Session open: function 'set_pbgroup_py_instance' not found

[x6207220@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "C:\\\D_disk\\\new project\\\AZG1\\\paper\\\Fig\\\Fig4\\\Fig4f-1.cxs"

Opened apo7.4.mrc as #2, grid size 240,240,240, pixel 0.851, shown at level
0.012, step 1, values float32  
Log from Sun Jan 1 23:38:00 2023UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4g-1.cxs"

Opened apo5.5_resampled.mrc as #2, grid size 240,240,240, pixel 0.851, shown
at level 0.016, step 1, values float32  

Frozen name "mc" not restored: nothing is selected by specifier  

Log from Sun Jan 1 23:14:01 2023UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "C:\\\D_disk\\\new project\\\AZG1\\\paper\\\Fig\\\Fig4\\\Fig4j-1.cxs"

Opened kinetin.mrc as #2, grid size 35,30,31, pixel 0.851,0.851,0.851, shown
at level 0.0109, step 1, values float32  
Opened Kinetin7.4_autob_resampled.mrc as #3, grid size 240,240,240, pixel
0.851, shown at level 0.02, step 1, values float32  
Log from Sun Jan 1 14:25:58 2023UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4j-3.cxs"

Opened kinetin.mrc as #2, grid size 35,30,31, pixel 0.851,0.851,0.851, shown
at level 0.0109, step 1, values float32  
Opened Kinetin7.4_autob_resampled.mrc as #3, grid size 240,240,240, pixel
0.851, shown at level 0.02, step 1, values float32  
Log from Sun Jan 1 14:12:25 2023UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4l-5.cxs"

Opened kinetin.mrc as #2, grid size 35,30,31, pixel 0.851,0.851,0.851, shown
at level 0.0109, step 1, values float32  
Opened Kinetin7.4_autob_resampled.mrc as #3, grid size 240,240,240, pixel
0.851, shown at level 0.017, step 1, values float32  
Log from Sat Dec 31 08:36:02 2022UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "C:\\\D_disk\\\new project\\\AZG1\\\paper\\\Fig\\\Fig4\\\Fig4l-1.cxs"

Opened kinetin.mrc as #2, grid size 35,30,31, pixel 0.851,0.851,0.851, shown
at level 0.0109, step 1, values float32  
Opened Kinetin7.4_autob_resampled.mrc as #3, grid size 240,240,240, pixel
0.851, shown at step 1, values float32  
Log from Fri Dec 30 21:16:08 2022UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "C:\\\D_disk\\\new project\\\AZG1\\\paper\\\Fig\\\Fig4\\\Fig4a.cxs"

Opened apo7.4.mrc as #2, grid size 240,240,240, pixel 0.851, shown at level
0.01, step 1, values float32  
Opened Kinetin7.4_autob_resampled.mrc as #5, grid size 240,240,240, pixel
0.851, shown at level 0.013, step 1, values float32  
Log from Thu Dec 29 23:26:36 2022UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\\\D_disk\\\new project\\\AZG1\\\structure\\\this
> work\\\apo7.4\\\apo7.4.pdb"

Chain information for apo7.4.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> open "C:\\\D_disk\\\new project\\\AZG1\\\structure\\\this
> work\\\apo7.4\\\apo7.4.mrc"

Opened apo7.4.mrc as #2, grid size 240,240,240, pixel 0.851, shown at level
0.00746, step 1, values float32  

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -70

> hide atoms

> select #1/A:162:390:440:601/E

22 atoms, 19 bonds, 3 residues, 1 model selected  

> show sel atoms

> hide H

> view #1/A:162:390:440/E

> volume zone #2 nearAtoms #10 range 5

no atoms specified for zone  

> surface zone #2 nearAtoms #1/A:162:390:440:601/E

> volume #2 level 0.017 style mesh

> color byhetero

> color #2 #909090

> volume #2 transparency 0.2

> volume #2 subdivideSurface true subdivisionLevels 1

> volume #2 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.1

> set bgColor white

> volume #2 level 0.01246

> volume #2 level 0.01

> volume #2 level 0.003853

> surface unzone #2

> volume #2 level 0.01

> cartoon style modeHelix default arrows true xsection oval width 1.5
> thickness 0.5

> setattr b radius 0.3

Assigning radius attribute to 8306 items  

> select /A:188

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

> transparency #2 70 cartoons

> transparency #2 10 cartoons

> transparency #1 10 cartoons

> transparency #1 70 cartoons

> volume #2 level 0.00678

> volume #2 level 0.005

> volume #2 level 0.006

> volume zone #2 nearAtoms #10 range 5

no atoms specified for zone  

> surface zone #2 nearAtoms #1/A:162:390:440:601/E

> volume #2 level 0.005

> hide atoms

> select #1/A:162:390:440:601/E

22 atoms, 19 bonds, 3 residues, 1 model selected  

> show sel atoms

> hide H

> view #1/A:162:390:440/E

> volume zone #2 nearAtoms #1 range 5

> surface zone #2 nearAtoms #1/A:162:390:440:601/E、

Invalid "nearAtoms" argument: only initial part "#1/A:162:390:440:601/E" of
atom specifier valid  

> surface zone #2 nearAtoms #1/A:162:390:440:601/E

> surface unzone #2

> volume #2 level 0.01

> hide sel cartoons

> select #2

4 models selected  

> select clear

> hide cartoons

> show cartoons

> hide cartoons

> show atoms

> select #1/A:162:390:440:601/E

22 atoms, 19 bonds, 3 residues, 1 model selected  

> color sel red

> color sel cyan

> show sel cartoons

[Repeated 1 time(s)]

> hide sel cartoons

> select clear

> show cartoons

> open "C:/D_disk/new project/AZG1/structure/this
> work/kinetin7.4/kinetin7.4-wat.pdb"

Chain information for kinetin7.4-wat.pdb #3  
---  
Chain | Description  
A B | No description available  
  

> open "C:/D_disk/new project/AZG1/structure/this
> work/kinetin7.4/Kinetin7.4_autob_resampled.mrc"

Opened Kinetin7.4_autob_resampled.mrc as #4, grid size 240,240,240, pixel
0.851, shown at level 0.0157, step 1, values float32  

> close #3#4

> open "C:/D_disk/new project/AZG1/structure/this
> work/kinetin7.4/kinetin7.4.pdb"

Chain information for kinetin7.4.pdb #3  
---  
Chain | Description  
A B | No description available  
  

> open "C:/D_disk/new project/AZG1/structure/this
> work/kinetin7.4/kinetin7.4-wat.pdb"

Chain information for kinetin7.4-wat.pdb #4  
---  
Chain | Description  
A B | No description available  
  

> open "C:/D_disk/new project/AZG1/structure/this
> work/kinetin7.4/Kinetin7.4_autob_resampled.mrc"

Opened Kinetin7.4_autob_resampled.mrc as #5, grid size 240,240,240, pixel
0.851, shown at level 0.0157, step 1, values float32  

> hide #1 models

> show #1 models

> hide #3 models

> hide #!2 models

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y 70

> hide atoms

> select #4/A:162:390:440:601/E

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

> show sel atoms

> view #4/A:162:390:440/E

> volume zone #5 nearAtoms #4 range 3

> surface zone #5 nearAtoms #4/A:162:390:440:601/E

> volume #5 level 0.013 style mesh

> color byhetero

> color #5 #909090

> volume #5 transparency 0.2

> hide H

> volume #5 subdivideSurface true subdivisionLevels 1

> volume #5 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.1

> hide #1 models

> cd "C:/D_disk/new project/AZG1/paper/Fig/Fig4"

Current working directory is: C:\D_disk\new project\AZG1\paper\Fig\Fig4  

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig.cxs"

——— End of log from Thu Dec 29 23:26:36 2022 ———

opened ChimeraX session  

> ui tool show Registration

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -70

> hide atoms

> select #3/A:452-435:152-168:376-404/E

364 atoms, 375 bonds, 46 residues, 1 model selected  

> show sel atoms

> hide H

> volume zone #4 nearAtoms #3 range 3

> surface zone #4 nearAtoms #3/A:452-435:152-168:376-404/E

No surfaces specified  

> volume #4 level 0.017 style mesh

No volumes specified  

> color byhetero

> color #4 #909090

> volume #4 transparency 0.2

No volumes specified  

> select clear

> hide atoms

> hide cartoons

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -70

> hide atoms

> select #4/A:452-435:152-168:376-404/E

365 atoms, 375 bonds, 47 residues, 1 model selected  

> show sel atoms

> hide H

> volume zone #5 nearAtoms #4 range 3

> surface zone #5 nearAtoms #4/A:452-435:152-168:376-404/E

> volume #5 level 0.017 style mesh

> color byhetero

> color #5 #909090

> volume #5 transparency 0.2

> volume #5 subdivideSurface true subdivisionLevels 1

> color #4 #aa55ff transparency 0

> color sel byhetero

> setattr b radius 0.1

Assigning radius attribute to 25026 items  

> setattr b radius 0.3

Assigning radius attribute to 25026 items  

> setattr b radius 0.2

Assigning radius attribute to 25026 items  

> select clear

> hide atoms

> hide cartoons

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -70

> hide atoms

> select #4/A:452-435:152-168:376-404:601/E

390 atoms, 402 bonds, 48 residues, 1 model selected  

> setattr b radius 0.1

Assigning radius attribute to 25026 items  

> show sel atoms

> hide H

> volume zone #5 nearAtoms #4 range 3

> surface zone #5 nearAtoms #4/A:452-435:152-168:376-404:601/E

> volume #5 level 0.017 style mesh

> color byhetero

> color #5 #909090

> volume #5 transparency 0.2

> volume #5 subdivideSurface true subdivisionLevels 1

> volume #5 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.1

> setattr b radius 0.2

Assigning radius attribute to 25026 items  

> volume #5 level 0.02

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -70

> turn y -20

> select #4/A:162:390:440:601

47 atoms, 46 bonds, 4 residues, 1 model selected  

> color sel light green

> color byhetero

> select clear

> hide #!5 models

> select #4/E:1@O

1 atom, 1 residue, 1 model selected  

> style sel stick

Changed 1 atom style  

> style sel sphere

Changed 1 atom style  

> size sel atomRadius 1

Changed 1 atom radii  

> size sel atomRadius 0。5

Invalid "atomRadius" argument: Expected 'default' or a number >= 0 or a +/-
delta  

> size sel atomRadius 0.5

Changed 1 atom radii  

> size sel atomRadius 0.3

Changed 1 atom radii  

> size sel atomRadius 0.4

Changed 1 atom radii  

> show #!5 models

> size sel atomRadius 0.5

Changed 1 atom radii  

> select clear

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -90

> volume #5 level 0.025

> volume #5 level 0.022

> view orient

[Repeated 1 time(s)]

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -70

> turn y -20

> select #4/A:162:390:440:601

47 atoms, 46 bonds, 4 residues, 1 model selected  

> color sel light green

> select clear

> hide atoms

> hide cartoons

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -70

> hide atoms

> select #4/A:435-452:152-168:376-404:601/E

518 atoms, 531 bonds, 66 residues, 1 model selected  

> setattr b radius 0.2

Assigning radius attribute to 25026 items  

> color byhetero

> show sel atoms

> hide H

> volume zone #5 nearAtoms #4 range 3

> surface zone #5 nearAtoms #4/A:452-435:152-168:376-404:601/E

> volume #5 level 0.017 style mesh

> color byhetero

> color #5 #909090

> volume #5 transparency 0.2

> volume #5 subdivideSurface true subdivisionLevels 1

> volume #5 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.1

> select #4/A:162:390:440:601

47 atoms, 46 bonds, 4 residues, 1 model selected  

> color sel light green

> color byhetero

> select /E

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> size sel atomRadius 0.4

Changed 1 atom radii  

> volume #5 level 0.02

> volume #5 level 0.022

> surface zone #5 nearAtoms #4/A:435-452:152-168:376-404:601/E

> ui tool show "Side View"

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -90

> turn x 90

> turn x -90

> turn x -10

[Repeated 1 time(s)]

> turn x 10

[Repeated 1 time(s)]

> turn y -10

[Repeated 3 time(s)]

> select #4/A:389@CA

1 atom, 1 residue, 1 model selected  

> hide #4 models

> show #4 models

> hide #!5 models

> select clear

> select #4/A:389@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

231 atoms, 238 bonds, 28 residues, 1 model selected  

> select down

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

> hide sel atoms

> show sel cartoons

> hide sel cartoons

> show #!5 models

> volume #5 level 0.02

> select clear

> hide #4 atoms

> select #4/A:435-452:152-168:376-404:601/E

518 atoms, 531 bonds, 66 residues, 1 model selected  

> show sel cartoons

> cartoon style modeHelix default arrows true xsection oval width 1.5
> thickness 0.5

> transparency #5 70

> transparency #5 30 cartoons

[Repeated 1 time(s)]

