudobonds, 20 residues, 4 models selected  

> select add /P:74@C

143 atoms, 140 bonds, 4 pseudobonds, 21 residues, 4 models selected  

> select up

145 atoms, 140 bonds, 4 pseudobonds, 22 residues, 4 models selected  

> select up

156 atoms, 152 bonds, 4 pseudobonds, 22 residues, 4 models selected  

> select add /P:78@C

157 atoms, 152 bonds, 4 pseudobonds, 23 residues, 4 models selected  

> select up

161 atoms, 157 bonds, 4 pseudobonds, 23 residues, 4 models selected  

> select add /P:79@CA

162 atoms, 157 bonds, 4 pseudobonds, 24 residues, 4 models selected  

> select up

168 atoms, 164 bonds, 4 pseudobonds, 24 residues, 4 models selected  

> name frozen bindsite sel

[Repeated 1 time(s)]

> select clear

> select bindsite

2638 atoms, 164 bonds, 17 pseudobonds, 344 residues, 2 models selected  

> color (#!1 & sel) red

> undo

> select clear

> select cattriad

2597 atoms, 19 bonds, 338 residues, 1 model selected  

> select clear

> select /D:239@CG

1 atom, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 2 models selected  

> select add /D:344

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select up

198 atoms, 198 bonds, 29 residues, 2 models selected  

> select down

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select add /D:122

24 atoms, 22 bonds, 3 residues, 2 models selected  

> name frozen cattriad sel

> select clear

> select cattriad

2597 atoms, 22 bonds, 338 residues, 1 model selected  

> select clear

> select /D:239

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

> select add /D:344

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select add /D:122

24 atoms, 22 bonds, 3 residues, 2 models selected  

> name cattriad sel

> select cattriad

2597 atoms, 22 bonds, 338 residues, 1 model selected  

> select cattriad

2597 atoms, 2649 bonds, 13 pseudobonds, 338 residues, 2 models selected  

> select #1/D:239,122,239

18 atoms, 17 bonds, 2 residues, 1 model selected  

> name cattriad sel

> select cattriad

2597 atoms, 17 bonds, 338 residues, 1 model selected  

> name cattriad #1/D:239,122,239

> select cattriad

18 atoms, 17 bonds, 2 residues, 1 model selected  

> name bindsite #1/P,D:340-344,158-163,238-240,190-192,122

> select bindsite

127 atoms, 124 bonds, 4 pseudobonds, 18 residues, 2 models selected  

> name notbindsite ~bindsite

> select notbindsite

2511 atoms, 2565 bonds, 22 pseudobonds, 326 residues, 4 models selected  

> hide notbindsite

> name bindsite #1/P,D:340-344,158-163,238-240,190-192,122

> select bindsite

127 atoms, 124 bonds, 4 pseudobonds, 18 residues, 2 models selected  

> show sel atoms

> select /P:74-75

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select /P:74-79

41 atoms, 40 bonds, 6 residues, 1 model selected  

> name bindsite #1/P:74-79,D:340-344,158-163,238-240,190-192,122

> show sel atoms

> hide notbindsite

> show cattriad

> graphics silhouettes true

> select notbindsite

2597 atoms, 2649 bonds, 26 pseudobonds, 338 residues, 4 models selected  

> name bindsite #1/P:74-79,D:340-344,158-163,238-240,190-192,122

> name notbindsite ~bindsite

> select notbindsite

2597 atoms, 2649 bonds, 26 pseudobonds, 338 residues, 4 models selected  

> select clear

[Repeated 2 time(s)]

> select notbindsite

2597 atoms, 2649 bonds, 26 pseudobonds, 338 residues, 4 models selected  

> select bindsite

41 atoms, 40 bonds, 6 residues, 1 model selected  

> select clear

[Repeated 2 time(s)]

> ui mousemode right select

> select clear

[Repeated 1 time(s)]

> select bindsite

41 atoms, 40 bonds, 6 residues, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select bindsite

41 atoms, 40 bonds, 6 residues, 1 model selected  

> select not bindsite

Expected an objects specifier or a keyword  

> select ~bindsite

2597 atoms, 2649 bonds, 26 pseudobonds, 338 residues, 4 models selected  

> hide sel atoms

> hide sel cartoons

> show sel cartoons

> select bindsite

41 atoms, 40 bonds, 6 residues, 1 model selected  

> show sel atoms

> select clear

> select bindsite

41 atoms, 40 bonds, 6 residues, 1 model selected  

> show sel atoms

> select clear

[Repeated 1 time(s)]

> select cattriad

18 atoms, 17 bonds, 2 residues, 1 model selected  

> show sel atoms

> select ~ bindsite

2597 atoms, 2649 bonds, 26 pseudobonds, 338 residues, 4 models selected  

> graphics silhouettes false

> hide sel cartoons

> show sel cartoons

> select bindsite

41 atoms, 40 bonds, 6 residues, 1 model selected  

> select add /D:344

47 atoms, 45 bonds, 7 residues, 2 models selected  

> show sel atoms

> select add /D:239

55 atoms, 52 bonds, 8 residues, 3 models selected  

> select add /D:122

65 atoms, 62 bonds, 9 residues, 3 models selected  

> name bindsite #1/P,D:340-344,158-163,238-240,190-192,122

> select ~ bindsite

2511 atoms, 2565 bonds, 22 pseudobonds, 326 residues, 4 models selected  

> hide sel cartoons

> show sel cartoons

> select clear

> transparency (~ bindsite) 100 target c

> graphics silhouettes true

> transparency (~ bindsite) 95 target c

> transparency (~ bindsite) 90 target c

> select clear

> select bindsite

127 atoms, 124 bonds, 4 pseudobonds, 18 residues, 2 models selected  

> select add /P:74

135 atoms, 131 bonds, 4 pseudobonds, 19 residues, 3 models selected  

> select add /P:75

141 atoms, 135 bonds, 4 pseudobonds, 20 residues, 4 models selected  

> select clear

> select bindsite

127 atoms, 124 bonds, 4 pseudobonds, 18 residues, 2 models selected  

> select add /P:75

133 atoms, 129 bonds, 4 pseudobonds, 19 residues, 3 models selected  

> name bindsite select #1/P:74-79,D:340-344,158-163,238-240,190-192,122

"select #1/P:74-79,D:340-344,158-163,238-240,190-192,122": invalid atom
specifier  

> name bindsite #1/P:74-79,D:340-344,158-163,238-240,190-192,122

> name notbindsite (~ bindsite )

> select clear

> select notbindsite

2597 atoms, 2649 bonds, 26 pseudobonds, 338 residues, 4 models selected  

> select bindsite

41 atoms, 40 bonds, 6 residues, 1 model selected  

> transparency (bindsite) 0 target c

Drag select of 6 residues  

> select clear

Drag select of 6 residues  

> undo

> lighting soft

> lighting simple

> lighting full

> graphics silhouettes false

> select bindsite

41 atoms, 40 bonds, 6 residues, 1 model selected  

> select #1/P:74-79,D:340-344,158-163,238-240,190-192,122

41 atoms, 40 bonds, 6 residues, 1 model selected  

> select #1/P:74-79

41 atoms, 40 bonds, 6 residues, 1 model selected  

> D:340-344,158-163,238-240,190-192,122

Unknown command: D:340-344,158-163,238-240,190-192,122  

> select #1/P:74-79,D:340-344,158-163,238-240,190-192,122

41 atoms, 40 bonds, 6 residues, 1 model selected  

> select #1/D:340-344,158-163,238-240,190-192,122

127 atoms, 124 bonds, 4 pseudobonds, 18 residues, 2 models selected  

> select add /P:74

135 atoms, 131 bonds, 4 pseudobonds, 19 residues, 3 models selected  

> select up

629 atoms, 631 bonds, 4 pseudobonds, 90 residues, 4 models selected  

> select down

135 atoms, 131 bonds, 4 pseudobonds, 19 residues, 4 models selected  

> select add /P:75

141 atoms, 136 bonds, 4 pseudobonds, 20 residues, 4 models selected  

> select add /P:76

147 atoms, 141 bonds, 4 pseudobonds, 21 residues, 4 models selected  

> select add /P:77

156 atoms, 149 bonds, 4 pseudobonds, 22 residues, 4 models selected  

> select add /P:79

163 atoms, 156 bonds, 4 pseudobonds, 23 residues, 4 models selected  

> select add /P:78

168 atoms, 159 bonds, 4 pseudobonds, 24 residues, 4 models selected  

> name bindsite2 sel

> select bindsite2

2638 atoms, 164 bonds, 17 pseudobonds, 344 residues, 2 models selected  

> select clear

> select bindsite

41 atoms, 40 bonds, 6 residues, 1 model selected  

> select cattriad

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select add /D:240

29 atoms, 27 bonds, 3 residues, 2 models selected  

> select add /D:238

33 atoms, 30 bonds, 4 residues, 2 models selected  

> select add /P:77

42 atoms, 38 bonds, 5 residues, 2 models selected  

> select add /P:78

47 atoms, 42 bonds, 6 residues, 3 models selected  

> select add /P:79

54 atoms, 48 bonds, 7 residues, 3 models selected  

> select add /P:76

60 atoms, 53 bonds, 8 residues, 3 models selected  

> select add /P:75

66 atoms, 58 bonds, 9 residues, 3 models selected  

> select add /P:74

74 atoms, 65 bonds, 10 residues, 3 models selected  

> select add /D:192

79 atoms, 69 bonds, 11 residues, 3 models selected  

> select add /D:245

88 atoms, 77 bonds, 12 residues, 3 models selected  

> select add /D:246

95 atoms, 83 bonds, 13 residues, 3 models selected  

> select add /D:191

99 atoms, 86 bonds, 14 residues, 3 models selected  

> select subtract /D:245

90 atoms, 78 bonds, 13 residues, 3 models selected  

> select subtract /D:246

83 atoms, 72 bonds, 12 residues, 3 models selected  

> select add /D:190

94 atoms, 83 bonds, 13 residues, 3 models selected  

> select add /D:160

102 atoms, 90 bonds, 14 residues, 3 models selected  

> select add /D:161

111 atoms, 98 bonds, 15 residues, 3 models selected  

> select add /D:162

117 atoms, 103 bonds, 16 residues, 3 models selected  

> select add /D:163

124 atoms, 109 bonds, 17 residues, 3 models selected  

> select add /D:159

131 atoms, 115 bonds, 18 residues, 3 models selected  

> select add /D:158

140 atoms, 123 bonds, 19 residues, 3 models selected  

> select add /D:343

146 atoms, 128 bonds, 20 residues, 3 models selected  

> select add /D:344

152 atoms, 133 bonds, 21 residues, 3 models selected  

> select subtract /P:79

145 atoms, 127 bonds, 20 residues, 3 models selected  

> select subtract /P:78

140 atoms, 123 bonds, 19 residues, 3 models selected  

> select add /P:78

145 atoms, 127 bonds, 20 residues, 3 models selected  

> select add /P:79

152 atoms, 133 bonds, 21 residues, 3 models selected  

> select add /D:342

156 atoms, 136 bonds, 22 residues, 3 models selected  

> select add /D:341

164 atoms, 143 bonds, 23 residues, 3 models selected  

> select add /D:340

168 atoms, 146 bonds, 24 residues, 3 models selected  

> name bindsite2 sel

> save figure_v1.png

> select add /D:270

177 atoms, 154 bonds, 25 residues, 3 models selected  

> select subtract /D:270

168 atoms, 146 bonds, 24 residues, 3 models selected  

> select subtract /D:343

162 atoms, 141 bonds, 11 pseudobonds, 23 residues, 4 models selected  

> select add /D:343

168 atoms, 146 bonds, 11 pseudobonds, 24 residues, 4 models selected  

> save figure_v1.png

> save figure_v1.png supersample 3

> cartoon style rounded

Expected an atoms specifier or a keyword  

> cartoon

> name frozen bindsite sel

[Repeated 1 time(s)]