> transparency #5 70 cartoons

> transparency #5 70

> transparency #1 70 cartoons

> transparency #1 30 cartoons

> select clear

> transparency #5 30 cartoons

> transparency #4 30 cartoons

> transparency #5 30

> transparency #5 70

> select #4/A:162:390:440:601

47 atoms, 46 bonds, 4 residues, 1 model selected  

> show sel atoms

> color sel light green

> color byhetero

> select /E

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> size sel atomRadius 0.4

Changed 1 atom radii  

> select /E

1 atom, 1 residue, 1 model selected  

> show sel atoms

> style sel sphere

Changed 1 atom style  

> size sel atomRadius 0.4

Changed 1 atom radii  

> hide H

> volume #5 level 0.023

> surface dust #5 size 8.51

> volume zone #5 nearAtoms #4 range 3

> surface zone #5 nearAtoms #4/A:435-452:152-168:376-404:601/E

> volume #5 level 0.017 style mesh

> volume zone #5 nearAtoms #4 range 5

> surface zone #5 nearAtoms #4/A:435-452:152-168:376-404:601/E

> volume zone #5 nearAtoms #4 range 1

> surface zone #5 nearAtoms #4/A:435-452:152-168:376-404:601/E

> surface zone #5 nearAtoms #4/A:162:390:440:601/E

> volume #5 level 0.02

> volume #5 level 0.022

> volume #5 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.1

> volume #5 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.5

> surface zone #5 nearAtoms #4/A:162:390:440:601

> surface zone #5 nearAtoms #4/A:162:390:440/E

> volume #5 level 0.02

> cartoon style modeHelix default arrows true xsection oval width 1.2
> thickness 0.5

> cartoon style modeHelix default arrows true xsection oval width 1 thickness
> 0.5

> color cylindrical purple

Missing or invalid "surfaces" argument: invalid surfaces specifier  

> color #4 #aa55ff color

Missing "color" keyword's argument  

> color #4 #aa55ff

> vop gaussian #4 sdev 1.5

> vop gaussian #4 sdev 3

> vop gaussian #4 sdev 0

> volume #5 level 0.021

> volume #5 level 0.018

> color sel byhetero

[Repeated 2 time(s)]

> select clear

> color #4 byhetero

> surface zone #5 nearAtoms #4/A:435-452:152-168:376-404:601/E

> select #4/A:435-452:152-168:376-404:601/E

518 atoms, 531 bonds, 66 residues, 1 model selected  

> setattr b radius 0.2

Assigning radius attribute to 25026 items  

> color byhetero

> show sel atoms

> select clear

> select #4/A:390

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

> select add #4/A:162

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

> select add #4/A:440

22 atoms, 19 bonds, 3 residues, 1 model selected  

> color sel orange red

> color sel byhetero

> select clear

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -90

> turn y -10

[Repeated 2 time(s)]

> turn y 10

> select #4/A:389

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

> hide sel atoms

> select #4/A:389

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

> show sel atoms

> select clear

> close #4

> open "C:/D_disk/new project/AZG1/structure/this
> work/kinetin7.4/kinetin7.4-wat.pdb"

Chain information for kinetin7.4-wat.pdb #4  
---  
Chain | Description  
A B | No description available  
  

> select clear

> hide atoms

> hide cartoons

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -90

> hide atoms

> select #4/A:435-452:152-168:376-404:601/E

518 atoms, 531 bonds, 66 residues, 1 model selected  

> setattr b radius 0.2

Assigning radius attribute to 25026 items  

> color byhetero

> show sel atoms

> hide H

> surface zone #5 nearAtoms #4/A:435-452:152-168:376-404:601/E

> volume #5 level 0.017 style mesh

> color byhetero

> color #5 #909090

> volume #5 transparency 0.2

> volume #5 subdivideSurface true subdivisionLevels 1

> volume #5 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.1

> select #4/A:162:390:440:601

47 atoms, 46 bonds, 4 residues, 1 model selected  

> show sel atoms

> color sel light green

> color byhetero

> select /E

1 atom, 1 residue, 1 model selected  

> show sel atoms

> style sel sphere

Changed 1 atom style  

> size sel atomRadius 0.4

Changed 1 atom radii  

> hide H

[Repeated 1 time(s)]

> volume #5 level 0.02

> show sel atoms

> color sel wheat

> color byhetero

> select #4/A:162:390:440:601

47 atoms, 46 bonds, 4 residues, 1 model selected  

> show sel atoms

> color sel wheat

> color byhetero

> select clear

> hide H

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -70

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -90

> turn x 30

> turn x -30

> surface zone #5 nearAtoms #4/A:162:390:440:601

> select

24425 atoms, 25026 bonds, 3257 residues, 7 models selected  

> select clear

> show #4/A:162:390:440:601 cartoons

> show #4/A:162:390:440:601 atoms

> hide atoms

> hide cartoons

> show #4/A:162:390:440:601 atoms

> volume #5 level 0.018

> surface zone #5 nearAtoms #4/A:162:390:440:601/E

> show #4/A:162:390:440:601/E atoms

> select clear

> hide H

> volume #5 level 0.01

> volume #5 level 0.025

> surface zone #5 nearAtoms #4/A:162:390:440/E

> open "C:/D_disk/new project/AZG1/paper/Fig/Fig3/kinetin.mrc"

Opened kinetin.mrc as #6, grid size 35,30,31, pixel 0.851,0.851,0.851, shown
at level 0.00193, step 1, values float32  

> volume #6 level 0.01822

> hide #4 models

> hide #!5 models

> surface dust #6 size 8.51

> surface dust #6 size 5

> surface dust #6 size 3

> volume #6 level 0.01027

> surface dust #6 size 3

> surface dust #6 size 5

> surface dust #6 size 8

> volume #6 subdivideSurface true subdivisionLevels 1

> volume #6 level 0.01 style mesh

> show #!5 models

> show #4 models

> volume #6 level 0.01104

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -90

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -90

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

> turn y -30

> turn y -10

> turn y 5

> volume #5 level 0.022

> hide #!5 models

Drag select of 4 atoms, 3 bonds  

> select clear

Drag select of 4 atoms, 3 bonds  

> select clear

Drag select of 4 atoms, 4 bonds  

> surface zone #5 nearAtoms sel

> show #!5 models

> select clear

Drag select of 7 atoms, 6 bonds  
Drag select of 1 bonds  

> select clear

> hide #!5 models

Drag select of 4 atoms, 3 bonds  
Drag select of 7 atoms, 6 bonds  
Drag select of 8 atoms, 6 bonds  

> surface zone #5 nearAtoms sel

> show #!5 models

> volume #5 subdivideSurface true subdivisionLevels 1

> volume #5 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.1

> volume #5 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.5

> volume #5 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.1

> select clear

> hide #!5 models

Drag select of 4 atoms, 4 bonds  

> select clear

Drag select of 4 atoms, 4 bonds  
Drag select of 3 atoms, 3 bonds  
[Repeated 1 time(s)]Drag select of 1 atoms  

> surface zone #5 nearAtoms sel

> show #!5 models

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -125

> select clear

> volume #5 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.1

> select clear

> hide #!5 models

> show #!5 models

> hide #!5 models

Drag select of 4 atoms, 4 bonds  

> select clear

Drag select of 4 atoms, 4 bonds  
Drag select of 2 atoms, 2 bonds  
Drag select of 3 atoms, 3 bonds  
Drag select of 4 atoms, 3 bonds  

> surface zone #5 nearAtoms sel

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -125

> show #!5 models

> select clear

> hide #!5 models

Drag select of 7 atoms, 6 bonds  

> select add #4/E:1@O

8 atoms, 6 bonds, 2 residues, 1 model selected  
Drag select of 2 atoms, 3 bonds  
Drag select of 1 atoms, 1 bonds, 6 kinetin.mrc  
Drag select of 4 atoms, 4 bonds  
Drag select of 2 atoms, 2 bonds  

> surface zone #5 nearAtoms sel

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -125

> show #!5 models

> volume #5 subdivideSurface true subdivisionLevels 1

> volume #5 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.1

> volume #5 subdivideSurface true subdivisionLevels 2

> volume #5 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.1

> volume #5 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.15

> volume #5 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.5

> volume #5 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.1

> select clear

> hide #!5 models

> undo

[Repeated 1 time(s)]

> hide #!5 models

Drag select of 1 atoms, 1 bonds  
Drag select of 2 atoms, 2 bonds  

> select up

16 atoms, 12 bonds, 4 residues, 1 model selected  

> select up

23 atoms, 19 bonds, 4 residues, 1 model selected  
Drag select of 2 atoms, 1 bonds  

> select subtract #4/A:390@N

20 atoms, 16 bonds, 4 residues, 1 model selected  

> select subtract #4/A:440@N

19 atoms, 15 bonds, 4 residues, 1 model selected  

> select subtract #4/A:440@O

18 atoms, 14 bonds, 4 residues, 1 model selected  

> select subtract #4/A:440@C

17 atoms, 13 bonds, 4 residues, 1 model selected  

> select subtract #4/A:162@N

16 atoms, 12 bonds, 4 residues, 1 model selected  

> surface zone #5 nearAtoms sel

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> select clear

Drag select of 4 atoms, 4 bonds  

> surface zone #5 nearAtoms sel

> show #!5 models

> hide #!5 models

Drag select of 2 atoms, 2 bonds  

> surface zone #5 nearAtoms sel

> show #!5 models

Drag select of 3 atoms, 3 bonds  
Drag select of 1 atoms  

> select add #4/A:440@OG1

11 atoms, 9 bonds, 4 residues, 1 model selected  

> select add #4/A:440@CG2

12 atoms, 11 bonds, 4 residues, 1 model selected  

> select clear

> undo

> surface zone #5 nearAtoms sel

> select clear

[Repeated 1 time(s)]

> undo

[Repeated 2 time(s)]

> hide #!5 models

> select add #4/A:162@CA

13 atoms, 12 bonds, 4 residues, 1 model selected  

> surface zone #5 nearAtoms sel

> show #!5 models

> hide #!5 models

Drag select of 2 atoms, 2 bonds  

> show #!5 models

> surface zone #5 nearAtoms sel

> select add #4/A:390@CA

12 atoms, 10 bonds, 4 residues, 1 model selected  

> surface zone #5 nearAtoms sel

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -125

> select subtract #4/A:390@CA

11 atoms, 9 bonds, 4 residues, 1 model selected  

> turn y -125

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -125

> surface zone #5 nearAtoms sel

> volume #5 subdivideSurface true subdivisionLevels 1

> volume #5 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.1

> volume #5 subdivideSurface true subdivisionLevels 2

> volume #6 subdivideSurface true subdivisionLevels 2

> color #5 #909090

> volume #5 transparency 0.2

> color #6 #909090

> volume #6 transparency 0.2

> save C:\Users\xly/Desktop/Fig/Fig4a-4.png width 2000 height 2000
> transparentBackground true

> save C:\Users\xly/Desktop/Fig/Fig4a-4.png width 2000 height 2000
> transparentBackground false

> close #1,3-4#2,5-6

> open "C:/D_disk/new project/AZG1/structure/this
> work/kinetin7.4/kinetin7.4-wat.pdb"

Chain information for kinetin7.4-wat.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> open "C:/D_disk/new project/AZG1/paper/Fig/Fig3/kinetin.mrc"

Opened kinetin.mrc as #2, grid size 35,30,31, pixel 0.851,0.851,0.851, shown
at level 0.00193, step 1, values float32  

> open "C:/D_disk/new project/AZG1/structure/this
> work/kinetin7.4/Kinetin7.4_autob_resampled.mrc"

Opened Kinetin7.4_autob_resampled.mrc as #3, grid size 240,240,240, pixel
0.851, shown at level 0.0157, step 1, values float32  

> select clear

> hide atoms

> hide cartoons

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -125

> hide atoms

> select #1/A:162:390:440

22 atoms, 19 bonds, 3 residues, 1 model selected  

> setattr b radius 0.3

Assigning radius attribute to 8360 items  

> show sel atoms

> color sel #abe5b7

> color byhetero

> select #1/601

Nothing selected  

> setattr b radius 0.3

Assigning radius attribute to 8360 items  

> show sel atoms

> color sel #f9b03d

> color byhetero

> hide H

> select #1/E

1 atom, 1 residue, 1 model selected  

> show sel atoms

> style sel sphere

Changed 1 atom style  

> size sel atomRadius 0.4

Changed 1 atom radii  

> surface zone #3 nearAtoms sel

> surface zone #2 nearAtoms #1/601

No atoms specified  

> color #2#3 #909090

> volume #2#3 transparency 0.2

> volume #2#3 subdivideSurface true subdivisionLevels 2

> volume #2#3 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.1

> select clear

Drag select of 4 atoms, 4 bonds  

> select /A:390@CA

1 atom, 1 residue, 1 model selected  

> select clear

Drag select of 4 atoms, 3 bonds  

> select add /A:390@CA

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

> hide #!2 models

> hide #!3 models

Drag select of 3 atoms, 3 bonds  
Drag select of 1 atoms  
Drag select of 3 atoms, 2 bonds  

> select add /A:162@CA

13 atoms, 9 bonds, 4 residues, 1 model selected  

> surface zone #3 nearAtoms sel

> surface zone #2 nearAtoms #1/601

No atoms specified  

> surface zone #2 nearAtoms #1:601

> surface zone #3 nearAtoms #1/601

No atoms specified  

> surface zone #3 nearAtoms sel

> show #!2 models

> show #!3 models

> volume #2 level 0.01613

> volume #2 level 0.00988

> hide #!3 models

> surface dust #2 size 8.51

> volume #3 level 0.01782

> volume #2 level 0.008055

> volume #2 level 0.01053

> volume #2#3 style mesh

> color #2#3 #909090

> volume #2#3 transparency 0.2

> volume #2#3 subdivideSurface true subdivisionLevels 2

> volume #2#3 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.1

> select #1/:601

Expected an objects specifier or a keyword  

> setattr b radius 0.3

Assigning radius attribute to 8360 items  

> show sel atoms

> color sel #f9b03d

> color byhetero

> hide H

> select #1/A:162:390:440

22 atoms, 19 bonds, 3 residues, 1 model selected  

> setattr b radius 0.3

Assigning radius attribute to 8360 items  

> show sel atoms

> color sel #abe5b7

> color byhetero

> select #1/:601

Expected an objects specifier or a keyword  

> setattr b radius 0.3

Assigning radius attribute to 8360 items  

> show sel atoms

> color sel #f9b03d

> color byhetero

> hide H

> select #1/A:162:390:440

22 atoms, 19 bonds, 3 residues, 1 model selected  

> setattr b radius 0.3

Assigning radius attribute to 8360 items  

> show sel atoms

> color sel #abe5b7

> color byhetero

> select #1:601

50 atoms, 54 bonds, 2 residues, 1 model selected  

> setattr b radius 0.3

Assigning radius attribute to 8360 items  

> show sel atoms

> color sel #f9b03d

> color byhetero

> hide H

> select #1/A:162:390:440

22 atoms, 19 bonds, 3 residues, 1 model selected  

> setattr b radius 0.3

Assigning radius attribute to 8360 items  

> show sel atoms

> color sel #abe5b7

> color byhetero

> select #1/A:601

25 atoms, 27 bonds, 1 residue, 1 model selected  

> setattr b radius 0.3

Assigning radius attribute to 8360 items  

> show sel atoms

> color sel #f9b03d

> color byhetero

> hide H

> select clear

> hide atoms

> select #1/A:162:390:440

22 atoms, 19 bonds, 3 residues, 1 model selected  

> setattr b radius 0.3

Assigning radius attribute to 8360 items  

> show sel atoms

> color sel #abe5b7

> color byhetero

> select #1/A:601

25 atoms, 27 bonds, 1 residue, 1 model selected  

> setattr b radius 0.3

Assigning radius attribute to 8360 items  

> show sel atoms

> color sel #f9b03d

> color byhetero

> hide H

> select #1/E

1 atom, 1 residue, 1 model selected  

> select #1/E

1 atom, 1 residue, 1 model selected  

> show sel atoms

> style sel sphere

Changed 1 atom style  

> size sel atomRadius 0.4

Changed 1 atom radii  

> select clear

> select #1/E

1 atom, 1 residue, 1 model selected  

> show sel atoms

> style sel sphere

Changed 1 atom style  

> size sel atomRadius 0.5

Changed 1 atom radii  

> select clear

> setattr b radius 0.2

Assigning radius attribute to 8360 items  

> volume #3 level 0.01699

> setattr b radius 0.25

Assigning radius attribute to 8360 items  

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -125

> volume #2 level 0.01092

> turn y -125setattr b radius 0.2

Expected a number or a keyword  

> setattr b radius 0.2

Assigning radius attribute to 8360 items  

> size sel atomRadius 0.4

Changed 0 atom radii  

> save C:\Users\xly/Desktop/Fig/Fig4a-3.png width 2000 height 2000
> transparentBackground true

> hide #!3 models

Drag select of 2 atoms, 2 bonds  

> select add /A:390@CA

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

> select add /A:390@N

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

> select subtract /A:390@CA

3 atoms, 1 bond, 1 residue, 1 model selected  

> select add /A:390@CA

4 atoms, 1 bond, 1 residue, 1 model selected  

> select subtract /A:390@CA

3 atoms, 1 bond, 1 residue, 1 model selected  

> hide sel atoms

> select add /A:162@N

4 atoms, 3 bonds, 2 residues, 1 model selected  

> select add /A:162@O

5 atoms, 6 bonds, 2 residues, 1 model selected  

> hide sel atoms

[Repeated 2 time(s)]

> select add /A:162@C

6 atoms, 6 bonds, 2 residues, 1 model selected  

> hide sel atoms

> select add /A:440@O

7 atoms, 6 bonds, 3 residues, 1 model selected  

> select add /A:440@C

8 atoms, 6 bonds, 3 residues, 1 model selected  

> select add /A:440@N

9 atoms, 7 bonds, 3 residues, 1 model selected  

> hide sel atoms

> show #!3 models

> undo

[Repeated 7 time(s)]

> select #1/A:162:390:440

22 atoms, 19 bonds, 3 residues, 1 model selected  

> show sel atoms

> color sel #abe5b7

> color byhetero

> select #1/A:601

25 atoms, 27 bonds, 1 residue, 1 model selected  

> setattr b radius 0.2

Assigning radius attribute to 8360 items  

> select clear

Drag select of 4 atoms, 3 bonds  

> select add /A:390@CA

5 atoms, 4 bonds, 1 residue, 1 model selected  
Drag select of 3 atoms, 3 bonds  
[Repeated 1 time(s)]

> open "C:/D_disk/new project/AZG1/structure/this
> work/kinetin7.4/kinetin7.4-wat.pdb"

Chain information for kinetin7.4-wat.pdb #4  
---  
Chain | Description  
A B | No description available  
  

> hide atoms

> select #1/A:162:390:440

22 atoms, 19 bonds, 3 residues, 1 model selected  

> show sel atoms

> color sel #abe5b7

> color byhetero

> select #1/A:601

25 atoms, 27 bonds, 1 residue, 1 model selected  

> setattr b radius 0.2

Assigning radius attribute to 16720 items  

> hdie c

Unknown command: hdie c  

> select clear

> hide cartoons

> hide #4 models

> show #4 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide atoms

> select #4/A:162:390:440

22 atoms, 19 bonds, 3 residues, 1 model selected  

> show sel atoms

> color sel #abe5b7

> color byhetero

> select #4/A:601

25 atoms, 27 bonds, 1 residue, 1 model selected  

> setattr b radius 0.2

Assigning radius attribute to 16720 items  

> hide #4 models

> show #4 models

> hide #1 models

> show #1 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #1 models

> hide #4 models

> show #1 models

> select #1/A:162:390:440

22 atoms, 19 bonds, 3 residues, 1 model selected  

> show sel atoms

> color sel #abe5b7

> color byhetero

> select #1/A:601

25 atoms, 27 bonds, 1 residue, 1 model selected  

> setattr b radius 0.2

Assigning radius attribute to 16720 items  

> show #4 models

> hide #4 models

> setattr b radius 0.4

Assigning radius attribute to 16720 items  

> show #4 models

> hide #1 models

> show #1 models

> hide #4 models

> show #4 models

> hide #1 models

> show #!3 models

> show #1 models

> hide #4 models

> surface #1/A:162 enclose #1/A:162

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #3.1 models

> show #3.1 models

> color #3.1 #639061cc

> select clear

> hide #!1 surfaces

> hide #3.1 models

> hide #!3 models

> show #!3 models

> hide #!3 models

Drag select of 4 atoms, 3 bonds  

> size sel pseudobondRadius 0.1

Changed 0 pseudobond radii  

> size pseudobondRadius 0.1

Changed 0 pseudobond radii  

> setattr sel b radius 0.2

Assigning radius attribute to 3 items  

> setattr sel a radius 0.2

Assigning radius attribute to 4 items  

> size sel atomRadius 0.2

Changed 4 atom radii  

> setattr sel atoms radius 0.2

Assigning radius attribute to 4 items  

> show #4 models

> hide #4 models

> hide #!1 models

> show #!1 models

> select clear

> select add #1/A:390@N

1 atom, 1 residue, 1 model selected  

> select add #1/A:390@C

2 atoms, 1 residue, 1 model selected  

> setattr sel atoms radius 0.2

Assigning radius attribute to 2 items  

> setattr atoms radius 0.2

Assigning radius attribute to 16318 items  

> setattr r radius 0.2

Assigning radius attribute to 2174 items  
Not creating attribute 'radius'; use 'create true' to override  

> setattr residues radius 0.2

Assigning radius attribute to 2174 items  
Not creating attribute 'radius'; use 'create true' to override  

> style sel ball

Changed 2 atom styles  

> setattr atoms radius 0.2

Assigning radius attribute to 16318 items  

> setattr sel atoms radius 0.2

Assigning radius attribute to 2 items  

> setattr sel atoms radius 0.5

Assigning radius attribute to 2 items  

> setattr sel atoms radius 0.6

Assigning radius attribute to 2 items  

> setattr sel atoms radius 1

Assigning radius attribute to 2 items  

> setattr sel atoms radius 0.5

Assigning radius attribute to 2 items  

> setattr sel atoms radius 0.8

Assigning radius attribute to 2 items  

> select clear

> select #1/A:390@CA

1 atom, 1 residue, 1 model selected  

> show #!3 models

> show #3.1 models

> setattr b radius 0.2

Assigning radius attribute to 16720 items  

> setattr b radius 0.4

Assigning radius attribute to 16720 items  

> setattr b radius 0.3

Assigning radius attribute to 16720 items  
Drag select of 4 atoms, 3 bonds, 3 Kinetin7.4_autob_resampled.mrc  

> hide #3.1 models

> setattr b radius 0.3

Assigning radius attribute to 16720 items  

> setattr sel b radius 0.2

Assigning radius attribute to 3 items  

> setattr sel atoms radius 1

Assigning radius attribute to 3 items  

> select clear

Drag select of 2 atoms, 1 bonds  

> select clear

> style #!1 stick

Changed 8159 atom styles  

> style #!1 ball

Changed 8159 atom styles  

> style #!1 sphere

Changed 8159 atom styles  

> style #!1 stick

Changed 8159 atom styles  

> style #!1 stick

Changed 8159 atom styles  

> style #!1 stick

Changed 8159 atom styles  

> select clear

> ringFill thick

Unknown command: ringFill thick  

> ringFill

Unknown command: ringFill  

> style ball ringFill think

Invalid "ringFill" argument: Should be one of 'off', 'on', 'thick', or 'thin'  

> style ball ringFill thick

Changed 16318 atom styles, 2174 residue ring styles  

> style stick ringFill thick

Changed 16318 atom styles, 2174 residue ring styles  

> style stick ringFill thin

Changed 16318 atom styles, 2174 residue ring styles  

> style stick ringFill on

Changed 16318 atom styles, 2174 residue ring styles  

> style stick ringFill off

Changed 16318 atom styles, 2174 residue ring styles  

> style stick

Changed 16318 atom styles  

> style stick dashes 1

Changed 16318 atom styles, 0 pseudobond dashes  

> style stick dashes 2

Changed 16318 atom styles, 0 pseudobond dashes  

> style stick dashes 0

Changed 16318 atom styles, 0 pseudobond dashes  

> style stick dashes 3

Changed 16318 atom styles, 0 pseudobond dashes  

> style #!1 ball

Changed 8159 atom styles  

> style bsll dashes 3

Expected a keyword  

> style ball dashes 3

Changed 16318 atom styles, 0 pseudobond dashes  

> select clear

> show #!1 atoms

> style ball dashes 3

Changed 16318 atom styles, 0 pseudobond dashes  

> style ball dashes 1

Changed 16318 atom styles, 0 pseudobond dashes  

> style ball dashes -1

Changed 16318 atom styles, 0 pseudobond dashes  

> style ball dashes -1

Changed 16318 atom styles, 0 pseudobond dashes  

> style ball ringFill on

Changed 16318 atom styles, 2174 residue ring styles  

> style ball ringFill thick

Changed 16318 atom styles, 2174 residue ring styles  

> style ball ringFill thin

Changed 16318 atom styles, 2174 residue ring styles  

> style #!1 stick

Changed 8159 atom styles  

> select clear

> style #!1 stick

Changed 8159 atom styles  

> set stickRadius -.2

Expected a keyword  

> set stickRadius 0.2

Expected a keyword  

> size sel stickRadius 0.2

Changed 0 bond radii  

> style #!1 stick

Changed 8159 atom styles  

> size sel stickRadius 0.2

Changed 0 bond radii  

> style #!1 ball

Changed 8159 atom styles  

> size sel stickRadius 0.2

Changed 0 bond radii  

> size stickRadius 0.2

Changed 16720 bond radii  

> style #!1 stick

Changed 8159 atom styles  

> size stickRadius 0.4

Changed 16720 bond radii  
Drag select of 3 atoms, 3 bonds, 1 shapes  

> size sel stickRadius 0.2

Changed 6 bond radii  

> select clear

> hide atoms

> hide cartoons

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -125

> hide atoms

> select #1/A:162:390:440

22 atoms, 19 bonds, 3 residues, 1 model selected  

> show sel atoms

> color sel #abe5b7

> color byhetero

> select #1/A:601

25 atoms, 27 bonds, 1 residue, 1 model selected  

> setattr b radius 0.3

Assigning radius attribute to 16720 items  

> show sel atoms

> color sel #f9b03d

> color byhetero

> hide H

> select clear

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -125

> close #4

> hide #!3 models

> show #!3 models

> hide #!2 models

> hide #!3 models

> hide cartoons

> select #1/A:435-452:152-168:376-404

492 atoms, 504 bonds, 64 residues, 1 model selected  

> show sel cartoons

> select #1/A:435-452:152-168:376-404

492 atoms, 504 bonds, 64 residues, 1 model selected  

> show sel cartoons

> color sel #f9b03d

> select #1/A:435-452:152-168:376-404

492 atoms, 504 bonds, 64 residues, 1 model selected  

> show sel cartoons

> color sel #909090

> select #1/A:435-452:152-168:376-404

492 atoms, 504 bonds, 64 residues, 1 model selected  

> show sel cartoons

> color sel #f9b03d

> cartoon style modeHelix default arrows true xsection oval width 1.2
> thickness 0.5