> select clear

[Repeated 1 time(s)]

> cartoon style xsection oval modeHelix default

> select bindsite

2638 atoms, 164 bonds, 17 pseudobonds, 344 residues, 2 models selected  

> select clear

> select notbindsite

2470 atoms, 2525 bonds, 9 pseudobonds, 320 residues, 4 models selected  

> select ~ notbindsite

168 atoms, 164 bonds, 17 pseudobonds, 24 residues, 2 models selected  

> select add /D:123

172 atoms, 167 bonds, 17 pseudobonds, 25 residues, 4 models selected  

> select add /D:121

178 atoms, 172 bonds, 17 pseudobonds, 26 residues, 4 models selected  

> show sel cartoons

> transparency sel 0

> transparency sel 0 target c

> select add /D:345

190 atoms, 184 bonds, 17 pseudobonds, 27 residues, 4 models selected  

> transparency sel 0 target c

> save /sci/labs/fora/projects/fusolisin/fusolisin_figure.cxs

——— End of log from Mon Jun 6 17:29:07 2022 ———

opened ChimeraX session  

failed to create compose table  

> save figure_v3.png width 2400 height 2400

> ui mousemode right translate

> save figure_v3.png width 2400 height 2400

> save figure_v3.png width 1600 height 1600

> save figure_v3.png width 2400 height 2400

> ui mousemode right zoom

> save figure_v3.png width 2400 height 2400

> 2dlabels text "HIS 144" bgColor white color light green size 14

> 2dlabels "HIS 144" bgColor white color light green size 16

Expected 'all' or a 2d label name or a label models specifier or a keyword  

> 2dlabels "HIS144" bgColor white color light green size 16

Expected 'all' or a 2d label name or a label models specifier or a keyword  

> 2dlabels HIS 144 bgColor white color light green size 16

Expected 'all' or a 2d label name or a label models specifier or a keyword  

> 2dlabels HIS144 bgColor white color light green size 16

Expected 'all' or a 2d label name or a label models specifier or a keyword  

> 2dlabels #2.1 bgColor white color light green size 16

> 2dlabels #2.1 bgColor white color light green size 120

> 2dlabels #2.1 bgColor white color light green size 20

> undo

No undo action is available  

> 2dlabels #2.1 bgColor white color light green size 20

> ui mousemode right label

> ui mousemode right "move label"

> 2dlabels #2.1 xpos 0.646 ypos 0.333

> 2dlabels text "SER 344" bgColor white color light green size 20

> 2dlabels #2.2 xpos 0.524 ypos 0.275

> select up

708 atoms, 711 bonds, 17 pseudobonds, 101 residues, 2 models selected  

> select down

190 atoms, 184 bonds, 17 pseudobonds, 27 residues, 4 models selected  

> 2dlabels #2.1 bgColor text "HIS 122" Color white color light green size 20

Invalid "bgColor" argument: Expected 'none' or a color  

> 2dlabels #2.1 text "HIS 122" bgColor white color light green size 20

> 2dlabels text "ASN 239" bgColor white color light green size 20

> 2dlabels #2.3 xpos 0.296 ypos 0.460

> 2dlabels text "ASN 239" bgColor white color light green size 20 bold true

> hide #2.3 models

> 2dlabels #2.4 xpos 0.302 ypos 0.455

> 2dlabels #2.1 bgColor white color light green size 20 bold true

> 2dlabels #2.2 bgColor white color light green size 20 bold true

> save figure_v3.png width 2400 height 2400

[Repeated 1 time(s)]

> 2dlabels #2.2 bgColor white color light green size 24 bold true

> 2dlabels #2.2 xpos 0.520 ypos 0.232

> 2dlabels #2.4 bgColor white color light green size 24 bold true

> 2dlabels #2.1 bgColor white color light green size 24 bold true

> 2dlabels #2.4 xpos 0.255 ypos 0.430

> 2dlabels #2.1 xpos 0.695 ypos 0.312

> save figure_v3.png width 2400 height 2400

> save /sci/labs/fora/projects/fusolisin/fusolisin_figure.cxs

> 2dlabels text "GLY 191" bgColor white color cornflower blue size 20 bold
> true

> 2dlabels #2.5 xpos 0.291 ypos 0.850

> 2dlabels text "LYS 161" bgColor white color cornflower blue size 20 bold
> true

> 2dlabels #2.6 xpos 0.706 ypos 0.822

> 2dlabels text P1 bgColor white color light salmon blue size 20 bold true

Expected a keyword  

> 2dlabels text P1 bgColor white color light salmon size 20 bold true

> 2dlabels #2.7 xpos 0.399 ypos 0.576

> 2dlabels #2.7 xpos 0.539 ypos 0.340

> 2dlabels #2.2 xpos 0.531 ypos 0.167

> 2dlabels #2.7 xpos 0.547 ypos 0.319

> 2dlabels text P2 bgColor white color light salmon size 20 bold true

> 2dlabels #2.8 xpos 0.437 ypos 0.225

> 2dlabels text P-2 bgColor white color light salmon size 20 bold true

> 2dlabels text P-1 bgColor white color light salmon size 20 bold true

> 2dlabels #2.9 xpos 0.552 ypos 0.619

> 2dlabels #2.10 xpos 0.394 ypos 0.570

> 2dlabels #2.8 xpos 0.401 ypos 0.129

> 2dlabels text "ILE 341" bgColor white color cornflower blue size 20 bold
> true

> 2dlabels #2.11 xpos 0.398 ypos -0.019

> save /sci/labs/fora/projects/fusolisin/fusolisin_figure.cxs

> save figure_v3.png width 2400 height 2400

> ui mousemode right translate

> undo

> hide #2.3 models

> ui mousemode right "move label"

> 2dlabels #2.11 xpos 0.309 ypos -0.084

> ui mousemode right translate

Alignment identifier is 1/D  
Alignment identifier is 1/P  

> 2dlabels text "SER 162" bgColor white color cornflower blue size 20 bold
> true

> ui mousemode right label

> ui mousemode right "move label"

> 2dlabels #2.12 xpos 0.589 ypos 1.092

> save figure_v3.png width 2400 height 2400

> 2dlabels text "PHE 190" bgColor white color cornflower blue size 20 bold
> true

> 2dlabels #2.13 xpos 0.399 ypos 0.690

> save figure_v3.png width 2400 height 2400

> 2dlabels #2.8 text P𠞢 bgColor white color light salmon size 20 bold true

[Repeated 1 time(s)]

> 2dlabels #2.8 text P𠢢 bgColor white color light salmon size 20 bold true

> 2dlabels #2.8 text P₊ bgColor white color light salmon size 20 bold true

> 2dlabels #2.8 text P₊ 2 bgColor white color light salmon size 20 bold true

Expected a keyword  

> 2dlabels #2.8 text "P\\\U+208A 2" bgColor white color light salmon size 20
> bold true

Traceback (most recent call last):  
File "/usr/local/hurcs/chimerax/1.3/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "/usr/local/hurcs/chimerax/1.3/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2817, in run  
self._process_keyword_arguments(final, prev_annos)  
File "/usr/local/hurcs/chimerax/1.3/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2743, in
_process_keyword_arguments  
value, text = self._parse_arg(anno, text, session, final)  
File "/usr/local/hurcs/chimerax/1.3/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2447, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
File "/usr/local/hurcs/chimerax/1.3/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 1020, in parse  
token, text, rest = next_token(text, convert=True)  
File "/usr/local/hurcs/chimerax/1.3/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 1798, in next_token  
token = unescape(token)  
File "/usr/local/hurcs/chimerax/1.3/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 1672, in unescape  
return unescape_with_index_map(text)[0]  
File "/usr/local/hurcs/chimerax/1.3/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 1701, in unescape_with_index_map  
if text[index + count] not in '01234567':  
IndexError: string index out of range  
  
IndexError: string index out of range  
  
File "/usr/local/hurcs/chimerax/1.3/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 1701, in unescape_with_index_map  
if text[index + count] not in '01234567':  
  
See log for complete Python traceback.  
  

> 2dlabels #2.8 text "P"\\\U+208A"" bgColor white color light salmon size 20
> bold true

> 2dlabels #2.8 text P𠢢 bgColor white color light salmon size 20 bold true

> 2dlabels #2.8 text P₊

> 2dlabels bgColor white color light salmon size 20 bold true

> delete #2.3

> hide #2.3 models

> 2dlabels #2.8 text u'P₊

> 2' bgColor white color light salmon size 20 bold true

Unknown command: 2' bgColor white color light salmon size 20 bold true  

> 2dlabels #2.8 text "u'P\\\U+208A'" bgColor white color light salmon size 20
> bold true

> 2dlabels #2.8 text "u'\\\U+208A'" bgColor white color light salmon size 20
> bold true

> 2dlabels #2.8 text u'ȈA' bgColor white color light salmon size 20 bold true

> 2dlabels #2.8 xpos 0.390 ypos 0.130

> 2dlabels #2.8 text u'the \u03b1 and \u03b2 subunits' bgColor white color
> light salmon size 20 bold true

Expected a keyword  

> 2dlabels #2.8 text u'the \U03b1 and \U03b2 subunits' bgColor white color
> light salmon size 20 bold true

Expected a keyword  

> 2dlabels #2.8 text u"the \U03b1 and \U03b2 subunits" bgColor white color
> light salmon size 20 bold true

Expected a keyword  

> 2dlabels #2.8 text u"α" bgColor white color light salmon size 20 bold true

> 2dlabels #2.8 text α bgColor white color light salmon size 20 bold true

> 2dlabels #2.8 text "\\\u"+208" bgColor white color light salmon size 20 bold
> true

> 2dlabels #2.8 text "\\\u"Ȉ" bgColor white color light salmon size 20 bold
> true

> 2dlabels #2.8 text "\\\u"⁺" bgColor white color light salmon size 20 bold
> true

> 2dlabels #2.8 text "\\\u"⁸" bgColor white color light salmon size 20 bold
> true

> 2dlabels #2.8 text "\\\u"Ȉ" bgColor white color light salmon size 20 bold
> true

> 2dlabels #2.8 text "\\\u"₊" bgColor white color light salmon size 20 bold
> true

> 2dlabels #2.8 text P"₊ bgColor white color light salmon size 20 bold true

> 2dlabels #2.8 text P₊ bgColor white color light salmon size 20 bold true

> 2dlabels #2.8 text "P\U+208A"2 bgColor white color light salmon size 20 bold
> true

Invalid "text" argument: incomplete quoted text  

> 2dlabels #2.8 text P₊ bgColor white color light salmon size 20 bold true

> 2dlabels #2.8 text P𠢢 bgColor white color light salmon size 20 bold true

> 2dlabels #2.8 text "P\\\U+208A 2" bgColor white color light salmon size 20
> bold true

> 2dlabels #2.8 text "P\\\U+208A""2" bgColor white color light salmon size 20
> bold true

> 2dlabels #2.8 text "P\\\U+208A𢂊" bgColor white color light salmon size 20
> bold true

> 2dlabels #2.8 text "P\\\U+208A₂" bgColor white color light salmon size 20
> bold true

> 2dlabels #2.8 text "P\\\U+208A ₂" bgColor white color light salmon size 20
> bold true

> 2dlabels #2.8 text "P \\\U+208A ₂" bgColor white color light salmon size 20
> bold true

> 2dlabels #2.8 text P"₊ \U+2082" bgColor white color light salmon size 20
> bold true

Expected a keyword  

> 2dlabels #2.8 text "P\\\U+208A₂" bgColor white color light salmon size 20
> bold true

> 2dlabels #2.8 text "u'P\\\U+208A\\\U+2082'" bgColor white color light salmon
> size 20 bold true

> 2dlabels #2.8 text "P\\\U+208A₂" bgColor white color light salmon size 20
> bold true

> 2dlabels #2.8 text "P'\\\U+208A'\\\U+2082'" bgColor white color light salmon
> size 20 bold true

> 2dlabels #2.8 text "P"'\U+208A''\U+2082' bgColor white color light salmon
> size 20 bold true

Invalid "text" argument: incomplete quoted text  

> 2dlabels #2.8 text "P"'\U+208A' '\U+2082' bgColor white color light salmon
> size 20 bold true

Invalid "text" argument: incomplete quoted text  

> 2dlabels #2.8 text "P"'\U+208A \U+2082' bgColor white color light salmon
> size 20 bold true

Invalid "text" argument: incomplete quoted text  

> 2dlabels #2.8 text "P'\U+208A \U+2082' bgColor white color light salmon size
> 20 bold true

Invalid "text" argument: incomplete quoted text  

> 2dlabels #2.8 text "P'\\\U+208A \\\U+2082'" bgColor white color light salmon
> size 20 bold true

> 2dlabels #2.8 text P'₊ \U+2082' bgColor white color light salmon size 20
> bold true

Expected a keyword  

> 2dlabels #2.8 text P₊ \U+2082 bgColor white color light salmon size 20 bold
> true

Expected a keyword  

> 2dlabels #2.8 text P"₊ \U+2082" bgColor white color light salmon size 20
> bold true

Expected a keyword  

> 2dlabels #2.8 text "P"\\\U+208A\\\U+2082"" bgColor white color light salmon
> size 20 bold true

> 2dlabels #2.8 text "P\\\U+208A₂" bgColor white color light salmon size 20
> bold true

> 2dlabels #2.8 text "P \\\U+208A₂" bgColor white color light salmon size 20
> bold true

> 2dlabels #2.8 text P2 bgColor white color light salmon size 20 bold true

> save figure_v3.png width 2400 height 2400

> save /sci/labs/fora/projects/fusolisin/fusolisin_figure.cxs

> save /sci/labs/fora/projects/fusolisin/fusolisin_figure_v2.cxs

> surface /D

> undo

> hide sel surfaces

> surface #1/D

> transparency 95 target s

> color byhetero target a

> graphics silhouettes true

> transparency 85 target s

> graphics silhouettes true width 1

> lighting soft

> color /D cornflower blue

> color /P light salmon

> transparency 95 target s

> color byhetero target a

> select ~ notbindsite

168 atoms, 164 bonds, 17 pseudobonds, 24 residues, 2 models selected  

> select notbindsite

2470 atoms, 2525 bonds, 9 pseudobonds, 320 residues, 18 models selected  

> show sel cartoons

> transparency notbindsite 0 target s

> transparency notbindsite 0 target a

> transparency notbindsite 0.95 target s

[Repeated 1 time(s)]

> transparency notbindsite 0.95 target a

> transparency notbindsite 0.95 target s

> transparency 0.95 target a

> transparency 0.95 target s

> transparency 0 target s

> transparency 1 target s

> hide #!1.1 models

> show #!1.1 models

> hide #1.2 models

> transparency 1 target s

> transparency 1 target a

> transparency 0 target a

> transparency 0 target s

> hide #!1.1 models

Alignment identifier is 1/D  

> ui mousemode right select

> select /D:340

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

> select clear

> select /D:340

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

> select add /D:341

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select add /D:345

24 atoms, 22 bonds, 3 residues, 2 models selected  

> select /D:344-345

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select /D:341-345

36 atoms, 36 bonds, 5 residues, 1 model selected  

> select clear

> select /D:341-342

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select /D:341-346

41 atoms, 41 bonds, 6 residues, 1 model selected  

> select clear

> select /D:340

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

> select add /D:345

16 atoms, 15 bonds, 2 residues, 2 models selected  

> select /D:341

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

> select /D:341-345

36 atoms, 36 bonds, 5 residues, 1 model selected  

> select /D:340

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

> select /D:340-346

45 atoms, 45 bonds, 7 residues, 1 model selected  

> select clear

> select /D:345

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select add /D:340

16 atoms, 15 bonds, 2 residues, 2 models selected  

> transparency 0 target a

> transparency 0.96 target c

> transparency 0 target c

> lighting gentle

> lighting soft

> ui tool show "Color Actions"

> color sel light salmon

> select clear

[Repeated 1 time(s)]

> select #1/D

2597 atoms, 2649 bonds, 13 pseudobonds, 338 residues, 2 models selected  

> color sel light salmon

> select #1/P

41 atoms, 40 bonds, 6 residues, 1 model selected  

> color sel cornflower blue

> select cattriad

18 atoms, 17 bonds, 2 residues, 1 model selected  

> color sel light green

> select /D:344

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

> color sel light green

> color sel byhetero

> select /D:122@CG

1 atom, 1 residue, 1 model selected  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 2 models selected  

> color sel byhetero

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

10 atoms, 10 bonds, 1 residue, 2 models selected  

> color sel byhetero

> select /P:77

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

> select clear

[Repeated 1 time(s)]

> select /P:76

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

> select up

41 atoms, 40 bonds, 6 residues, 2 models selected  

> color sel byhetero

> select notbindsite

2470 atoms, 2525 bonds, 9 pseudobonds, 320 residues, 18 models selected  

> transparency 0.95 target notbindsite

Invalid "target" argument: Character 'n' is not an allowed target, must be one
of acrsbmpfl  

> transparency 0.95 notbindsite target a

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> transparency 0.95 notbindsite target c

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> transparency 0.95 target c

Drag select of 4 residues  
Drag select of 2 residues  

> clip front 10

> clip front 20

> clip front -10

> clip front 10

> clip front -20

> clip front 0

> clip front 10

> clip front 20

> clip front -5

> clip back

Missing "back" keyword's argument  

> clip back 5

> clip back 10

> clip back 15

> ui mousemode right translate

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting full

> lighting soft

> lighting full

> lighting shadows false

> lighting shadows true

> graphics silhouettes false

> lighting soft

[Repeated 2 time(s)]

> lighting full

> lighting simple

> save sample.png width 2400 height 2400

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting simple

> lighting soft

> lighting flat

> lighting full

> lighting shadows false

> lighting shadows true

> surface #1/D

> transparency 0.95 target s

> show #1.2 models

> hide #1.2 models

> hide #1.1.2 models

> hide #1.1.1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1 models

> show #!1 models

> transparency 0 target s

> transparency 0.98 target s

> transparency 1 target s

> select clear

> transparency 1 target s

[Repeated 1 time(s)]

> select clear

> transparency 95 target s

> hide #!1.1 models

> show #!1.1 models

> show #1.1.1 models

> show #1.1.2 models

> show #1.2 models

> hide #1.2 models

> show cartoons

> select #1/P

41 atoms, 40 bonds, 6 residues, 1 model selected  

> hide sel cartoons

> transparency 98 target s

> transparency 90 target s

> select bindsite

2638 atoms, 164 bonds, 17 pseudobonds, 344 residues, 2 models selected  

> select notbindsite

2470 atoms, 2525 bonds, 9 pseudobonds, 320 residues, 18 models selected  

> select ~ notbindsite

168 atoms, 164 bonds, 17 pseudobonds, 24 residues, 2 models selected  

> show sel atoms

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> select up

629 atoms, 631 bonds, 17 pseudobonds, 90 residues, 4 models selected  

> show sel cartoons

> transparency 0 target c

> transparency 0.5 target c

> transparency 50 target c

[Repeated 1 time(s)]

> transparency 10 target c

> transparency 0 target c

> ui mousemode right "move label"

> 2dlabels #2.1 xpos 0.692 ypos 0.497

> 2dlabels #2.2 xpos 0.526 ypos 0.367

> 2dlabels #2.7 xpos 0.499 ypos 0.405

> 2dlabels #2.3 xpos 0.269 ypos 0.540

> transparency 1 target c

> transparency 1 notbindsite target c

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> transparency 0 notbindsite target c

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> transparency notbindsite 0 target c

> transparency notbindsite 50 target c

> transparency ( ~ notbindsite) 0 target c

> hide sel surfaces

[Repeated 1 time(s)]

> select #1/D

2597 atoms, 2649 bonds, 13 pseudobonds, 338 residues, 2 models selected  

> hide sel surfaces

> graphics silhouettes false

> clip front 0

[Repeated 1 time(s)]

> clip front 10

> clip front 20

> clip front 0

> clip front 10

> clip front -30

> clip back 10

> clip back -10

> clip back 0

> clip back 30

> clip back -30

> clip back -50

> clip back -60

clip back plane is in front of front plane  

> clip back -55

clip back plane is in front of front plane  

> clip back -50

clip back plane is in front of front plane  

> clip back -40

clip back plane is in front of front plane  

> clip back 0

clip back plane is in front of front plane  

> clip back 200

> ui mousemode right translate

> graphics silhouettes true

> graphics silhouettes false

> select clear

> clip back 10

> clip back -20

> clip back -5

> ui mousemode right select

> select /D:190@CB

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 11 bonds, 1 residue, 2 models selected  