> hide cartoons

> select #1/A:435-452:152-168:376-404

492 atoms, 504 bonds, 64 residues, 1 model selected  

> show sel cartoons

> color sel #abe5b7

> transparency #1 0.2 cartoons

> transparency #1 70 cartoons

> select clear

> select #1/A:162:390:440

22 atoms, 19 bonds, 3 residues, 1 model selected  

> show sel atoms

> color sel #abe5b7

> color byhetero

> select clear

> select #1/A:162:390:440/E

23 atoms, 19 bonds, 4 residues, 1 model selected  

> show sel atoms

> color sel #abe5b7

> color byhetero

> transparency #1 70 cartoons

> select clear

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -125

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -130

> show #!3 models

> show #!2 models

> hide #!2 models

> hide #!3 models

> show #!3 models

> show stick ringFill off

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

> show bonds stick ringFill off

Expected ',' or a keyword  

> select /A:601@C13

1 atom, 1 residue, 1 model selected  

> select up

25 atoms, 27 bonds, 1 residue, 1 model selected  

> select up

4051 atoms, 4150 bonds, 541 residues, 1 model selected  

> select down

25 atoms, 27 bonds, 1 residue, 2 models selected  

> show sel stick ringFill off

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

> style sel stick ringFill off

Changed 25 atom styles, 1 residue ring style  

> cd "C:/D_disk/new project/AZG1/paper/Fig/Fig4"

Current working directory is: C:\D_disk\new project\AZG1\paper\Fig\Fig4  

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4l-1.cxs"

——— End of log from Fri Dec 30 21:16:08 2022 ———

opened ChimeraX session  

> hide atoms

> select #1/A:162:390:440:160:442

41 atoms, 37 bonds, 5 residues, 1 model selected  

> hide atoms

> select #1/A:162:390:440:160:442

41 atoms, 37 bonds, 5 residues, 1 model selected  

> show sel atoms

> color sel #abe5b7

> color byhetero

> select #1/A:601

25 atoms, 27 bonds, 1 residue, 1 model selected  

> setattr b radius 0.3

Assigning radius attribute to 8360 items  

> show sel atoms

> color sel #f9b03d

> color byhetero

> hide H

> select #1/E

1 atom, 1 residue, 1 model selected  

> show sel atoms

> style sel sphere

Changed 1 atom style  

> size sel atomRadius 0.4

Changed 1 atom radii  
Drag select of 4 atoms, 4 bonds  
Drag select of 6 atoms, 2 residues, 6 bonds, 1 shapes  

> select clear

> select /A:160

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

> select add /A:443

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

> select subtract /A:443

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

> select add /A:442

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

> select add /A:440

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

> select add /A:161

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

> select subtract /A:161

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

> select add /A:162

33 atoms, 30 bonds, 4 residues, 1 model selected  

> select add /A:389

40 atoms, 36 bonds, 5 residues, 2 models selected  

> select subtract /A:389

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

> select add /A:390@CA

34 atoms, 30 bonds, 5 residues, 2 models selected  

> select clear

> hide cartoons

Drag select of 4 atoms, 4 bonds  
Drag select of 6 atoms, 7 bonds, 1 shapes  

> select add /A:442@CB

11 atoms, 12 bonds, 2 residues, 1 model selected  
Drag select of 4 atoms, 3 bonds  
Drag select of 3 atoms, 3 bonds  
Drag select of 2 atoms, 3 bonds  

> select add /A:440@CG2

21 atoms, 22 bonds, 5 residues, 2 models selected  

> select add /E:1@O

22 atoms, 22 bonds, 6 residues, 2 models selected  

> style sel sphere

Changed 22 atom styles  

> undo

> surface zone #3 nearAtoms sel

> size sel stickRadius 0.2surface zone #3 near sel

Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta  

> surface zone #3 nearAtoms sel

> show #!2 models

> hide #!2 models

> hide #!3 models

> show #!3 models

> volume #2#3 style mesh

> select clear

> undo

> hide #!3 models

Drag select of 1 atoms, 1 bonds  

> select add /A:160@CA

24 atoms, 23 bonds, 6 residues, 2 models selected  

> select add /A:160@O

25 atoms, 25 bonds, 6 residues, 2 models selected  

> select add /A:160@N

26 atoms, 25 bonds, 6 residues, 2 models selected  

> select add /A:160@C

27 atoms, 26 bonds, 6 residues, 2 models selected  

> surface zone #3 nearAtoms sel

> show #!2 models

> show #!3 models

> select #1/A:435-452:152-168:376-404

492 atoms, 504 bonds, 64 residues, 1 model selected  

> show sel cartoons

> select clear

> hide #!2 models

> hide #!3 models

> select /A:160

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

> select add /A:159

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select add /A:158

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

> select subtract /A:158

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select clear

> select add /A:160

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

> select add /A:161

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select subtract /A:161

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

> select add /A:162

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

> select add /A:161

19 atoms, 16 bonds, 3 residues, 2 models selected  

> select add /A:440

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

> select add /A:441

33 atoms, 28 bonds, 5 residues, 2 models selected  

> select add /A:442

44 atoms, 39 bonds, 6 residues, 2 models selected  

> select add /A:390

52 atoms, 46 bonds, 7 residues, 2 models selected  

> surface zone #3 nearAtoms sel

> show #!3 models

> show #!2 models

> hide #!3 models

> select subtract /A:442

41 atoms, 35 bonds, 6 residues, 2 models selected  

> select add /A:442

52 atoms, 46 bonds, 7 residues, 2 models selected  

> select subtract /A:441

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

> select subtract /A:161

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

> surface zone #3 nearAtoms sel

> show #!3 models

> select add /E:1@O

42 atoms, 37 bonds, 6 residues, 2 models selected  

> surface zone #3 nearAtoms sel

> select clear

> hide #!3 models

> show #!3 models

> hide #!2 models

> cd "C:/D_disk/new project/AZG1/paper/Fig/Fig4"

Current working directory is: C:\D_disk\new project\AZG1\paper\Fig\Fig4  

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4l-1.cxs"

——— End of log from Sat Dec 31 08:36:02 2022 ———

opened ChimeraX session  

> hide #!3 models

> select clear

> hide cartoons

Drag select of 4 atoms, 4 bonds  
Drag select of 3 atoms, 2 bonds  

> select subtract /A:162@CG2

6 atoms, 6 bonds, 2 residues, 2 models selected  
Drag select of 3 atoms, 3 bonds  

> select subtract /A:390@OD2

8 atoms, 9 bonds, 3 residues, 2 models selected  
Drag select of 3 atoms, 3 bonds  
Drag select of 1 atoms  
Drag select of 7 atoms, 7 bonds, 1 shapes  

> name frozen map sel

> style stick ringFill off

Changed 8159 atom styles, 1087 residue ring styles  

> surface zone #3 nearAtoms sel

> show #!3 models

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4l-5.cxs"

> select add /A:440@CA

20 atoms, 20 bonds, 6 residues, 2 models selected  

> surface zone #3 nearAtoms sel

> select subtract /A:440@CA

19 atoms, 19 bonds, 6 residues, 2 models selected  

> surface zone #3 nearAtoms sel

> select clear

> hide #!3 models

Drag select of 2 atoms, 2 bonds  
Drag select of 1 atoms  
Drag select of 2 atoms, 1 bonds  
Drag select of 1 atoms, 1 bonds  

> select subtract /A:162@C

5 atoms, 4 bonds, 2 residues, 2 models selected  
Drag select of 1 atoms, 1 bonds  
Drag select of 2 atoms, 1 bonds  

> select subtract /A:390@C

7 atoms, 6 bonds, 3 residues, 2 models selected  

> select subtract /A:390@O

6 atoms, 6 bonds, 3 residues, 2 models selected  

> select add /A:390@O

7 atoms, 7 bonds, 3 residues, 2 models selected  
Drag select of 2 atoms, 2 bonds  
Drag select of 1 atoms  
Drag select of 2 atoms, 2 bonds  
Drag select of 1 atoms, 1 bonds  

> name frozen map sel

> name frozen mc sel

> select clear

Drag select of 7 atoms, 8 bonds  
Drag select of 3 atoms, 2 bonds  
Drag select of 4 atoms, 4 bonds  
Drag select of 3 atoms, 3 bonds  
Drag select of 1 atoms  
Drag select of 4 atoms, 4 bonds  

> select subtract /A:390@OD2

21 atoms, 21 bonds, 6 residues, 2 models selected  

> select subtract /A:162@CG2

20 atoms, 20 bonds, 6 residues, 2 models selected  

> name frozen map sel

> surface zone #3 nearAtoms sel

> show #!3 models

> surface zone #3 nearAtoms sel

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -125

> select #1/A:435-452:152-168:376-404

492 atoms, 504 bonds, 64 residues, 1 model selected  

> show sel cartoons

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -125

> select clear

> volume #2#3 style mesh

> color #2#3 #909090

> volume #2#3 transparency 0.2

> volume #2#3 subdivideSurface true subdivisionLevels 2

> volume #2#3 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.1

> select clear

> volume #3 level 0.02

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4l-5.cxs"

> ui tool show "Side View"

> select #1/A:434-452:152-168:376-404

500 atoms, 512 bonds, 65 residues, 1 model selected  

> select clear

> show sel cartoons

> select #1/A:434-452:152-168:376-404

500 atoms, 512 bonds, 65 residues, 1 model selected  

> show sel cartoons

> select clear

> color sel #abe5b7

> select clear

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4l-5.cxs"

> view name 1

> select clear

> hide cartoons

> select mc

18 atoms, 14 bonds, 5 residues, 1 model selected  

> hide sel atoms

> undo

[Repeated 1 time(s)]

> hide #!3 models

> select subtract /A:162@OG1

17 atoms, 14 bonds, 5 residues, 2 models selected  

> select subtract /A:162@CG2

16 atoms, 14 bonds, 5 residues, 2 models selected  

> hide sel atoms

> undo

> hide sel atoms

> show sel atoms

> hide sel atoms

> show sel atoms

> hide sel atoms

> show sel atoms

> hide sel atoms

[Repeated 2 time(s)]

> show sel atoms

> select add /A:390@C

17 atoms, 14 bonds, 5 residues, 2 models selected  

> select subtract /A:162@CA

16 atoms, 13 bonds, 5 residues, 2 models selected  

> select add /A:162@CA

17 atoms, 15 bonds, 5 residues, 2 models selected  

> select subtract /A:162@CA

16 atoms, 13 bonds, 5 residues, 2 models selected  

> hide sel atoms

[Repeated 1 time(s)]

> show sel atoms

> select subtract /A:162@CB

15 atoms, 15 bonds, 5 residues, 2 models selected  

> hide sel atoms

> show sel atoms

> hide sel atoms

> show sel atoms

> hide sel atoms

> show sel atoms

> hide sel atoms

> show sel atoms

> name frozen mc sel

> hide sel atoms

> select #1/A:434-452:152-168:376-404

500 atoms, 512 bonds, 65 residues, 1 model selected  

> show sel cartoons

> view 1

> select clear

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4j-1.cxs"

> select clear

> hide atoms

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4j-1.cxs"

> undo

> select clear

> hide cartoons

> show #!3 models

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4j-2.cxs"

> select clear

> hide #!3 models

> select #1/A:434-452:152-168:376-404

500 atoms, 512 bonds, 65 residues, 1 model selected  

> show sel cartoons

> select clear

> ui mousemode right distance

> distance /E:1@O /A:440@OG1

Distance between /E HOH 1 O and /A THR 440 OG1: 3.3777Å  

> distance /A:162@OG1 /E:1@O

Distance between /A THR 162 OG1 and /E HOH 1 O: 2.5646Å  

> distance /A:390@OD1 /E:1@O

Distance between /A ASP 390 OD1 and /E HOH 1 O: 3.1296Å  

> hide #4.1 models

> select /E:1@O

1 atom, 1 residue, 1 model selected  

> size sel atomRadius 0.4

Changed 1 atom radii  

> select clear

> select /A:160@CA

1 atom, 1 residue, 1 model selected  

> select /A:160@CA

1 atom, 1 residue, 1 model selected  

> select clear

> select #1/A:160:442@ca

9 atoms, 7 bonds, 2 residues, 1 model selected  

> select #1/A:160@ca:442@ca

2 atoms, 2 residues, 1 model selected  

> style sel ball

Changed 2 atom styles  

> style sel ball

Changed 2 atom styles  

> style sel ball

Changed 2 atom styles  

> style sel sphere

Changed 2 atom styles  

> style sel sphere

Changed 2 atom styles  

> style sel sphere

Changed 2 atom styles  

> style sel sphere

Changed 2 atom styles  

> style sel sphere

Changed 2 atom styles  

> size sel atomRadius 2

Changed 2 atom radii  

> size sel atomRadius 1

Changed 2 atom radii  

> size sel atomRadius 0.8

Changed 2 atom radii  

> size sel atomRadius 0.5

Changed 2 atom radii  

> size sel atomRadius 0.4

Changed 2 atom radii  

> color sel forest green

> select clear

> undo

> select #1/A:160@ca:442@ca

2 atoms, 2 residues, 1 model selected  

> style sel sphere

Changed 2 atom styles  

> color sel #abe5b7

> select clear

> open "C:/D_disk/new project/AZG1/structure/this
> work/kinetin7.4/kinetin7.4-wat.pdb"

Chain information for kinetin7.4-wat.pdb #5  
---  
Chain | Description  
A B | No description available  
  

> hide #4 atoms

> hide #4 cartoons

> select #4/A:160@ca:442@ca

Nothing selected  

> show sel atoms

> style sel sphere

Changed 0 atom styles  

> size sel atomRadius 0.4

Changed 0 atom radii  

> hide #5 atoms

> hide #5 cartoons

> select #5/A:160@ca:442@ca

2 atoms, 2 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 2 atom styles  

> size sel atomRadius 0.4

Changed 2 atom radii  

> color sel forest green

> hide #5 models

> show #5 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #5 models

> select #1/A:442

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

> select add #1/A:160

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

> style sel stick

Changed 19 atom styles  

> select clear

> show #5 models

> select clear

> cd "C:/D_disk/new project/AZG1/paper/Fig/Fig4"