> hide sel atoms

> select /D:163@CB

1 atom, 1 residue, 1 model selected  

> select up

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

> hide sel atoms

> select /D:161@CG

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> select up

11 atoms, 9 bonds, 2 residues, 2 models selected  

> select up

20 atoms, 18 bonds, 2 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel byhetero

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

7 atoms, 6 bonds, 1 residue, 2 models selected  

> hide sel atoms

> clip back -3

> clip back 3

> clip back -1

> clip back 1

> 2dlabels #2.1 color light green

> ui mousemode right "move label"

> 2dlabels #2.1 xpos 0.659 ypos 0.303

> 2dlabels #2.2 color light green

> 2dlabels #2.2 xpos 0.550 ypos 0.192

> 2dlabels #2.4 color light green

> 2dlabels #2.4 xpos 0.317 ypos 0.455

> 2dlabels #2.7 color cornflower blue

> 2dlabels #2.7 xpos 0.572 ypos 0.442

> 2dlabels #2.8 color cornflower blue

> 2dlabels #2.8 xpos 0.595 ypos 0.295

> 2dlabels #2.7 xpos 0.509 ypos 0.430

> 2dlabels #2.9 color cornflower blue

> 2dlabels #2.10 color cornflower blue

> 2dlabels #2.10 xpos 0.424 ypos 0.475

> 2dlabels #2.9 xpos 0.506 ypos 0.548

> 2dlabels #2.6 xpos 0.710 ypos 0.588

> 2dlabels #2.5 xpos 0.300 ypos 0.653

> 2dlabels #2.13 xpos 0.408 ypos 0.543

> 2dlabels #2.3 xpos 0.144 ypos 0.610

> 2dlabels #2.4 text "ARG 240"

> 2dlabels #2.4 text "ASN 239"

> hide #2.3 models

> select /D:240@CG

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 10 bonds, 1 residue, 2 models selected  

> hide sel atoms

> select /D:341@CB

1 atom, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 2 models selected  

> hide sel atoms

> ui mousemode right translate

> ui mousemode right label

> ui mousemode right "move label"

> 2dlabels #2.8 xpos 0.616 ypos 0.273

> 2dlabels #2.7 xpos 0.530 ypos 0.373

> select /P:78

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

> select clear

> 2dlabels #2.8 xpos 0.603 ypos 0.255

> 2dlabels #2.2 xpos 0.546 ypos 0.172

> 2dlabels #2.4 xpos 0.292 ypos 0.389

> 2dlabels #2.10 xpos 0.419 ypos 0.458

> 2dlabels #2.13 xpos 0.409 ypos 0.548

> 2dlabels #2.6 xpos 0.718 ypos 0.592

> 2dlabels text "VAL 163" color light salmon bgColor white size 20

> 2dlabels #2.14 color light salmon bgColor white size 20 bold

Missing "bold" keyword's argument  

> 2dlabels #2.14 color light salmon bgColor white size 20 bold true

> 2dlabels #2.14 xpos 0.560 ypos 0.726

> hide atoms

> undo

> hide sel

[Repeated 1 time(s)]

> save figure_v4.png width 2400 height 2400

> ui mousemode right "move label"

> 2dlabels #2.4 xpos 0.299 ypos 0.413

> ui mousemode right rotate

> ui mousemode right select

> select clear

> ui mousemode right "move label"

> 2dlabels #2.5 xpos 0.379 ypos 0.649

> 2dlabels #2.4 xpos 0.312 ypos 0.377

> 2dlabels #2.13 xpos 0.410 ypos 0.558

> 2dlabels #2.6 xpos 0.719 ypos 0.588

> select #2.12

1 model selected  

> ~select #2.12

Nothing selected  

> hide #2.12 models

> save figure_v4.png width 2400 height 2400

> ui mousemode right zoom

> 2dlabels #2.11 xpos 0 ypos 0

> ui mousemode right "move label"

> 2dlabels #2.11 xpos 0.417 ypos -0.007

> save figure_v4.png width 2400 height 2400

> lighting soft

> lighting full

> lighting simple

> lighting shadows true

> lighting full

> save /sci/labs/fora/projects/fusolisin/fusolisin_figure_v2.cxs

> graphics silhouettes true

> save figure_v5.png width 2400 height 2400

> hide #1.1.1 models

> hide #1.1.2 models

> show #1.1.2 models

> show #1.1.1 models

> ui mousemode right label

> select /D:162

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

> label #1/P:75

> ui mousemode right "move label"

> label #1.3 color cornflower blue

> color #1.3 #729fcf models transparency 0

> label #1.3 color cornflower blue bgColor white

> label #1/P:75 color cornflower blue bgColor white

> label #1/P:76 color cornflower blue bgColor white text P-2

> label #1/P:76 color cornflower blue bgColor white text P-2 bold true

Expected a keyword  

> label #1/P:76 color cornflower blue bgColor white text P-2 font Arial bold

Expected a keyword  

> label listfonts

599 fonts available:  
Accanthis ADF Std  
Accanthis ADF Std No2  
Accanthis ADF Std No3  
Aharoni CLM  
Aharoni [Glyf]  
Aharoni [culmus]  
Amiri  
Amiri Quran  
Amiri Quran Colored  
Andale Mono  
Angerthas Moria  
Arial  
Arial Black  
Arial Narrow  
Arial Unicode MS  
Arimo  
Asana Math  
Batang  
BatangChe  
Berenis ADF Pro  
Berenis ADF Pro SC  
Bitstream Charter  
Bitstream Cyberbit  
Bitstream Vera Sans  
Bitstream Vera Sans Mono  
Bitstream Vera Serif  
Bold Oblique  
Cabin  
Caladea  
Caladings  
Caladings CLM  
Calibri  
Cambria  
Cambria Math  
Candara  
Cantarell  
Cantarell Extra Bold  
Cantarell Light  
Cantarell Thin  
Carlito  
Century Schoolbook L  
Comfortaa  
Comfortaa Light  
Comic Sans MS  
Consolas  
Constantia  
Corbel  
Courier  
Courier 10 Pitch  
Courier New  
Courier-Hebrew  
Cousine  
David CLM  
David Transparent  
David [Glyf]  
David [bitstream]  
DejaVu Math TeX Gyre  
DejaVu Sans  
DejaVu Sans Condensed  
DejaVu Sans Mono  
DejaVu Serif  
DejaVu Serif Condensed  
DilleniaUPC  
Dingbats  
Dotum  
DotumChe  
Droid Sans Fallback  
Drugulin  
Drugulin CLM  
Dwarf Runes  
EB Garamond  
EB Garamond 08  
EB Garamond 12  
EB Garamond 12 All SC  
EB Garamond Initials  
EB Garamond Initials Fill1  
EB Garamond Initials Fill2  
EB Garamond SC  
EB Garamond SC 08  
EB Garamond SC 12  
Ellinia  
Ellinia CLM  
Estrangelo Edessa  
EucrosiaUPC  
Everson Mono Unicode  
Fira Code  
Fira Code Light  
Fira Code Medium  
Fira Code Retina  
Fixed Miriam Transparent  
FontAwesome  
Frank Ruehl  
Frank Ruehl CLM  
FrankRuehl  
FreeMono [GNU ]  
FreeMono [PfEd]  
FreeSans [GNU ]  
FreeSans [PfEd]  
FreeSerif [GNU ]  
FreeSerif [PfEd]  
FreesiaUPC  
GFS Artemisia  
GFS Baskerville  
GFS Complutum  
GFS Didot  
GFS Neohellenic  
GFS Olga  
GFS Porson  
GFS Solomos  
GLYPHICONS Halflings  
Garuda  
Gautami  
Gentium  
Gentium Basic  
Gentium Book Basic  
Gentium Plus  
Gentium Plus Compact  
GentiumAlt  
Georgia  
Gillius ADF  
Gillius ADF Cond  
Gillius ADF No2  
Gillius ADF No2 Cond  
Go  
Go Medium  
Go Mono  
Go Smallcaps  
Gulim  
GulimChe  
Gungsuh  
GungsuhChe  
Guttman Adii  
Guttman Adii-Light  
Guttman Aharoni  
Guttman Calligraphic  
Guttman David  
Guttman Drogolin  
Guttman Frank  
Guttman Frnew  
Guttman Haim  
Guttman Haim-Condensed  
Guttman Hatzvi  
Guttman Hodes  
Guttman Kav  
Guttman Kav-Light  
Guttman Keren  
Guttman Logo1  
Guttman Mantova  
Guttman Mantova-Bold  
Guttman Mantova-Decor  
Guttman Miryam  
Guttman Myamfix  
Guttman Rashi  
Guttman Stam  
Guttman Stam1  
Guttman Vilna  
Guttman Yad  
Guttman Yad-Brush  
Guttman Yad-Light  
Guttman-Aharoni  
Guttman-Aram  
Guttman-CourMir  
Guttman-Soncino [ALTS]  
Guttman-Soncino [MS ]  
Guttman-Toledo  
Hadasim CLM  
Impact  
IrisUPC  
JasmineUPC  
Junicode  
Keter YG [YG ]  
Keter YG [YGNT]  
Kinnari  
KodchiangUPC  
Ktav Yad  
LM Mono 10  
LM Mono 12  
LM Mono 8  
LM Mono 9  
LM Mono Caps 10  
LM Mono Light 10  
LM Mono Light Cond 10  
LM Mono Prop 10  
LM Mono Prop Light 10  
LM Mono Slanted 10  
LM Roman 10  
LM Roman 12  
LM Roman 17  
LM Roman 5  
LM Roman 6  
LM Roman 7  
LM Roman 8  
LM Roman 9  
LM Roman Caps 10  
LM Roman Demi 10  
LM Roman Dunhill 10  
LM Roman Slanted 10  
LM Roman Slanted 12  
LM Roman Slanted 17  
LM Roman Slanted 8  
LM Roman Slanted 9  
LM Roman Unslanted 10  
LM Sans 10  
LM Sans 12  
LM Sans 17  
LM Sans 8  
LM Sans 9  
LM Sans Demi Cond 10  
LM Sans Quot 8  
Laksaman  
Latha  
Latin Modern Math  
Latin Modern Mono  
Latin Modern Mono Caps  
Latin Modern Mono Light  
Latin Modern Mono Light Cond  
Latin Modern Mono Prop  
Latin Modern Mono Prop Light  
Latin Modern Mono Slanted  
Latin Modern Roman  
Latin Modern Roman Caps  
Latin Modern Roman Demi  
Latin Modern Roman Dunhill  
Latin Modern Roman Slanted  
Latin Modern Roman Unslanted  
Latin Modern Sans  
Latin Modern Sans Demi Cond  
Latin Modern Sans Quotation  
Lato  
Lato Black  
Lato Hairline  
Lato Heavy  
Lato Light  
Lato Medium  
Lato Semibold  
Lato Thin  
Levenim MT  
Liberation Mono  
Liberation Sans  
Liberation Sans Narrow  
Liberation Serif  
LilyUPC  
Linux Biolinum Keyboard O  
Linux Biolinum O  
Linux Libertine Display O  
Linux Libertine Initials O  
Linux Libertine Mono O  
Linux Libertine O  
Lobster Two  
Loma  
Lucida Console  
Lucida Sans  
Lucida Sans Unicode  
MS Gothic  
MS Mincho  
MS PGothic  
MS PMincho  
MS UI Gothic  
Marlett  
MathJax_AMS  
MathJax_Caligraphic  
MathJax_Fraktur  
MathJax_Main  
MathJax_Math  
MathJax_SansSerif  
MathJax_Script  
MathJax_Size1  
MathJax_Size2  
MathJax_Size3  
MathJax_Size4  
MathJax_Typewriter  
MathJax_Vector  
MathJax_Vector-Bold  
MathJax_WinChrome  
MathJax_WinIE6  
Mathematica1  
Mathematica1Mono  
Mathematica2  
Mathematica2Mono  
Mathematica3  
Mathematica3Mono  
Mathematica4  
Mathematica4Mono  
Mathematica5  
Mathematica5Mono  
Mathematica6  
Mathematica6Mono  
Mathematica7  
Mathematica7Mono  
MingLiU  
Miriam  
Miriam CLM  
Miriam Fixed  
Miriam Mono  
Miriam Mono CLM  
Miriam Transparent  
Monospace  
Moon Runes  
NSimSun  
Nachlieli  
Nachlieli CLM  
Narkisim  
Nimbus Mono L  
Nimbus Roman No9 L  
Nimbus Sans L  
Norasi  
Noto Color Emoji  
Noto Kufi Arabic  
Noto Mono  
Noto Music  
Noto Naskh Arabic  
Noto Naskh Arabic UI  
Noto Nastaliq Urdu  
Noto Sans  
Noto Sans Adlam  
Noto Sans Adlam Unjoined  
Noto Sans Anatolian Hieroglyphs  
Noto Sans Arabic  
Noto Sans Arabic UI  
Noto Sans Armenian  
Noto Sans Avestan  
Noto Sans Bamum  
Noto Sans Bassa Vah  
Noto Sans Batak  
Noto Sans Bengali  
Noto Sans Bengali UI  
Noto Sans Bhaiksuki  
Noto Sans Brahmi  
Noto Sans Buginese  
Noto Sans Buhid  
Noto Sans Canadian Aboriginal  
Noto Sans Carian  
Noto Sans Caucasian Albanian  
Noto Sans Chakma  
Noto Sans Cham  
Noto Sans Cherokee  
Noto Sans Coptic  
Noto Sans Cuneiform  
Noto Sans Cypriot  
Noto Sans Deseret  
Noto Sans Devanagari  
Noto Sans Devanagari UI  
Noto Sans Display  
Noto Sans Duployan  
Noto Sans Egyptian Hieroglyphs  
Noto Sans Elbasan  
Noto Sans Ethiopic  
Noto Sans Georgian  
Noto Sans Glagolitic  
Noto Sans Gothic  
Noto Sans Grantha  
Noto Sans Gujarati  
Noto Sans Gujarati UI  
Noto Sans Gurmukhi  
Noto Sans Gurmukhi UI  
Noto Sans Hanunoo  
Noto Sans Hatran  
Noto Sans Hebrew  
Noto Sans Imperial Aramaic  
Noto Sans Inscriptional Pahlavi  
Noto Sans Inscriptional Parthian  
Noto Sans Javanese  
Noto Sans Kaithi  
Noto Sans Kannada  
Noto Sans Kannada UI  
Noto Sans Kayah Li  
Noto Sans Kharoshthi  
Noto Sans Khmer  
Noto Sans Khmer UI  
Noto Sans Khudawadi  
Noto Sans Lao  
Noto Sans Lao UI  
Noto Sans Lepcha  
Noto Sans Limbu  
Noto Sans Linear A  
Noto Sans Linear B  
Noto Sans Lisu  
Noto Sans Lycian  
Noto Sans Lydian  
Noto Sans Mahajani  
Noto Sans Malayalam  
Noto Sans Malayalam UI  
Noto Sans Mandaic  
Noto Sans Manichaean  
Noto Sans Marchen  
Noto Sans Meetei Mayek  
Noto Sans Mende Kikakui  
Noto Sans Meroitic  
Noto Sans Miao  
Noto Sans Modi  
Noto Sans Mongolian  
Noto Sans Mono  
Noto Sans Mro  
Noto Sans Multani  
Noto Sans Myanmar  
Noto Sans Myanmar UI  
Noto Sans NKo  
Noto Sans Nabataean  
Noto Sans New Tai Lue  
Noto Sans Newa  
Noto Sans Ogham  
Noto Sans Ol Chiki  
Noto Sans Old Hungarian  
Noto Sans Old Italic  
Noto Sans Old North Arabian  
Noto Sans Old Permic  
Noto Sans Old Persian  
Noto Sans Old South Arabian  
Noto Sans Old Turkic  
Noto Sans Oriya  
Noto Sans Oriya UI  
Noto Sans Osage  
Noto Sans Osmanya  
Noto Sans Pahawh Hmong  
Noto Sans Palmyrene  
Noto Sans Pau Cin Hau  
Noto Sans PhagsPa  
Noto Sans Phoenician  
Noto Sans Psalter Pahlavi  
Noto Sans Rejang  
Noto Sans Runic  
Noto Sans Samaritan  
Noto Sans Saurashtra  
Noto Sans Sharada  
Noto Sans Shavian  
Noto Sans Sinhala  
Noto Sans Sinhala UI  
Noto Sans Sora Sompeng  
Noto Sans Sundanese  
Noto Sans Syloti Nagri  
Noto Sans Symbols  
Noto Sans Symbols2  
Noto Sans Syriac  
Noto Sans Syriac Eastern  
Noto Sans Syriac Estrangela  
Noto Sans Syriac Western  
Noto Sans Tagalog  
Noto Sans Tagbanwa  
Noto Sans Tai Le  
Noto Sans Tai Tham  
Noto Sans Tai Viet  
Noto Sans Takri  
Noto Sans Tamil  
Noto Sans Tamil UI  
Noto Sans Telugu  
Noto Sans Telugu UI  
Noto Sans Thaana  
Noto Sans Thai  
Noto Sans Thai UI  
Noto Sans Tibetan  
Noto Sans Tifinagh  
Noto Sans Tirhuta  
Noto Sans Ugaritic  
Noto Sans Vai  
Noto Sans Warang Citi  
Noto Sans Yi  
Noto Serif  
Noto Serif Ahom  
Noto Serif Armenian  
Noto Serif Balinese  
Noto Serif Bengali  
Noto Serif Devanagari  
Noto Serif Display  
Noto Serif Ethiopic  
Noto Serif Georgian  
Noto Serif Gujarati  
Noto Serif Gurmukhi  
Noto Serif Hebrew  
Noto Serif Kannada  
Noto Serif Khmer  
Noto Serif Lao  
Noto Serif Malayalam  
Noto Serif Myanmar  
Noto Serif Sinhala  
Noto Serif Tamil  
Noto Serif Tamil Slanted  
Noto Serif Telugu  
Noto Serif Thai  
Noto Serif Tibetan  
Oblique  
Open Sans  
Open Sans Condensed  
Open Sans Condensed Light  
Open Sans Extrabold  
Open Sans Light  
Open Sans Semibold  
OpenSymbol  
OrtIsraelClassic  
PMingLiU  
Padauk  
Padauk Book [PYRS]  
Padauk Book [SIL ]  
Purisa  
Quicksand  
Quicksand Light  
Quicksand Medium  
Roboto  
Roboto Black  
Roboto Condensed  
Roboto Condensed Light  
Roboto Condensed Medium  
Roboto Light  
Roboto Medium  
Roboto Slab  
Roboto Thin  
Rod  
Rod Transparent  
STIX  
STIX Math  
STIXGeneral  
STIXIntegralsD  
STIXIntegralsSm  
STIXIntegralsUp  
STIXIntegralsUpD  
STIXIntegralsUpSm  
STIXNonUnicode  
STIXSizeFiveSym  
STIXSizeFourSym  
STIXSizeOneSym  
STIXSizeThreeSym  
STIXSizeTwoSym  
STIXVariants  
Sans Serif  
Sawasdee  
Serif  
Shofar  
Shruti  
SimHei  
SimSun  
Simple CLM  
Stam Ashkenaz CLM  
Stam Sefarad CLM  
Standard Symbols L  
Sylfaen  
SylfaenARM  
Symbol  
Tahoma [MS ]  
Tahoma [MS]  
TeX Gyre Adventor  
TeX Gyre Bonum  
TeX Gyre Bonum Math  
TeX Gyre Chorus  
TeX Gyre Cursor  
TeX Gyre DejaVu Math  
TeX Gyre Heros  
TeX Gyre Heros Cn  
TeX Gyre Pagella  
TeX Gyre Pagella Math  
TeX Gyre Schola  
TeX Gyre Schola Math  
TeX Gyre Termes  
TeX Gyre Termes Math  
Tengwar Cursive  
Tengwar Sindarin  
Tengwar-Gandalf  
Times New Roman  
Times-Hebrew  
Times-Roman-Hebrew  
Tinos  
Tlwg Mono  
Tlwg Typewriter  
Tlwg Typist  
Tlwg Typo  
Tolkien  
TopType Soncino  
Traditional Arabic  
Trebuchet MS  
Tunga  
URW Bookman L  
URW Chancery L  
URW Gothic L  
URW Palladio L  
Umpush  
UnBatang  
UnDinaru  
UnDotum  
UnGraphic  
UnGungseo  
UnPilgi  
Universalis ADF Std  
Universalis ADF Std Cond  
Utopia  
Verdana  
Waree  
Webdings  
Wingdings  
Yehuda CLM  
cmex10  
cmmi10  
cmr10  
cmsy10  
elusiveicons  
esint10  
eufm10  
msam10  
msbm10  
rsfs10  
stmary10  
wasy10  

> label #1/P:76 color cornflower blue bgColor white text P-2 font Arial black

Expected a keyword  

> label #1/P:76 color cornflower blue bgColor white text P-2 font "Arial
> black"