Current working directory is: C:\D_disk\new project\AZG1\paper\Fig\Fig4  

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4j-3.cxs"

> ui tool show Distances

> distance style color #555500

[Repeated 2 time(s)]

> color #4.1 #636363 models transparency 0

> distance style color red

[Repeated 2 time(s)]

> close #4

> ui mousemode right distance

> distance #1/A:442@CB #5/A:160@CA

Distance between kinetin7.4-wat.pdb #1/A PHE 442 CB and kinetin7.4-wat.pdb
#5/A MET 160 CA: 8.9591Å  
Must select one or more distances in the table  

> ~distance #1/A:442@CB #5/A:160@CA

> distance #5/A:160@CA #5/A:442@CA

Distance between kinetin7.4-wat.pdb #5/A MET 160 CA and PHE 442 CA: 9.1810Å  

> distance style dashes 5

[Repeated 2 time(s)]

> distance style dashes 4

[Repeated 2 time(s)]

> distance style dashes 5

[Repeated 2 time(s)]

> distance style dashes 6

[Repeated 2 time(s)]

> distance style dashes 7

[Repeated 2 time(s)]

> distance style dashes 8

[Repeated 2 time(s)]

> distance style dashes 9

[Repeated 2 time(s)]

> distance style dashes 10

[Repeated 2 time(s)]

> color pbonds #636363

> select #1/A:162@OG1

1 atom, 1 residue, 1 model selected  

> select #1/E:1@O

1 atom, 1 residue, 1 model selected  

> distance #1/A:162@OG1 #1/E:1@O

Distance between kinetin7.4-wat.pdb #1/A THR 162 OG1 and /E HOH 1 O: 2.5646Å  

> distance #1/A:440@OG1 #1/E:1@O

Distance between kinetin7.4-wat.pdb #1/A THR 440 OG1 and /E HOH 1 O: 3.3777Å  

> distance #1/A:390@OD1 #1/E:1@O

Distance between kinetin7.4-wat.pdb #1/A ASP 390 OD1 and /E HOH 1 O: 3.1296Å  

> distance style dashes 9

[Repeated 2 time(s)]

> distance style dashes 8

[Repeated 2 time(s)]

> distance style dashes 7

[Repeated 2 time(s)]

> hide #4.1 models

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4j-3.cxs"

> select clear

> style pbound dashes 9

Expected a keyword  

> style pbond dashes 9

Expected a keyword  

> style pseudobond dashes 9

Expected a keyword  

> style

> style

> distance style dashes 8

[Repeated 2 time(s)]

> distance style dashes 7

[Repeated 2 time(s)]

> distance style dashes 6

[Repeated 2 time(s)]

> distance style dashes 7

[Repeated 2 time(s)]

> distance style dashes 8

[Repeated 2 time(s)]

> distance style dashes 7

[Repeated 2 time(s)]

> distance style dashes 8

[Repeated 2 time(s)]

> distance style dashes 7

[Repeated 2 time(s)]

> distance style dashes 6

[Repeated 2 time(s)]

> distance style dashes 7

[Repeated 2 time(s)]

> distance save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/1.pb"

> distance style dashes 6

[Repeated 2 time(s)]

> distance style dashes 7

[Repeated 2 time(s)]

> distance style dashes 6

[Repeated 2 time(s)]

> distance style dashes 7

[Repeated 2 time(s)]

> select #5/A:160@CA

1 atom, 1 residue, 1 model selected  

> select clear

> select #5/A:442@CA

1 atom, 1 residue, 1 model selected  

> open "C:/D_disk/new project/AZG1/paper/Fig/Fig4/3.pb"

Opened Pseudobonds 3.pb, 1 bonds  

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> close #6

> open "C:/D_disk/new project/AZG1/paper/Fig/Fig4/3.pb"

Opened Pseudobonds 3.pb, 1 bonds  

> hide #!4 models

> show #!4 models

> distance style dashes 6

[Repeated 2 time(s)]

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> select clear

> select #1/E:1@O

1 atom, 1 residue, 1 model selected  

> select #1/A:440@OG1

1 atom, 1 residue, 1 model selected  

> select clear

> select #1/A:390@OD1

1 atom, 1 residue, 1 model selected  

> select clear

> select #1/A:162@OG1

1 atom, 1 residue, 1 model selected  

> open "C:/D_disk/new project/AZG1/paper/Fig/Fig4/4.pb"

Opened Pseudobonds 4.pb, 3 bonds  

> hide #!4 models

> show #!4 models

> hide #!4 models

> close #4

> close #6-7

> open "C:/D_disk/new project/AZG1/paper/Fig/Fig4/3.pb" "C:/D_disk/new
> project/AZG1/paper/Fig/Fig4/4.pb"

Opened Pseudobonds 3.pb, 1 bonds  
Opened Pseudobonds 4.pb, 3 bonds  

> select clear

> view 1

> turn y -10

> turn y 10

[Repeated 2 time(s)]

> view 1

> turn y 10

> view 1

> select #5/A:160@CA

1 atom, 1 residue, 1 model selected  

> hide #4 models

> show #4 models

> hide #5 models

> show #5 models

> select #5/A:442@CA

1 atom, 1 residue, 1 model selected  

> select add #1/A:160

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

> select clear

> select #5/A:160@CA

1 atom, 1 residue, 1 model selected  

> select add #5/A:442@CA

2 atoms, 2 residues, 1 model selected  

> select add #1/E:1@O

3 atoms, 3 residues, 2 models selected  

> size sel atomRadius 0.5

Changed 3 atom radii  

> select clear

> select #1/E:1@O

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> select clear

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4j-3.cxs"

——— End of log from Sun Jan 1 14:12:25 2023 ———

opened ChimeraX session  

> save C:\Users\xly/Desktop/Fig/Fig4j-3.png width 2000 height 2000
> transparentBackground true

> hide #6 models

> hide #5 models

> hide #4 models

> hide #!1 atoms

> save C:\Users\xly/Desktop/Fig/Fig4j-1.png width 2000 height 2000
> transparentBackground true

> transparency #1 50 cartoons

> save C:\Users\xly/Desktop/Fig/Fig4j-1.png width 2000 height 2000
> transparentBackground true

> undo

> show #!3 models

> hide #!3 models

> show #!3 models

> save C:\Users\xly/Desktop/Fig/Fig4j-1.png width 2000 height 2000
> transparentBackground true

> volume #2#3 transparency 0.4

> volume #1 transparency 0.3

No volumes specified  

> volume #1 transparency 30 c

Expected keyword "center", "change", "close", "color", "calculateSurfaces",
"capFaces", "centerIndex", "colorMode", "colormapSize", "coordinateSystem",
"colormapExtendLeft", "colormapExtendRight", or "colormapOnGpu"  

> transparency #1 30 cartoons

> volume #2#3 transparency 1

> volume #2#3 transparency 0

> color #3 #c1c1c1cc models

> color #3 #b4b4b4cc models

> color #3 #878787cc models

> color #3 #969696cc models

> color #3 #737373cc models

> volume #2#3 transparency 0

> color #2 #b5b5b5cc models

> volume #2#3 transparency 0

> color #3 #a8a8a8cc models

> volume #2#3 transparency 0

> transparency #1 70 cartoons

> save C:\Users\xly/Desktop/Fig/Fig4j-1.png width 2000 height 2000
> transparentBackground false

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4j-1.cxs"

——— End of log from Sun Jan 1 14:25:58 2023 ———

opened ChimeraX session  

> close #4-6#1-3

> open "C:/D_disk/new project/AZG1/structure/this work/BAP7.4/BAP7.4-wat.pdb"

Chain information for BAP7.4-wat.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> open "C:/D_disk/new project/AZG1/paper/Fig/Fig3/BAP.mrc"

Opened BAP.mrc as #2, grid size 38,23,26, pixel 0.851,0.851,0.851, shown at
level 0.00411, step 1, values float32  

> open "C:/D_disk/new project/AZG1/structure/this
> work/BAP7.4/BAP7.4_resampled.mrc"

Opened BAP7.4_resampled.mrc as #3, grid size 240,240,240, pixel 0.851, shown
at level 0.00918, step 1, values float32  

> open "C:/D_disk/new project/AZG1/structure/this work/BAP7.4/BAP7.4-wat.pdb"

Chain information for BAP7.4-wat.pdb #4  
---  
Chain | Description  
A B | No description available  
  

> cd "C:/D_disk/new project/AZG1/paper/Fig/Fig4"

Current working directory is: C:\D_disk\new project\AZG1\paper\Fig\Fig4  

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4i-1.cxs"

> view 1

> dssp

> setattr :47-74 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :47-74 res ss_id 200

Assigning ss_id attribute to 112 items  

> setattr :84-87 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :84-87 res ss_id 201

Assigning ss_id attribute to 16 items  

> setattr :102-106 res ss_type 2

Assigning ss_type attribute to 20 items  

> setattr :102-106 res ss_id 202

Assigning ss_id attribute to 20 items  

> setattr :160-171 res ss_type 1

Assigning ss_type attribute to 48 items  

> setattr :160-171 res ss_id 203

Assigning ss_id attribute to 48 items  

> setattr :172-180 res ss_type 3

Assigning ss_type attribute to 36 items  

> setattr :172-180 res ss_id 204

Assigning ss_id attribute to 36 items  

> setattr :181-201 res ss_type 1

Assigning ss_type attribute to 84 items  

> setattr :181-201 res ss_id 228

Assigning ss_id attribute to 84 items  

> setattr :203-209 res ss_type 1

Assigning ss_type attribute to 28 items  

> setattr :203-209 res ss_id 205

Assigning ss_id attribute to 28 items  

> setattr :213-232 res ss_type 1

Assigning ss_type attribute to 80 items  

> setattr :213-232 res ss_id 206

Assigning ss_id attribute to 80 items  

> setattr :241-244 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :241-244 res ss_id 207

Assigning ss_id attribute to 16 items  

> setattr :248-251 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :248-251 res ss_id 208

Assigning ss_id attribute to 16 items  

> setattr :259-261 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :259-261 res ss_id 209

Assigning ss_id attribute to 12 items  

> setattr :262-264 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :262-264 res ss_id 210

Assigning ss_id attribute to 12 items  

> setattr :265-268 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :265-268 res ss_id 211

Assigning ss_id attribute to 16 items  

> setattr :271-275 res ss_type 2

Assigning ss_type attribute to 20 items  

> setattr :271-275 res ss_id 212

Assigning ss_id attribute to 20 items  

> setattr :279-282 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :279-282 res ss_id 213

Assigning ss_id attribute to 16 items  

> setattr :285-287 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :285-287 res ss_id 214

Assigning ss_id attribute to 12 items  

> setattr :318-331 res ss_type 1

Assigning ss_type attribute to 56 items  

> setattr :318-331 res ss_id 215

Assigning ss_id attribute to 56 items  

> setattr :344-354 res ss_type 1

Assigning ss_type attribute to 44 items  

> setattr :344-354 res ss_id 216

Assigning ss_id attribute to 44 items  

> setattr :377-403 res ss_type 1

Assigning ss_type attribute to 108 items  

> setattr :377-403 res ss_id 217

Assigning ss_id attribute to 108 items  

> setattr :417-434 res ss_type 1

Assigning ss_type attribute to 72 items  

> setattr :417-434 res ss_id 218

Assigning ss_id attribute to 72 items  

> setattr :443-451 res ss_type 1

Assigning ss_type attribute to 36 items  

> setattr :443-451 res ss_id 219

Assigning ss_id attribute to 36 items  

> setattr :457-469 res ss_type 1

Assigning ss_type attribute to 52 items  

> setattr :457-469 res ss_id 220

Assigning ss_id attribute to 52 items  

> setattr :473-478 res ss_type 1

Assigning ss_type attribute to 24 items  

> setattr :473-478 res ss_id 221

Assigning ss_id attribute to 24 items  

> setattr :481-501 res ss_type 1

Assigning ss_type attribute to 84 items  

> setattr :481-501 res ss_id 222

Assigning ss_id attribute to 84 items  

> setattr :507-522 res ss_type 1

Assigning ss_type attribute to 64 items  

> setattr :507-522 res ss_id 223

Assigning ss_id attribute to 64 items  

> setattr :526-553 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :526-553 res ss_id 224

Assigning ss_id attribute to 112 items  

> setattr :252-258 res ss_type 3

Assigning ss_type attribute to 28 items  

> setattr :252-258 res ss_id 225

Assigning ss_id attribute to 28 items  

> setattr :107-117 res ss_type 3

Assigning ss_type attribute to 44 items  

> setattr :107-117 res ss_id 226

Assigning ss_id attribute to 44 items  

> setattr :88-101 res ss_type 3

Assigning ss_type attribute to 56 items  

> setattr :88-101 res ss_id 227

Assigning ss_id attribute to 56 items  

> setattr :75-83 res ss_type 3

Assigning ss_type attribute to 36 items  

> setattr :75-83 res ss_id 227

Assigning ss_id attribute to 36 items  

> setattr :40-42 res ss_type 1

Assigning ss_type attribute to 12 items  

> setattr :40-42 res ss_id 228

Assigning ss_id attribute to 12 items  

> setattr :156-158 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :156-158 res ss_id 229

Assigning ss_id attribute to 12 items  

> setattr :439-441 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :439-441 res ss_id 230