> label #1/P:76 color cornflower blue bgColor white text P-2 bold true

Expected a keyword  

> label #1/P:77 color cornflower blue bgColor white text P-1 bold true

Expected a keyword  

> label #1/P:77 color cornflower blue bgColor white text P-1

> label #1/P:78 color cornflower blue bgColor white text P1

> label #1/P:79 color cornflower blue bgColor white text P2

> hide #2.8 models

> hide #2.7 models

> hide #2.9 models

> hide #2.10 models

> delete label #1/P:75

Missing or invalid "atoms" argument: invalid atoms specifier  

> label delete #1/P:75

> label #1/P:76 color cornflower blue bgColor white text P-2

> label delete #1/P:76

> label #1/P:76 color cornflower blue bgColor white text P-2

> label #1/D:239 color light green bgColor white text ASN239

> label #1/D:344 color light green bgColor white text ASN344

> label #1/D:344 color light green bgColor white text SER344

> label #1/D:122 color light green bgColor white text HIS122

> hide #2.1 models

> hide #2.2 models

> hide #2.4 models

> label #1/D:161 color light salmon bgColor white text LYS161

> hide #2.6 models

> label #1/D:163 color light salmon bgColor white text Val163

> hide #2.14 models

> label #1/D:190 color light salmon bgColor white text PHE190

> label #1/D:163 color light salmon bgColor white text VAL163

> label #1/D:191 color light salmon bgColor white text GLY191

> hide #2.5 models

> label #1/D:190 color light salmon bgColor white text PHE190

> hide #2.13 models

> label #1/D:341 color light salmon bgColor white text ILE341

> hide #2.11 models

> label #1/D:161 color light salmon bgColor white text LYS161

> hide #!2 models

> ui mousemode right "move label"

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

6 atoms, 5 bonds, 1 residue, 2 models selected  

> hide sel atoms

Drag select of 1 residues  

> select clear

> ui mousemode right translate

> ui mousemode right "move label"

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> hide sel atoms

> select clear

> ui mousemode right translate

> ui mousemode right "crop volume"

> rainbow

> undo

> interfaces ~solvent

1 buried areas: D P 538  

> ui mousemode right label

> ui mousemode right "move label"

> ui mousemode right clip

> clip front -10

> clip back 3

> clip back -3

> clip back 3

> clip back 5

> clip back 3

> clip back 10

> clip back -5

[Repeated 1 time(s)]

> clip back -2

> clip back -1

> ui mousemode right translate

> clip front 1

> clip front -3

[Repeated 3 time(s)]

> clip front -1

> clip back -1

> save /sci/labs/fora/projects/fusolisin/fusolisin_figure_v2.cxs

QXcbConnection: XCB error: 3 (BadWindow), sequence: 14676, resource id:
14255297, major code: 40 (TranslateCoords), minor code: 0  

> select notbindsite

2470 atoms, 2525 bonds, 9 pseudobonds, 320 residues, 18 models selected  

> transparency 0.95 target s notbindsite

Expected a keyword  

> transparency notbindsite 0.95 target s

> transparency notbindsite 95 target s

> transparency notbindsite 95 target c

> transparency notbindsite 50 target s

> transparency notbindsite 50 target c

> transparency notbindsite 80 target c

> select clear

> save /sci/labs/fora/projects/fusolisin/fusolisin_figure_v2.cxs

——— End of log from Tue Jun 7 11:23:29 2022 ———

opened ChimeraX session  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 2 models selected  

> ui tool show "Color Actions"

> color sel light salmon

> color sel byhetero

> select /D:240

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

> select /D:238

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

> select clear

> select /D:240

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

> select /D:238

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

> transparency 0.85 sele target c

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> transparency sele 0.85 target c

Missing or invalid "percent" argument: Expected a number  

> transparency 0.85 target c

> undo

> transparency notbindsite 95 target c

> select nobindsite

Expected an objects specifier or a keyword  

> select notbindsite

2470 atoms, 2525 bonds, 9 pseudobonds, 320 residues, 18 models selected  

> select /D:240

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

> select /D:238

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

> select up

164 atoms, 164 bonds, 24 residues, 2 models selected  

> transparency notbindsite 95 target c

> transparency notbindsite 85 target c

> select up

2597 atoms, 2649 bonds, 338 residues, 2 models selected  

> select up

2638 atoms, 2689 bonds, 344 residues, 2 models selected  

> select notbindsite

2470 atoms, 2525 bonds, 9 pseudobonds, 320 residues, 18 models selected  

> select /D:240

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

> select notbindsite

2470 atoms, 2525 bonds, 9 pseudobonds, 320 residues, 18 models selected  

> select add /D:240

2481 atoms, 2535 bonds, 9 pseudobonds, 321 residues, 19 models selected  

> select add /D:238

2485 atoms, 2538 bonds, 9 pseudobonds, 322 residues, 19 models selected  

> select add /D:158

2494 atoms, 2546 bonds, 9 pseudobonds, 323 residues, 19 models selected  

> select add /D:159

2501 atoms, 2552 bonds, 9 pseudobonds, 324 residues, 19 models selected  

> select add /D:160

2509 atoms, 2559 bonds, 9 pseudobonds, 325 residues, 19 models selected  

> select add /D:340

2513 atoms, 2562 bonds, 9 pseudobonds, 326 residues, 19 models selected  

> select add /D:342

2517 atoms, 2565 bonds, 9 pseudobonds, 327 residues, 19 models selected  

> select subtract /D:342

2513 atoms, 2563 bonds, 9 pseudobonds, 326 residues, 19 models selected  

> select up

2522 atoms, 2566 bonds, 9 pseudobonds, 332 residues, 19 models selected  

> select down

2513 atoms, 2564 bonds, 9 pseudobonds, 326 residues, 19 models selected  

> select add /D:343

2519 atoms, 2567 bonds, 9 pseudobonds, 327 residues, 19 models selected  

> name frozen notbindsite sel

[Repeated 1 time(s)]

> transparency notbindsite 85 target c

> select /D:343

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

> hide sel atoms

[Repeated 1 time(s)]

> select /D:342

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

> hide sel atoms

> select /D:160

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

> hide sel atoms

> select /D:276

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

> select #1/P

41 atoms, 40 bonds, 6 residues, 1 model selected  

> hide sel cartoons

> label #1/D:239 color light salmon

> ui tool show H-Bonds

> select /D:342

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

> transparency sel 85 target c

> select /D:343

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

> select subtract /D:343

1 model selected  

> select /D:342

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

> select /D:343

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

> select add /D:342

10 atoms, 8 bonds, 2 residues, 2 models selected  

> transparency sel 85 target c

> hbonds sel color #00aaff restrict cross

7 hydrogen bonds found  

> hide atoms

> show atoms

> undo

[Repeated 1 time(s)]

> hbonds reveal true

353 hydrogen bonds found  

> hbonds reveal true

353 hydrogen bonds found  

> ~hbonds

> select /D:240@CG

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 10 bonds, 1 residue, 2 models selected  

> undo

[Repeated 2 time(s)]

> hide atoms

> select cattriad

18 atoms, 17 bonds, 2 residues, 1 model selected  

> show sel atoms

> select add /D:344

24 atoms, 22 bonds, 3 residues, 2 models selected  

> show sel atoms

> select #1/P

41 atoms, 40 bonds, 6 residues, 1 model selected  

> show sel atoms

> select #1/P

41 atoms, 40 bonds, 6 residues, 1 model selected  

> ui mousemode right translate

> select #1/P

41 atoms, 40 bonds, 6 residues, 1 model selected  

> hbonds sel reveal true

14 hydrogen bonds found  

> color #1.4 #ffff7f models transparency 0

> select #1/D:88

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

> select #1/D:88,344,122

24 atoms, 22 bonds, 3 residues, 1 model selected  

> name frozen cattriad sel

> show sel atoms

> show sel surfaces

> transparency sel 0

[Repeated 2 time(s)]

> volume style image

No volumes specified  

> volume style mesh

No volumes specified  

> volume style surface

No volumes specified  

> volume showOutlineBox true

No volumes specified  

> volume hide

No volumes specified  

> hide sel surfaces

> ui tool show "Color Actions"

> color sel light green

> color sel byhetero

> select up

148 atoms, 147 bonds, 20 residues, 2 models selected  

> select #1/D:88,344,122

24 atoms, 22 bonds, 3 residues, 1 model selected  

> select add /P:77@CA

25 atoms, 22 bonds, 4 residues, 2 models selected  

> select #1/D:88,344,122,P

24 atoms, 22 bonds, 3 residues, 1 model selected  

> select #1/D:88,344,122 #1/P

65 atoms, 62 bonds, 4 pseudobonds, 9 residues, 2 models selected  

> hbonds sel reveal true

22 hydrogen bonds found  

> color #1.4 #ffff7f models transparency 0

> select add /D:189

6 atoms, 5 bonds, 2 pseudobonds, 1 residue, 2 models selected  

> select add /D:120@CB

7 atoms, 5 bonds, 4 pseudobonds, 2 residues, 3 models selected  

> select subtract /D:120

6 atoms, 5 bonds, 4 pseudobonds, 1 residue, 3 models selected  

> hide sel

> hide cartoons

> show cartoons

> hide atoms

> show atoms

> undo

[Repeated 1 time(s)]

> hide sel

[Repeated 3 time(s)]

> select /D:120

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

> hide sel

> select clear

> select #1/P

41 atoms, 40 bonds, 1 pseudobond, 6 residues, 2 models selected  

> hide sel cartoons

> save V:/projects/fusolisin/fusolisin_figure_v2.cxs

> select clear

> ui mousemode right "move label"

Drag select of 1 residues  

> select clear

> select /D:190

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

> select up

131 atoms, 133 bonds, 17 residues, 2 models selected  

> select up

2597 atoms, 2649 bonds, 338 residues, 2 models selected  

> select /D:190

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

> transparency sel 85 target c

> select clear

> clip back 5

> clip back -10

> clip back 2

> save fusolisin_v6.png width 2400 height 2400

> ui mousemode right translate

> ui tool show "Color Actions"

> color #1.4 black models transparency 0

> color #1.4 #565656 models transparency 0

> color #1.4 white models transparency 0

> color #1.4 #4c4c4c models transparency 0

> color #1.4 #6c6c6c models transparency 0

> undo

> select #1/D

2597 atoms, 2649 bonds, 8 pseudobonds, 338 residues, 2 models selected  

> show sel surfaces

> ui mousemode right clip

> ui mousemode right select

> ui mousemode right clip

> hide sel surfaces

> ui mousemode right "move label"

> ui mousemode right select

> lighting soft

> lighting full

> lighting simple

> lighting soft

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting soft

> graphics silhouettes true

> lighting soft

[Repeated 1 time(s)]

> lighting flat

> lighting shadows true intensity 0.5

> lighting soft

> lighting shadows true intensity 0.5

> lighting simple

> lighting gentle

> udo

Unknown command: udo  

> undo

> lighting shadows true intensity 0.5

> lighting flat

[Repeated 1 time(s)]

> lighting soft

> lighting simple

> lighting full

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> select 1#/D:211

Expected an objects specifier or a keyword  

> select #1/D:211

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

> show sel atoms

> clip back 5

> color #1.4 #6d6c6c models transparency 0

> color #1.4 #026c6c models transparency 0

> color #1.4 #ff6c6c models transparency 0

> color #1.4 #ffcc00 models transparency 0

> color #1.4 white models transparency 0

> color #1.4 #ff02ff models transparency 0

> color #1.4 #ffcdff models transparency 0

> color #1.4 #ff14ff models transparency 0

> color #1.4 #ffcc00 models transparency 0

> ui mousemode right "move label"

> clip front 5

clip back plane is in front of front plane  

> clip front -5

> clip front -10

> clip front -3

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

14 atoms, 15 bonds, 1 residue, 2 models selected  

> hide sel atoms

> ui mousemode right "move label"

> clip front 2

> clip front -5

> clip front 1

[Repeated 1 time(s)]

> clip front -1

> clip front 0.5

> clip front -0.5

> select notbindsite

2597 atoms, 2569 bonds, 3 pseudobonds, 338 residues, 18 models selected  

> transparency notbindsite 0.5 target c

> transparency notbindsite 50 target c

> transparency notbindsite 30 target c

> transparency notbindsite 90 target c

> transparency notbindsite 95 target c

> select #1/D?162

Nothing selected  

> select #1/D:162

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

> show sel atoms

[Repeated 1 time(s)]

> select #1/D:163

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

> hide sel atoms

> select #1/D:162

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

> hide sel atoms

> select #1/D:163

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

> select #1/D:163

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

> show sel atoms

> hide sel atoms

> select #1/D:162

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

> show sel atoms

> hide sel atoms

> select #1/D:190

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

> show sel atoms

[Repeated 1 time(s)]

> select #1/D:165

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

> show sel atoms

[Repeated 1 time(s)]

> select #1/D:189

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

> show sel atoms

> select #1/D:192

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

> select #1/D:189

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

> hide sel atoms

> select #1/D:165

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

> hide sel atoms

> select #1/D:192

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

> show sel atoms

> hide sel atoms

> select #1/D:358

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

> select #1/D:258

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

> show sel atoms

> hide sel atoms

> select #1/D:238

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

> show sel atoms

> hide sel cartoons

> show sel cartoons

> select #1/D:343

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

> open C:/Users/jvarg/Downloads/fusolisin.pdb

Chain information for fusolisin.pdb #3  
---  
Chain | Description  
D | No description available  
  

> delete #2

> delete #3

> save V:/projects/fusolisin/figures/fusolisin_figure_v2.cxs

Cannot save 'V:/projects/fusolisin/figures/fusolisin_figure_v2.cxs': [WinError
995] The I/O operation has been aborted because of either a thread exit or an
application request:
'V:/projects/fusolisin/figures/fusolisin_figure_v2.cxs.8360.tmp'  

> save V:/projects/fusolisin/figures/fusolisin_figure_v2.cxs

> save V:/projects/fusolisin/figures/binding_site.png width 2000 height 1200
> supersample 3

> 2dlabels "ASP88" color light green bgColor white

Expected 'all' or a 2d label name or a label models specifier or a keyword  

> label #1/D:88 text ASP88 color light green bgColor white

> label #1/D:88 text ASP88 color light green bgColor white size 12

> label #1/D:88 text ASP88 color light green bgColor white size 14

Drag select of 1 residues  

> select clear

> save V:/projects/fusolisin/figures/binding_site.png width 1338 height 775
> supersample 3

> save V:/projects/fusolisin/figures/fusolisin_figure_v2.cxs

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

11 atoms, 11 bonds, 1 residue, 2 models selected  

> hide sel atoms

> save V:/projects/fusolisin/figures/fusolisin_figure_v2.cxs

> save V:/projects/fusolisin/figures/binding_site.png width 1338 height 775
> supersample 3

> select clear

> save V:/projects/fusolisin/figures/binding_site.png width 1338 height 775
> supersample 3

> save V:/projects/fusolisin/figures/binding_site.png height 2400 width 2400
> supersample 3

> save V:/projects/fusolisin/figures/fusolisin_figure_v2.cxs

> select #1/D:345

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel atoms

> select #1/D:340

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

> show sel atoms

[Repeated 1 time(s)]

> hide sel atoms

> select #1/D:343

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

> show sel atoms

> hide sel atoms

> select clear

[Repeated 1 time(s)]

> select /D:344

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

> select clear

> hide sel

> save V:/projects/fusolisin/figures/fusolisin_figure_v2.cxs

[Errno 20] Not a directory: 'V:/projects/fusolisin/figures'  

> save V:/projects/fusolisin/figures/fusolisin_figure_v2.cxs

——— End of log from Mon Jun 13 21:11:39 2022 ———

opened ChimeraX session  

> select #2.7

1 model selected  

> 2dlabels #2.7 text P1'

> hide #2.7 models

> show #2.7 models

> hide #2.4 models

> hide #2.2 models

> show #2.2 models

> hide #2.2 models

> hide #2.1 models

> 2dlabels #2.8 text P2'

> 2dlabels #2.9 text P2'

> 2dlabels #2.9 text P2

> 2dlabels #2.10 text P1

> ~select #2.7

Nothing selected  

> select #2.7

1 model selected  

> ~select #2.7

Nothing selected  

> hide #2.7 models

> show #2.7 models

> hide #2.8 models

> show #2.8 models

> ui mousemode right label

> label delete residues

[Repeated 1 time(s)]

> ui mousemode right "move label"

> undo

[Repeated 9 time(s)]

> 2dlabels #2.3 xpos 0.289 ypos 0.205

> show #2.2 models

> 2dlabels #2.2 xpos 0.397 ypos 0.194

> 2dlabels #2.6 xpos 0.650 ypos 0.581

> 2dlabels #2.14 xpos 0.637 ypos 0.775

> 2dlabels #2.5 xpos 0.383 ypos 0.718

> 2dlabels #2.5 size 14

> 2dlabels #2.5 size 16

> 2dlabels #2.5 xpos 0.385 ypos 0.733

> 2dlabels #2.2 size 16

> 2dlabels #2.3 size 16

> 2dlabels #2.3 xpos 0.289 ypos 0.219

> 2dlabels #2.3 size 16 bold false

> 2dlabels #2.11 size 16 bold false

> 2dlabels #2.11 xpos 0.384 ypos 0.025

> 2dlabels #2.11 size 16 bold false text ILE341

> 2dlabels #2.11 xpos 0.388 ypos 0.029

> 2dlabels #2.3 size 16 bold false text ASN239

> 2dlabels #2.3 xpos 0.281 ypos 0.245

> 2dlabels #2.2 size 16 bold true text SER344

> 2dlabels #2.1 size 16 bold true text HIS122

> 2dlabels #2.1 xpos 0.639 ypos 0.304

> 2dlabels #2.13 size 16 bold false text PHE190

> 2dlabels #2.13 xpos 0.423 ypos 0.646

> 2dlabels #2.5 size 16 bold false text GLY191

> 2dlabels #2.14 size 16 bold false text VAL163

> 2dlabels #2.6 size 16 bold false text LYS161

> 2dlabels #2.6 size 16 bold true text LYS161

> 2dlabels #2.14 size 16 bold true text VAL163

> 2dlabels #2.5 size 16 bold true text GLY191

> 2dlabels #2.13 size 16 bold true

> 2dlabels #2.3 size 16 bold true

> 2dlabels #2.11 size 16 bold true

> ui mousemode right translate

> ui mousemode right "move label"

> 2dlabels #2.8 xpos 0.579 ypos 0.137

> 2dlabels #2.7 xpos 0.558 ypos 0.262

> 2dlabels #2.10 xpos 0.415 ypos 0.508

> 2dlabels #2.9 xpos 0.557 ypos 0.550

> save binding_site.png width 1200 height 1200 supersample 3

> save binding_site.png width 800 height 800 supersample 3

> save binding_site.png width 1200 height 1200 supersample 3

> save binding_site.png width 2000 height 2000 supersample 3

> save binding_site.png width 500 height 500 supersample 3

> save binding_site.png width 1000 height 1000 supersample 3

> save binding_site.png width 1000 height 1000 supersample 5

> 2dlabels ASP88 size 16 bold true color green text ASP88

Expected 'all' or a 2d label name or a label models specifier or a keyword  

> 2dlabels size 16 bold true color green text ASP88

> ui tool show "Color Actions"

> 2dlabels size 16 bold true color pale green text ASP88

> hide #2.15 models

> 2dlabels #2.16 size 16 bold true color pale green text ASP88 bgColor white

> 2dlabels #2.16 size 16 bold true color light green text ASP88 bgColor white

> 2dlabels #2.16 xpos 0.695 ypos 0.439

> 2dlabels #2.1 xpos 0.624 ypos 0.292

> 2dlabels #2.16 size 18 bold true color light green text ASP88 bgColor white

> 2dlabels #2.16 xpos 0.687 ypos 0.439

> 2dlabels #2.2 size 18 bold true color light green bgColor white

> 2dlabels #2.2 xpos 0.392 ypos 0.194

> 2dlabels #2.1 size 18 bold true color light green bgColor white

> 2dlabels #2.1 xpos 0.613 ypos 0.292

> 2dlabels #2.7 xpos 0.553 ypos 0.260

> 2dlabels #2.8 xpos 0.575 ypos 0.137

> save binding_site.png width 1000 height 1000 supersample 5

> graphics silhouettes color gray

> save binding_site.png supersample 5

> 2dlabels text P3 color cornflower blue size 16 bold true

> 2dlabels 2.17 text "P3" color cornflower blue size 16 bold true bgColor
> white

Expected 'all' or a 2d label name or a label models specifier or a keyword  

> 2dlabels #2.17 text P3 color cornflower blue size 16 bold true bgColor white

> 2dlabels #2.17 xpos 0.533 ypos 0.658

> 2dlabels #2.17 text P3 color cornflower blue size 18 bold true bgColor white

> 2dlabels #2.17 text P3 color cornflower blue size 20 bold true bgColor white

> 2dlabels #2.17 xpos 0.530 ypos 0.654

> 2dlabels text P4 color cornflower blue size 20 bold true bgColor white

> 2dlabels #2.18 xpos 0.507 ypos 0.831

> save V:/projects/fusolisin/figures/fusolisin_figure.cxs

> select up

1 model selected  

> select up

1 model selected  

> save binding_site_new.png supersample 5

> save binding_site_new.png supersample 8

> save binding_site_new.png supersample 8 height 1400

> save V:/projects/fusolisin/figures/fusolisin_figure.cxs

——— End of log from Tue Jul 12 00:05:22 2022 ———

opened ChimeraX session  

> clip back 5

[Repeated 1 time(s)]