Assigning ss_id attribute to 12 items  

> setattr :377-404 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :377-404 res ss_id 231

Assigning ss_id attribute to 112 items  

> set bgColor white

> cartoon style modeHelix default arrows true xsection oval width 1.5
> thickness 0.5

> hide #!2 models

> hide #!3 models

> hide #4 models

> select clear

> hide atoms

> hide cartoons

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -125

> hide atoms

> select #1/A:162:390:440:160:442

41 atoms, 37 bonds, 5 residues, 1 model selected  

> show sel atoms

> hide #1 models

> show #1 models

> show sel atoms

[Repeated 1 time(s)]

> show sel cartoons

> hide atoms

> select #1/A:162:390:440:160:442

41 atoms, 37 bonds, 5 residues, 1 model selected  

> show sel atoms

> ui tool show "Side View"

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -125

> select clear

> hide atoms

> hide cartoons

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -125

> hide atoms

> select #1/A:162:390:440:160:442

41 atoms, 37 bonds, 5 residues, 1 model selected  

> show sel atoms

> color sel #abe5b7

> color byhetero

> select #1/A:601

28 atoms, 30 bonds, 1 residue, 1 model selected  

> setattr b radius 0.3

Assigning radius attribute to 16732 items  

> show sel atoms

> color sel #f9b03d

> color byhetero

> hide H

[Repeated 1 time(s)]

> view orient

> turn y 90

> turn z 90

> turn y -10

> turn y 180

> turn y -125

> view 1

> select clear

Drag select of 4 atoms, 4 bonds  
Drag select of 3 atoms, 2 bonds  
Drag select of 2 atoms, 2 bonds  

> select add #1/A:440@OG1

10 atoms, 9 bonds, 3 residues, 1 model selected  
Drag select of 4 atoms, 4 bonds  
Drag select of 5 atoms, 5 bonds  
Drag select of 1 atoms, 2 bonds  

> hide sel atoms

> show sel atoms

> name frozen map sel

> select #1/E

1 atom, 1 residue, 1 model selected  

> show sel atoms

> style sel sphere

Changed 1 atom style  

> size sel atomRadius 0.4

Changed 1 atom radii  

> select #1/E

1 atom, 1 residue, 1 model selected  

> show sel atoms

> style sel sphere

Changed 1 atom style  

> size sel atomRadius 0.5

Changed 1 atom radii  

> surface zone #3 nearAtoms sel

> volume #3 style mesh

> color #3 #a8a8a8

> volume #2#3 subdivideSurface true subdivisionLevels 2

> volume #2#3 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.1

> show #!3 models

> select map

20 atoms, 22 bonds, 5 residues, 1 model selected  

> hide #!3 models

> select add #1/E:1@O

21 atoms, 22 bonds, 6 residues, 1 model selected  

> name frozen map sel

> surface zone #3 nearAtoms sel

> show #!3 models

> hide #!3 models

> select subtract #1/A:162@CG2

20 atoms, 21 bonds, 6 residues, 1 model selected  

> select subtract #1/A:390@OD2

19 atoms, 20 bonds, 6 residues, 1 model selected  

> surface zone #3 nearAtoms sel

> show #!3 models

> surface zone #3 nearAtoms sel

> volume #3 level 0.02

> hide #!3 models

> ui mousemode right distance

> select clear

> select add #1/A:440@OG1

1 atom, 1 residue, 1 model selected  

> select clear

> distance #1/E:1@O #1/A:440@OG1

Distance between BAP7.4-wat.pdb #1/E HOH 1 O and /A THR 440 OG1: 3.8822Å  

> close #1

> close #3

> open "C:/D_disk/new project/AZG1/structure/this work/BAP7.4/BAP7.4-wat.pdb"

Chain information for BAP7.4-wat.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> open "C:/D_disk/new project/AZG1/structure/this work/BAP7.4/BAP7.4-wat.pdb"

Chain information for BAP7.4-wat.pdb #3  
---  
Chain | Description  
A B | No description available  
  

> select clear

> hide atoms

> hide cartoons

> view 1

> select #1/A:162:390:440:160:442

41 atoms, 37 bonds, 5 residues, 1 model selected  

> show sel atoms

> color sel #78a0ff

> color byhetero

> select #1/A:601

28 atoms, 30 bonds, 1 residue, 1 model selected  

> setattr b radius 0.3

Assigning radius attribute to 25098 items  

> show sel atoms

> color sel #fa8072

> color byhetero

> hide H

> select #1/E

1 atom, 1 residue, 1 model selected  

> show sel atoms

> style sel sphere

Changed 1 atom style  

> size sel atomRadius 0.5

Changed 1 atom radii  
Drag select of 4 atoms, 4 bonds  
Drag select of 3 atoms, 2 bonds  

> select subtract #1/E:1@O

7 atoms, 7 bonds, 2 residues, 1 model selected  
Drag select of 2 atoms, 3 bonds  

> select add #1/A:390@OD2

10 atoms, 10 bonds, 3 residues, 1 model selected  

> select add #1/A:390@CB

11 atoms, 11 bonds, 3 residues, 1 model selected  

> select add #1/E:1@O

12 atoms, 11 bonds, 4 residues, 1 model selected  
Drag select of 3 atoms, 2 bonds  
Drag select of 6 atoms, 7 bonds  

> select add #1/A:442@CB

22 atoms, 22 bonds, 6 residues, 1 model selected  

> hide sel atoms

> show sel atoms

> name frozen map sel

> select map

22 atoms, 22 bonds, 6 residues, 1 model selected  

> surface zone #3 nearAtoms sel

No surfaces specified  

> close #3

> open "C:/D_disk/new project/AZG1/structure/this
> work/BAP7.4/BAP7.4_resampled.mrc"

Opened BAP7.4_resampled.mrc as #3, grid size 240,240,240, pixel 0.851, shown
at level 0.00918, step 1, values float32  

> surface zone #3 nearAtoms sel

> volume #3 style mesh

> color #3 #a8a8a8

> volume #2#3 subdivideSurface true subdivisionLevels 2

> volume #2#3 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.1

> volume #3 level 0.02

> volume #3 level 0.018

> volume #3 level 0.01

> volume #3 level 0.012

> volume #3 level 0.015

> volume #3 level 0.013

> select subtract #1/A:390@OD2

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

> select subtract #1/A:162@CG2

20 atoms, 21 bonds, 6 residues, 1 model selected  

> hide #!3 models

> name frozen map sel

> surface zone #3 nearAtoms sel

> show #!3 models

> view 1

> select clear

> cartoon style modeHelix default arrows true xsection oval width 1.5
> thickness 0.5

> cartoon style modeHelix default arrows true xsection oval width 1.2
> thickness 0.5

> hide cartoons

> select #1/A:434-452:152-168:376-404

500 atoms, 512 bonds, 65 residues, 1 model selected  

> show sel cartoons

> hide cartoons

> select #1/A:434-452:152-168:376-404

500 atoms, 512 bonds, 65 residues, 1 model selected  

> show sel cartoons

> color byhetero

> transparency #1 70 cartoons

> hide cartoons

> select #1/A:434-452:152-168:376-404

500 atoms, 512 bonds, 65 residues, 1 model selected  

> show sel cartoons

> color sel #78a0ff

> color byhetero

> transparency #1 70 cartoons

> hide #4 atoms

> hide #4 cartoons

> select #4/A:160@ca:442@ca

2 atoms, 2 residues, 1 model selected  

> show sel atoms

> show #4 models

> style sel sphere

Changed 2 atom styles  

> size sel atomRadius 0.5

Changed 2 atom radii  

> ui tool show "Color Actions"

> color sel blue

> color sel #0000ffff

> color sel #0000c3ff

> color sel #0000d3ff

> color sel #0000d8ff

> color sel #0000f0ff

> color sel #0000ffff

> color sel #3f2effff

> color sel #3c2effff

> color sel #1a25ffff

> color sel #3333ffff

> color sel #3d47ffff

> color sel #3e48ffff

> color sel #414affff

> color sel #5b55ffff

> color sel #4567ffff

> color sel #4a6bffff

> color sel #4f84ffff

> color sel #5084ffff

> color sel #5286ffff

> color sel #5a8cffff

> color sel #3d8bffff

> color sel #2b80ffff

> color sel #237bffff

> color sel #2079ffff

> color sel #205bffff

> color sel #2054ffff

> color sel #20a6ffff

> color sel #2084ffff

> color sel #2075ffff

> color sel #2256ffff

> color sel #2050ffff

> select clear

> open "C:/D_disk/new project/AZG1/paper/Fig/Fig4/1.pb" "C:/D_disk/new
> project/AZG1/paper/Fig/Fig4/2.pb"

Opened Pseudobonds 1.pb, 1 bonds  
Opened Pseudobonds 2.pb, 3 bonds  

> select clear

> volume #3 level 0.015

> volume #3 level 0.017

> volume #3 level 0.018

> volume #3 level 0.016

> volume #3 level 0.015

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4i-1.cxs"

> hide #7 models

> hide #6 models

> hide #5 models

> show #5 models

> hide #4 models

> show #4 models

> hide #4 models

> save C:\Users\xly/Desktop/Fig/Fig4i-1.png width 2000 height 2000
> transparentBackground false

> hide #!3 models

> show #7 models

> show #6 models

> show #4 models

> view 1

> save C:\Users\xly/Desktop/Fig/Fig4i-2.png width 2000 height 2000
> transparentBackground false

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4i-2.cxs"

> hide #5 models

> hide #6 models

> hide #7 models

> hide #4 models

> show #!3 models

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4i-1.cxs"

> volume #3 level 0.013

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4i-1.cxs"

> save C:\Users\xly/Desktop/Fig/Fig4i-1.png width 2000 height 2000
> transparentBackground false

> close #1,4-7#2-3

> open "C:/D_disk/new project/AZG1/structure/this work/tZ7.4/tZ7.4_add
> wat.pdb"

Chain information for tZ7.4_add wat.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> open "C:/D_disk/new project/AZG1/paper/Fig/Fig3/tZ.mrc"

Opened tZ.mrc as #2, grid size 38,23,26, pixel 0.851,0.851,0.851, shown at
level 0.00426, step 1, values float32  

> open "C:/D_disk/new project/AZG1/structure/this
> work/tZ7.4/tZ7.4_resamped.mrc"

Opened tZ7.4_resamped.mrc as #3, grid size 240,240,240, pixel 0.851, shown at
level 0.00934, step 1, values float32  

> open "C:/D_disk/new project/AZG1/structure/this work/tZ7.4/tZ7.4_add
> wat.pdb"

Chain information for tZ7.4_add wat.pdb #4  
---  
Chain | Description  
A B | No description available  
  

> dssp

> setattr :47-74 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :47-74 res ss_id 200

Assigning ss_id attribute to 112 items  

> setattr :84-87 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :84-87 res ss_id 201

Assigning ss_id attribute to 16 items  

> setattr :102-106 res ss_type 2

Assigning ss_type attribute to 20 items  

> setattr :102-106 res ss_id 202

Assigning ss_id attribute to 20 items  

> setattr :160-171 res ss_type 1

Assigning ss_type attribute to 48 items  

> setattr :160-171 res ss_id 203

Assigning ss_id attribute to 48 items  

> setattr :172-180 res ss_type 3

Assigning ss_type attribute to 36 items  

> setattr :172-180 res ss_id 204

Assigning ss_id attribute to 36 items  

> setattr :181-201 res ss_type 1

Assigning ss_type attribute to 84 items  

> setattr :181-201 res ss_id 228

Assigning ss_id attribute to 84 items  

> setattr :203-209 res ss_type 1

Assigning ss_type attribute to 28 items  

> setattr :203-209 res ss_id 205

Assigning ss_id attribute to 28 items  

> setattr :213-232 res ss_type 1

Assigning ss_type attribute to 80 items  

> setattr :213-232 res ss_id 206

Assigning ss_id attribute to 80 items  

> setattr :241-244 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :241-244 res ss_id 207

Assigning ss_id attribute to 16 items  

> setattr :248-251 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :248-251 res ss_id 208

Assigning ss_id attribute to 16 items  

> setattr :259-261 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :259-261 res ss_id 209

Assigning ss_id attribute to 12 items  

> setattr :262-264 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :262-264 res ss_id 210

Assigning ss_id attribute to 12 items  

> setattr :265-268 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :265-268 res ss_id 211

Assigning ss_id attribute to 16 items  

> setattr :271-275 res ss_type 2

Assigning ss_type attribute to 20 items  

> setattr :271-275 res ss_id 212

Assigning ss_id attribute to 20 items  

> setattr :279-282 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :279-282 res ss_id 213

Assigning ss_id attribute to 16 items  

> setattr :285-287 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :285-287 res ss_id 214

Assigning ss_id attribute to 12 items  

> setattr :318-331 res ss_type 1

Assigning ss_type attribute to 56 items  

> setattr :318-331 res ss_id 215

Assigning ss_id attribute to 56 items  

> setattr :344-354 res ss_type 1

Assigning ss_type attribute to 44 items  

> setattr :344-354 res ss_id 216

Assigning ss_id attribute to 44 items  

> setattr :377-403 res ss_type 1

Assigning ss_type attribute to 108 items  

> setattr :377-403 res ss_id 217

Assigning ss_id attribute to 108 items  

> setattr :417-434 res ss_type 1

Assigning ss_type attribute to 72 items  

> setattr :417-434 res ss_id 218

Assigning ss_id attribute to 72 items  

> setattr :443-451 res ss_type 1

Assigning ss_type attribute to 36 items  

> setattr :443-451 res ss_id 219

Assigning ss_id attribute to 36 items  

> setattr :457-469 res ss_type 1

Assigning ss_type attribute to 52 items  

> setattr :457-469 res ss_id 220

Assigning ss_id attribute to 52 items  

> setattr :473-478 res ss_type 1

Assigning ss_type attribute to 24 items  

> setattr :473-478 res ss_id 221

Assigning ss_id attribute to 24 items  

> setattr :481-501 res ss_type 1

Assigning ss_type attribute to 84 items  

> setattr :481-501 res ss_id 222

Assigning ss_id attribute to 84 items  

> setattr :507-522 res ss_type 1

Assigning ss_type attribute to 64 items  

> setattr :507-522 res ss_id 223

Assigning ss_id attribute to 64 items  

> setattr :526-553 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :526-553 res ss_id 224