> hide #!2 models

> lighting shadows false

> lighting shadows true

> lighting full

> lighting soft

> lighting simple

> lighting full

> select /D:211

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

> show sel atoms

> select /D:210

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

> select /D:209

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /D:200

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

> select /D:199

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

> show sel atoms

> select /D:200

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

> show sel atoms

> select /D:172

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

> show sel atoms

> hide sel atoms

> select /D:166

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

> select /D:164

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

> show sel atoms

> hide sel atoms

> select /D:210

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

> select add /D:209

19 atoms, 18 bonds, 2 residues, 2 models selected  

> show sel atoms

> select /D:210

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

> hide sel atoms

> select /D:192

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

> show sel atoms

> select /D:165

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

> select /D:164

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

> select add /D:165

15 atoms, 14 bonds, 2 residues, 2 models selected  

> show sel atoms

> hide sel atoms

> select /D:164

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

> hide sel atoms

> select /D:200

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

> select add /D:199

12 atoms, 11 bonds, 2 residues, 2 models selected  

> hide sel atoms

> select /D:209@CZ

1 atom, 1 residue, 1 model selected  

> select add /D:211@CB

2 atoms, 2 residues, 2 models selected  

> select add /D:165

9 atoms, 7 bonds, 3 residues, 2 models selected  

> select add /D:192

14 atoms, 11 bonds, 4 residues, 2 models selected  

> select up

38 atoms, 38 bonds, 4 residues, 2 models selected  

> select up

311 atoms, 316 bonds, 42 residues, 2 models selected  

> select down

38 atoms, 38 bonds, 4 residues, 2 models selected  

> show sel atoms

> style sel sphere

Changed 38 atom styles  

> select /D:258

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

> show sel atoms

> style sel sphere

Changed 9 atom styles  

> select /D:165@N

1 atom, 1 residue, 1 model selected  

> select /D:211@CA

1 atom, 1 residue, 1 model selected  

> select add /D:165@N

2 atoms, 2 residues, 2 models selected  

> select add /D:192@CB

3 atoms, 3 residues, 2 models selected  

> select add /D:258@OE2

4 atoms, 4 residues, 2 models selected  

> select add /D:209@CA

5 atoms, 5 residues, 2 models selected  

> select up

47 atoms, 46 bonds, 5 residues, 2 models selected  

> color sel byhetero

> select /D:187

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

> select add /D:188

17 atoms, 15 bonds, 2 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> hide sel atoms

> select /D:190

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

> show sel atoms

> style sel sphere

Changed 11 atom styles  

> select /D:209@CA

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 12 bonds, 1 residue, 2 models selected  

> hide sel atoms

> select clear

> select /D:191

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

> show sel atoms

> style sel sphere

Changed 4 atom styles  

> style sel sphere

Changed 4 atom styles  

> style sel sphere

Changed 4 atom styles  

> style sel sphere

Changed 4 atom styles  

> style sel sphere

Changed 4 atom styles  

> select /D:191

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

> select /D:191

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

> show sel atoms

> style sel stick

Changed 4 atom styles  

> style sel ball

Changed 4 atom styles  

> style sel sphere

Changed 4 atom styles  

> select /D:211@CD2

1 atom, 1 residue, 1 model selected  

> select add /D:165@CD

2 atoms, 2 residues, 2 models selected  

> select add /D:190@CD2

3 atoms, 3 residues, 2 models selected  

> select add /D:192@CA

4 atoms, 4 residues, 2 models selected  

> select up

37 atoms, 37 bonds, 4 residues, 2 models selected  

> style sel ball

Changed 37 atom styles  

> select /D:258@CA

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> style sel ball

Changed 9 atom styles  

> name phobpocket #1/D:192,211,190,165

> select phobpocket

37 atoms, 37 bonds, 4 residues, 1 model selected  

> style sel sphere

Changed 37 atom styles  

> name phobpocket #1/D:192,211,190,165, 258

> select phobpocket

46 atoms, 45 bonds, 5 residues, 1 model selected  

> style sel sphere

Changed 46 atom styles  

> select add /P:77@N

1 atom, 1 bond, 1 residue, 1 model selected  

> select up

4 atoms, 2 bonds, 2 residues, 2 models selected  

> hbonds sel

2 hydrogen bonds found  

> hide sel

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> select up

41 atoms, 40 bonds, 6 residues, 2 models selected  

> select up

2638 atoms, 2689 bonds, 344 residues, 2 models selected  

> select down

41 atoms, 40 bonds, 6 residues, 3 models selected  

> select up

2638 atoms, 2689 bonds, 344 residues, 2 models selected  

> select down

41 atoms, 40 bonds, 6 residues, 3 models selected  

> hbonds sel

14 hydrogen bonds found  

> color #1.4 #f9e559 models transparency 0

> select phobpocket

46 atoms, 45 bonds, 5 residues, 1 model selected  

> style sel stick

Changed 46 atom styles  

> style sel sphere

Changed 46 atom styles  

> style sel ball

Changed 46 atom styles  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> select up

11 atoms, 9 bonds, 2 residues, 2 models selected  

> style sel ball

Changed 11 atom styles  

> style sel stick

Changed 11 atom styles  

> select clear

> select phobpocket

46 atoms, 45 bonds, 5 residues, 1 model selected  

> style sel stick

Changed 46 atom styles  

> style sel sphere

Changed 46 atom styles  

> save C:/Users/jvarg/Documents/huji/fusolisin/fusolisin_figure.cxs

——— End of log from Sat Jul 23 20:33:38 2022 ———

opened ChimeraX session  

> clip front -5

[Repeated 3 time(s)]

> save 6mer_binding.png supersample 5 pixelSize 0.05

> clip front -5

> save 6mer_binding.png supersample 5 pixelSize 0.05

[Repeated 3 time(s)]

> save C:\Users\jvarg\Documents\huji\fusolisin\fusolisin_figure.cx

No known data format for file suffix '.cx'  

> save C:\Users\jvarg\Documents\huji\fusolisin\fusolisin_figure.cxs

> save C:\Users\jvarg\Documents\huji\fusolisin\fusolisin_figure_surface.cxs

——— End of log from Sun Jul 24 00:35:18 2022 ———

opened ChimeraX session  

> select /D:211@CE3

1 atom, 1 residue, 1 model selected  

> select phobpocket

46 atoms, 45 bonds, 5 residues, 1 model selected  

> hide sel atoms

> clip back -10

> clip back 20

[Repeated 2 time(s)]

> select #1/D

2597 atoms, 2649 bonds, 338 residues, 1 model selected  

> show sel surfaces

> hide sel surfaces

> ui tool show "Color Actions"

> color sel light salmon

> color sel byhetero

> show sel surfaces

> coulombic sel

Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -15.26, mean -1.22, maximum 13.83  
To also show corresponding color key, enter the above coulombic command and
add key true  

> lighting simple

> lighting shadows true

> lighting shadows false

> clip near 10

[Repeated 1 time(s)]

> clip near -10

> clip near 5

> clip near -5

[Repeated 1 time(s)]

> clip near -2

[Repeated 4 time(s)]

> clip near 1

> clip model #1/D true

> clip model #1/P false

> clip model #1 false

> clip model #1.1 true

> clip model #!1 false

> clip model #!1 true

> clip near -1

[Repeated 1 time(s)]

> mlp protein surfaces #1.1

Map values for surface "relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface": minimum -30.77, mean -6.378, maximum 21.71  
Map values for surface "cap near": minimum -49.37, mean -9.307, maximum 41.72  

> coulombic protein surfaces #1.1 offset 0

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -119.55, mean -2.01, maximum 27.46  
Coulombic values for cap near #1.1.1: minimum, -2687.41, mean -0.60, maximum
9332.59  

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> lighting simple

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows true

> select #1/D

2597 atoms, 2649 bonds, 338 residues, 1 model selected  

> coulombic sel

Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -15.26, mean -1.22, maximum 13.83  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic protein surfaces #1.1

Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -3348.00, mean -1.46, maximum 4600.26  
Coulombic values for cap near #1.1.1: minimum, -1218.72, mean 1.09, maximum
1147.31  

> coulombic protein surfaces #1.1 offset 1

Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -667.65, mean -1.52, maximum 297.80  
Coulombic values for cap near #1.1.1: minimum, -7034.86, mean -0.94, maximum
3342.96  

> coulombic protein surfaces #1.1 offset 10

Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -73530.64, mean -0.56, maximum 13140.35  
Coulombic values for cap near #1.1.1: minimum, -6824.58, mean -1.65, maximum
3156.92  

> coulombic protein surfaces #1.1 offset 1.4

Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -3348.00, mean -1.46, maximum 4600.26  
Coulombic values for cap near #1.1.1: minimum, -1218.72, mean 1.09, maximum
1147.31  

> color (#!1 & sel) white

> ui tool show "Color Actions"

> color sel white

> color sel yellow

> color sel white

> color zone #1.2.1 near protein distance 3 sharpEdges true update true

color zone: No surfaces specified.  

> color zone #1.1 near protein distance 3 sharpEdges true update true

> coulombic protein surfaces #1.1

Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -3348.00, mean -1.17, maximum 21139.05  
Coulombic values for cap near #1.1.1: minimum, -1218.72, mean 0.97, maximum
1147.31  

> coulombic sel

Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -15.26, mean -1.23, maximum 13.83  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color zone #1.1 near protein distance 3 sharpEdges true update true

> transparency #1.1 30

> color sel white target acpf

> color sel white

> color sel medium blue

> color sel white

> clip near 1

> clip near -2

> coulombic protein surfaces

Missing "surfaces" keyword's argument  

> coulombic protein surfaces #/1.1

Invalid "surfaces" argument: invalid surfaces specifier  

> coulombic protein surfaces #/1.1

Invalid "surfaces" argument: invalid surfaces specifier  

> coulombic protein surfaces /1.1

Invalid "surfaces" argument: only initial part "/1" of atom specifier valid  

> coulombic #1.1

> coulombic protein surfaces #1.1

Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -3348.00, mean -1.17, maximum 21139.05  
Coulombic values for cap near #1.1.1: minimum, -2887.66, mean -2.69, maximum
1017.62  

> transparency #1.1 30

> transparency #1.1 50

> clip near -1

> coulombic protein surfaces #1.1

Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -3348.00, mean -1.17, maximum 21139.05  
Coulombic values for cap near #1.1.1: minimum, -3523.44, mean -3.76, maximum
548.46  

> color sel white

> clip near -.01

> clip near -1

> clip near -10

> 10

Unknown command: 10  

> clip near 10

> color sel white

> select #1/D

2597 atoms, 2649 bonds, 338 residues, 1 model selected  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1650, in
_update_graphics_if_needed  
s[i].update_graphics_if_needed()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\structure.py", line 359, in update_graphics_if_needed  
update()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 563, in update_selection  
tmask = self._atom_triangle_mask(asel)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 351, in _atom_triangle_mask  
logical_and(shown_vertices[t[:,0]], shown_vertices[t[:,1]], shown_triangles)  
IndexError: index 196228 is out of bounds for axis 0 with size 195879  
  
Error processing trigger "graphics update":  
IndexError: index 196228 is out of bounds for axis 0 with size 195879  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 351, in _atom_triangle_mask  
logical_and(shown_vertices[t[:,0]], shown_vertices[t[:,1]], shown_triangles)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.9749
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Manufacturer: LENOVO
Model: 20LS0015XS
OS: Microsoft Windows 10 Pro (Build 19043)
Memory: 8,437,047,296
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

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