Assigning ss_id attribute to 112 items  

> setattr :252-258 res ss_type 3

Assigning ss_type attribute to 28 items  

> setattr :252-258 res ss_id 225

Assigning ss_id attribute to 28 items  

> setattr :107-117 res ss_type 3

Assigning ss_type attribute to 44 items  

> setattr :107-117 res ss_id 226

Assigning ss_id attribute to 44 items  

> setattr :88-101 res ss_type 3

Assigning ss_type attribute to 56 items  

> setattr :88-101 res ss_id 227

Assigning ss_id attribute to 56 items  

> setattr :75-83 res ss_type 3

Assigning ss_type attribute to 36 items  

> setattr :75-83 res ss_id 227

Assigning ss_id attribute to 36 items  

> setattr :40-42 res ss_type 1

Assigning ss_type attribute to 12 items  

> setattr :40-42 res ss_id 228

Assigning ss_id attribute to 12 items  

> setattr :156-158 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :156-158 res ss_id 229

Assigning ss_id attribute to 12 items  

> setattr :439-441 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :439-441 res ss_id 230

Assigning ss_id attribute to 12 items  

> setattr :377-404 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :377-404 res ss_id 231

Assigning ss_id attribute to 112 items  

> set bgColor white

> cartoon style modeHelix default arrows true xsection oval width 1.2
> thickness 0.5

> select clear

> hide atoms

> hide cartoons

> view 1

> select #1/A:162:390:440:160:442

41 atoms, 37 bonds, 5 residues, 1 model selected  

> show sel atoms

> color sel #78a0ff

> color byhetero

> select #1/A:601

29 atoms, 30 bonds, 1 residue, 1 model selected  

> setattr b radius 0.3

Assigning radius attribute to 16732 items  

> show sel atoms

> color sel #fa8072

> color byhetero

> hide H

> select #1/E

1 atom, 1 residue, 1 model selected  

> show sel atoms

> style sel sphere

Changed 1 atom style  

> size sel atomRadius 0.5

Changed 1 atom radii  

> select clear

> hide atoms

> hide cartoons

> view 1

> select #1/A:162:390:440:160:442

41 atoms, 37 bonds, 5 residues, 1 model selected  

> show sel atoms

> color sel #ffaaff

> color byhetero

> select #1/A:601

29 atoms, 30 bonds, 1 residue, 1 model selected  

> setattr b radius 0.3

Assigning radius attribute to 16732 items  

> show sel atoms

> color sel #87ceeb

> color byhetero

> hide H

> select #1/E

1 atom, 1 residue, 1 model selected  

> show sel atoms

> style sel sphere

Changed 1 atom style  

> size sel atomRadius 0.5

Changed 1 atom radii  

> hide #!3 models

> hide #!2 models

Drag select of 4 atoms, 4 bonds  
Drag select of 3 atoms, 3 bonds  
[Repeated 1 time(s)]

> select add #1/A:390@CB

12 atoms, 10 bonds, 4 residues, 1 model selected  

> select subtract #1/A:390@CB

11 atoms, 9 bonds, 4 residues, 1 model selected  

> select add #1/A:390@CB

12 atoms, 10 bonds, 4 residues, 1 model selected  

> select subtract #1/A:390@CB

11 atoms, 9 bonds, 4 residues, 1 model selected  
Drag select of 3 atoms, 3 bonds  
Drag select of 6 atoms, 6 bonds  

> select add #1/A:442@CD1

21 atoms, 19 bonds, 6 residues, 1 model selected  

> close #1

> close #4

> open "C:/D_disk/new project/AZG1/structure/this work/tZ7.4/tZ7.4_add
> wat.pdb"

Chain information for tZ7.4_add wat.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> open "C:/D_disk/new project/AZG1/structure/this work/tZ7.4/tZ7.4.pdb"

Chain information for tZ7.4.pdb #4  
---  
Chain | Description  
A B | No description available  
  

> close #4

> open "C:/D_disk/new project/AZG1/structure/this work/tZ7.4/tZ7.4_add
> wat_mono.pdb"

Chain information for tZ7.4_add wat_mono.pdb #4  
---  
Chain | Description  
A | No description available  
  

> open "C:/D_disk/new project/AZG1/structure/this work/tZ7.4/tZ7.4_add
> wat.pdb"

Chain information for tZ7.4_add wat.pdb #5  
---  
Chain | Description  
A B | No description available  
  

> close #5

> close #4

> open "C:/D_disk/new project/AZG1/structure/this work/tZ7.4/tZ7.4_add
> wat.pdb"

Chain information for tZ7.4_add wat.pdb #4  
---  
Chain | Description  
A B | No description available  
  

> dssp

> setattr :47-74 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :47-74 res ss_id 200

Assigning ss_id attribute to 112 items  

> setattr :84-87 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :84-87 res ss_id 201

Assigning ss_id attribute to 16 items  

> setattr :102-106 res ss_type 2

Assigning ss_type attribute to 20 items  

> setattr :102-106 res ss_id 202

Assigning ss_id attribute to 20 items  

> setattr :160-171 res ss_type 1

Assigning ss_type attribute to 48 items  

> setattr :160-171 res ss_id 203

Assigning ss_id attribute to 48 items  

> setattr :172-180 res ss_type 3

Assigning ss_type attribute to 36 items  

> setattr :172-180 res ss_id 204

Assigning ss_id attribute to 36 items  

> setattr :181-201 res ss_type 1

Assigning ss_type attribute to 84 items  

> setattr :181-201 res ss_id 228

Assigning ss_id attribute to 84 items  

> setattr :203-209 res ss_type 1

Assigning ss_type attribute to 28 items  

> setattr :203-209 res ss_id 205

Assigning ss_id attribute to 28 items  

> setattr :213-232 res ss_type 1

Assigning ss_type attribute to 80 items  

> setattr :213-232 res ss_id 206

Assigning ss_id attribute to 80 items  

> setattr :241-244 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :241-244 res ss_id 207

Assigning ss_id attribute to 16 items  

> setattr :248-251 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :248-251 res ss_id 208

Assigning ss_id attribute to 16 items  

> setattr :259-261 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :259-261 res ss_id 209

Assigning ss_id attribute to 12 items  

> setattr :262-264 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :262-264 res ss_id 210

Assigning ss_id attribute to 12 items  

> setattr :265-268 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :265-268 res ss_id 211

Assigning ss_id attribute to 16 items  

> setattr :271-275 res ss_type 2

Assigning ss_type attribute to 20 items  

> setattr :271-275 res ss_id 212

Assigning ss_id attribute to 20 items  

> setattr :279-282 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :279-282 res ss_id 213

Assigning ss_id attribute to 16 items  

> setattr :285-287 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :285-287 res ss_id 214

Assigning ss_id attribute to 12 items  

> setattr :318-331 res ss_type 1

Assigning ss_type attribute to 56 items  

> setattr :318-331 res ss_id 215

Assigning ss_id attribute to 56 items  

> setattr :344-354 res ss_type 1

Assigning ss_type attribute to 44 items  

> setattr :344-354 res ss_id 216

Assigning ss_id attribute to 44 items  

> setattr :377-403 res ss_type 1

Assigning ss_type attribute to 108 items  

> setattr :377-403 res ss_id 217

Assigning ss_id attribute to 108 items  

> setattr :417-434 res ss_type 1

Assigning ss_type attribute to 72 items  

> setattr :417-434 res ss_id 218

Assigning ss_id attribute to 72 items  

> setattr :443-451 res ss_type 1

Assigning ss_type attribute to 36 items  

> setattr :443-451 res ss_id 219

Assigning ss_id attribute to 36 items  

> setattr :457-469 res ss_type 1

Assigning ss_type attribute to 52 items  

> setattr :457-469 res ss_id 220

Assigning ss_id attribute to 52 items  

> setattr :473-478 res ss_type 1

Assigning ss_type attribute to 24 items  

> setattr :473-478 res ss_id 221

Assigning ss_id attribute to 24 items  

> setattr :481-501 res ss_type 1

Assigning ss_type attribute to 84 items  

> setattr :481-501 res ss_id 222

Assigning ss_id attribute to 84 items  

> setattr :507-522 res ss_type 1

Assigning ss_type attribute to 64 items  

> setattr :507-522 res ss_id 223

Assigning ss_id attribute to 64 items  

> setattr :526-553 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :526-553 res ss_id 224

Assigning ss_id attribute to 112 items  

> setattr :252-258 res ss_type 3

Assigning ss_type attribute to 28 items  

> setattr :252-258 res ss_id 225

Assigning ss_id attribute to 28 items  

> setattr :107-117 res ss_type 3

Assigning ss_type attribute to 44 items  

> setattr :107-117 res ss_id 226

Assigning ss_id attribute to 44 items  

> setattr :88-101 res ss_type 3

Assigning ss_type attribute to 56 items  

> setattr :88-101 res ss_id 227

Assigning ss_id attribute to 56 items  

> setattr :75-83 res ss_type 3

Assigning ss_type attribute to 36 items  

> setattr :75-83 res ss_id 227

Assigning ss_id attribute to 36 items  

> setattr :40-42 res ss_type 1

Assigning ss_type attribute to 12 items  

> setattr :40-42 res ss_id 228

Assigning ss_id attribute to 12 items  

> setattr :156-158 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :156-158 res ss_id 229

Assigning ss_id attribute to 12 items  

> setattr :439-441 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :439-441 res ss_id 230

Assigning ss_id attribute to 12 items  

> setattr :377-404 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :377-404 res ss_id 231

Assigning ss_id attribute to 112 items  

> set bgColor white

> cartoon style modeHelix default arrows true xsection oval width 1.2
> thickness 0.5

> select clear

> hide atoms

> hide cartoons

> view 1

> select #1/A:162:390:440:160:442

41 atoms, 37 bonds, 5 residues, 1 model selected  

> show sel atoms

> color sel #ffaaff

> color byhetero

> select #1/A:601

29 atoms, 30 bonds, 1 residue, 1 model selected  

> setattr b radius 0.3

Assigning radius attribute to 16732 items  

> show sel atoms

> color sel #87ceeb

> color byhetero

> hide H

> select #1/E

1 atom, 1 residue, 1 model selected  

> show sel atoms

> style sel sphere

Changed 1 atom style  

> size sel atomRadius 0.5

Changed 1 atom radii  
Drag select of 4 atoms, 4 bonds  
Drag select of 3 atoms, 3 bonds  

> select subtract #1/E:1@O

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

> select add #1/E:1@O

8 atoms, 7 bonds, 3 residues, 1 model selected  
Drag select of 2 atoms, 3 bonds  

> select add #1/A:390@CB

11 atoms, 10 bonds, 4 residues, 1 model selected  

> select subtract #1/A:390@CB

10 atoms, 9 bonds, 4 residues, 1 model selected  

> select add #1/A:390@CB

11 atoms, 11 bonds, 4 residues, 1 model selected  
Drag select of 3 atoms, 3 bonds  

> select subtract #1/A:162@CG2

13 atoms, 13 bonds, 5 residues, 1 model selected  
Drag select of 4 atoms, 4 bonds  

> select add #1/A:442@CD1

18 atoms, 19 bonds, 6 residues, 1 model selected  

> select add #1/A:442@CG

19 atoms, 20 bonds, 6 residues, 1 model selected  

> select add #1/A:442@CB

20 atoms, 21 bonds, 6 residues, 1 model selected  

> hide sel atoms

[Repeated 1 time(s)]

> show sel atoms

> select map

Expected an objects specifier or a keyword  

> surface zone #3 nearAtoms sel

> name frozen map sel

> select map

20 atoms, 22 bonds, 6 residues, 1 model selected  

> surface zone #3 nearAtoms sel

> show #!3 models

> volume #3 style mesh

> color #3 #a8a8a8

> volume #2#3 subdivideSurface true subdivisionLevels 2

> volume #2#3 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.1

> hide cartoons

> select #1/A:434-452:152-168:376-404

500 atoms, 512 bonds, 65 residues, 1 model selected  

> show sel cartoons

> color sel #ffaaff

> color byhetero

> transparency #1 70 cartoons

> volume #3 level 0.02

> volume #3 level 0.017

> volume #3 level 0.015

> volume #3 level 0.012

> close #1

> close #4

> open "C:/D_disk/new project/AZG1/structure/this work/tZ7.4/tZ7.4_add
> wat.pdb"

Chain information for tZ7.4_add wat.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> open "C:/D_disk/new project/AZG1/structure/this work/tZ7.4/tZ7.4_add
> wat.pdb"

Chain information for tZ7.4_add wat.pdb #4  
---  
Chain | Description  
A B | No description available  
  

> dssp

> setattr :47-74 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :47-74 res ss_id 200

Assigning ss_id attribute to 112 items  

> setattr :84-87 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :84-87 res ss_id 201

Assigning ss_id attribute to 16 items  

> setattr :102-106 res ss_type 2

Assigning ss_type attribute to 20 items  

> setattr :102-106 res ss_id 202

Assigning ss_id attribute to 20 items  

> setattr :160-171 res ss_type 1

Assigning ss_type attribute to 48 items  

> setattr :160-171 res ss_id 203

Assigning ss_id attribute to 48 items  

> setattr :172-180 res ss_type 3

Assigning ss_type attribute to 36 items  

> setattr :172-180 res ss_id 204

Assigning ss_id attribute to 36 items  

> setattr :181-201 res ss_type 1

Assigning ss_type attribute to 84 items  

> setattr :181-201 res ss_id 228

Assigning ss_id attribute to 84 items  

> setattr :203-209 res ss_type 1

Assigning ss_type attribute to 28 items  

> setattr :203-209 res ss_id 205

Assigning ss_id attribute to 28 items  

> setattr :213-232 res ss_type 1

Assigning ss_type attribute to 80 items  

> setattr :213-232 res ss_id 206

Assigning ss_id attribute to 80 items  

> setattr :241-244 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :241-244 res ss_id 207

Assigning ss_id attribute to 16 items  

> setattr :248-251 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :248-251 res ss_id 208

Assigning ss_id attribute to 16 items  

> setattr :259-261 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :259-261 res ss_id 209

Assigning ss_id attribute to 12 items  

> setattr :262-264 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :262-264 res ss_id 210

Assigning ss_id attribute to 12 items  

> setattr :265-268 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :265-268 res ss_id 211

Assigning ss_id attribute to 16 items  

> setattr :271-275 res ss_type 2

Assigning ss_type attribute to 20 items  

> setattr :271-275 res ss_id 212

Assigning ss_id attribute to 20 items  

> setattr :279-282 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :279-282 res ss_id 213

Assigning ss_id attribute to 16 items  

> setattr :285-287 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :285-287 res ss_id 214

Assigning ss_id attribute to 12 items  

> setattr :318-331 res ss_type 1

Assigning ss_type attribute to 56 items  

> setattr :318-331 res ss_id 215

Assigning ss_id attribute to 56 items  

> setattr :344-354 res ss_type 1

Assigning ss_type attribute to 44 items  

> setattr :344-354 res ss_id 216

Assigning ss_id attribute to 44 items  

> setattr :377-403 res ss_type 1

Assigning ss_type attribute to 108 items  

> setattr :377-403 res ss_id 217

Assigning ss_id attribute to 108 items  

> setattr :417-434 res ss_type 1

Assigning ss_type attribute to 72 items  

> setattr :417-434 res ss_id 218

Assigning ss_id attribute to 72 items  

> setattr :443-451 res ss_type 1

Assigning ss_type attribute to 36 items  

> setattr :443-451 res ss_id 219

Assigning ss_id attribute to 36 items  

> setattr :457-469 res ss_type 1

Assigning ss_type attribute to 52 items  

> setattr :457-469 res ss_id 220

Assigning ss_id attribute to 52 items  

> setattr :473-478 res ss_type 1

Assigning ss_type attribute to 24 items  

> setattr :473-478 res ss_id 221

Assigning ss_id attribute to 24 items  

> setattr :481-501 res ss_type 1

Assigning ss_type attribute to 84 items  

> setattr :481-501 res ss_id 222

Assigning ss_id attribute to 84 items  

> setattr :507-522 res ss_type 1

Assigning ss_type attribute to 64 items  

> setattr :507-522 res ss_id 223

Assigning ss_id attribute to 64 items  

> setattr :526-553 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :526-553 res ss_id 224

Assigning ss_id attribute to 112 items  

> setattr :252-258 res ss_type 3

Assigning ss_type attribute to 28 items  

> setattr :252-258 res ss_id 225

Assigning ss_id attribute to 28 items  

> setattr :107-117 res ss_type 3

Assigning ss_type attribute to 44 items  

> setattr :107-117 res ss_id 226

Assigning ss_id attribute to 44 items  

> setattr :88-101 res ss_type 3

Assigning ss_type attribute to 56 items  

> setattr :88-101 res ss_id 227

Assigning ss_id attribute to 56 items  

> setattr :75-83 res ss_type 3

Assigning ss_type attribute to 36 items  

> setattr :75-83 res ss_id 227

Assigning ss_id attribute to 36 items  

> setattr :40-42 res ss_type 1

Assigning ss_type attribute to 12 items  

> setattr :40-42 res ss_id 228

Assigning ss_id attribute to 12 items  

> setattr :156-158 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :156-158 res ss_id 229

Assigning ss_id attribute to 12 items  

> setattr :439-441 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :439-441 res ss_id 230

Assigning ss_id attribute to 12 items  

> setattr :377-404 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :377-404 res ss_id 231

Assigning ss_id attribute to 112 items  

> set bgColor white

> cartoon style modeHelix default arrows true xsection oval width 1.2
> thickness 0.5

> select clear

> hide atoms

> hide cartoons

> view 1

> select #1/A:162:390:440:160:442

41 atoms, 37 bonds, 5 residues, 1 model selected  

> show sel atoms

> color sel #ffaaff

> color byhetero

> select #1/A:601

29 atoms, 30 bonds, 1 residue, 1 model selected  

> setattr b radius 0.3

Assigning radius attribute to 16732 items  

> show sel atoms

> color sel #87ceeb

> color byhetero

> hide H

> select #1/E

1 atom, 1 residue, 1 model selected  

> show sel atoms

> style sel sphere

Changed 1 atom style  

> size sel atomRadius 0.5

Changed 1 atom radii  

> select map

Expected an objects specifier or a keyword  

> surface zone #3 nearAtoms sel

> volume #3 style mesh

> color #3 #a8a8a8

> volume #2#3 subdivideSurface true subdivisionLevels 2

> volume #2#3 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.1

> hide cartoons

> select #1/A:434-452:152-168:376-404

500 atoms, 512 bonds, 65 residues, 1 model selected  

> show sel cartoons

> color sel #ffaaff

> color byhetero

> transparency #1 70 cartoons

> select clear

> hide #4 models

> show #4 models

> select clear

> hide cartoons

Drag select of 4 atoms, 4 bonds  

> hide #!3 models

Drag select of 4 atoms, 3 bonds  
Drag select of 4 atoms, 4 bonds  
Drag select of 3 atoms, 3 bonds  
Drag select of 7 atoms, 8 bonds  

> hide sel atoms

> show sel atoms

> name frozen map sel

> select map

22 atoms, 22 bonds, 6 residues, 1 model selected  

> surface zone #3 nearAtoms sel

> show #!3 models

> select subtract #1/A:390@OD2

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

> select add #1/A:390@OD2

22 atoms, 21 bonds, 6 residues, 1 model selected  

> hide #!3 models

> select subtract #1/A:162@CG2

21 atoms, 20 bonds, 6 residues, 1 model selected  

> select add #1/A:162@CG2

22 atoms, 20 bonds, 6 residues, 1 model selected  

> select subtract #1/A:162@CG2

21 atoms, 20 bonds, 6 residues, 1 model selected  

> select add #1/A:162@CG2

22 atoms, 20 bonds, 6 residues, 1 model selected  

> select subtract #1/A:162@CG2

21 atoms, 20 bonds, 6 residues, 1 model selected  

> surface zone #3 nearAtoms sel

> show #!3 models

> select subtract #1/A:390@OD2

20 atoms, 21 bonds, 6 residues, 1 model selected  

> surface zone #3 nearAtoms sel

> volume #3 level 0.013

> volume #3 level 0.014

> volume #3 level 0.02

> volume #3 level 0.012

> volume #3 level 0.01

> volume #3 level 0.015

> volume #3 level 0.014

> view 1

> hide cartoons

> select #1/A:434-452:152-168:376-404

500 atoms, 512 bonds, 65 residues, 1 model selected  

> show sel cartoons

> color sel #ffaaff

> color byhetero

> transparency #1 70 cartoons

> hide #4 models

> show #4 models

> select clear

> save C:\Users\xly/Desktop/Fig/Fig4h-1.png width 2000 height 2000
> transparentBackground false

> cd "C:/D_disk/new project/AZG1/paper/Fig/Fig4"

Current working directory is: C:\D_disk\new project\AZG1\paper\Fig\Fig4  

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4h-1.cxs"

> hide #!3 models

> hide #4 atoms

> hide #4 cartoons

> select #4/A:160@ca:442@ca

2 atoms, 2 residues, 1 model selected  

> show sel atoms

> color sel

> style sel sphere

Changed 2 atom styles  

> size sel atomRadius 0.5

Changed 2 atom radii  

> color sel hot pink

> color sel magenta

> select clear

> open "C:/D_disk/new project/AZG1/paper/Fig/Fig4/1.pb" "C:/D_disk/new
> project/AZG1/paper/Fig/Fig4/2.pb"

Opened Pseudobonds 1.pb, 1 bonds  
Opened Pseudobonds 2.pb, 3 bonds  

> save C:\Users\xly/Desktop/Fig/Fig4h-2.png width 2000 height 2000
> transparentBackground false

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4h-2.cxs"

> close #1,4#2-3

> open "C:/D_disk/new project/AZG1/structure/this work/apo5.5/apo5.5-wat.pdb"

Chain information for apo5.5-wat.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> open "C:/D_disk/new project/AZG1/structure/this
> work/apo5.5/apo5.5_resampled.mrc"

Opened apo5.5_resampled.mrc as #2, grid size 240,240,240, pixel 0.851, shown
at level 0.0091, step 1, values float32  

> open "C:/D_disk/new project/AZG1/structure/this work/apo5.5/apo5.5-wat.pdb"

Chain information for apo5.5-wat.pdb #3  
---  
Chain | Description  
A B | No description available  
  

> hide #3 models

> hide #!2 models

> show #3 models

> dssp

> setattr :47-74 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :47-74 res ss_id 200

Assigning ss_id attribute to 112 items  

> setattr :84-87 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :84-87 res ss_id 201

Assigning ss_id attribute to 16 items  

> setattr :102-106 res ss_type 2

Assigning ss_type attribute to 20 items  

> setattr :102-106 res ss_id 202

Assigning ss_id attribute to 20 items  

> setattr :160-171 res ss_type 1

Assigning ss_type attribute to 48 items  

> setattr :160-171 res ss_id 203

Assigning ss_id attribute to 48 items  

> setattr :172-180 res ss_type 3

Assigning ss_type attribute to 36 items  

> setattr :172-180 res ss_id 204

Assigning ss_id attribute to 36 items  

> setattr :181-201 res ss_type 1

Assigning ss_type attribute to 84 items  

> setattr :181-201 res ss_id 228

Assigning ss_id attribute to 84 items  

> setattr :203-209 res ss_type 1

Assigning ss_type attribute to 28 items  

> setattr :203-209 res ss_id 205

Assigning ss_id attribute to 28 items  

> setattr :213-232 res ss_type 1

Assigning ss_type attribute to 80 items  

> setattr :213-232 res ss_id 206

Assigning ss_id attribute to 80 items  

> setattr :241-244 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :241-244 res ss_id 207

Assigning ss_id attribute to 16 items  

> setattr :248-251 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :248-251 res ss_id 208

Assigning ss_id attribute to 16 items  

> setattr :259-261 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :259-261 res ss_id 209

Assigning ss_id attribute to 12 items  

> setattr :262-264 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :262-264 res ss_id 210

Assigning ss_id attribute to 12 items  

> setattr :265-268 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :265-268 res ss_id 211

Assigning ss_id attribute to 16 items  

> setattr :271-275 res ss_type 2

Assigning ss_type attribute to 20 items  

> setattr :271-275 res ss_id 212

Assigning ss_id attribute to 20 items  

> setattr :279-282 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :279-282 res ss_id 213

Assigning ss_id attribute to 16 items  

> setattr :285-287 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :285-287 res ss_id 214

Assigning ss_id attribute to 12 items  

> setattr :318-331 res ss_type 1

Assigning ss_type attribute to 56 items  

> setattr :318-331 res ss_id 215

Assigning ss_id attribute to 56 items  

> setattr :344-354 res ss_type 1

Assigning ss_type attribute to 44 items  

> setattr :344-354 res ss_id 216

Assigning ss_id attribute to 44 items  

> setattr :377-403 res ss_type 1

Assigning ss_type attribute to 108 items  

> setattr :377-403 res ss_id 217

Assigning ss_id attribute to 108 items  

> setattr :417-434 res ss_type 1

Assigning ss_type attribute to 72 items  

> setattr :417-434 res ss_id 218

Assigning ss_id attribute to 72 items  

> setattr :443-451 res ss_type 1

Assigning ss_type attribute to 36 items  

> setattr :443-451 res ss_id 219

Assigning ss_id attribute to 36 items  

> setattr :457-469 res ss_type 1

Assigning ss_type attribute to 52 items  

> setattr :457-469 res ss_id 220

Assigning ss_id attribute to 52 items  

> setattr :473-478 res ss_type 1

Assigning ss_type attribute to 24 items  

> setattr :473-478 res ss_id 221

Assigning ss_id attribute to 24 items  

> setattr :481-501 res ss_type 1

Assigning ss_type attribute to 84 items  

> setattr :481-501 res ss_id 222

Assigning ss_id attribute to 84 items  

> setattr :507-522 res ss_type 1

Assigning ss_type attribute to 64 items  

> setattr :507-522 res ss_id 223

Assigning ss_id attribute to 64 items  

> setattr :526-553 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :526-553 res ss_id 224

Assigning ss_id attribute to 112 items  

> setattr :252-258 res ss_type 3

Assigning ss_type attribute to 28 items  

> setattr :252-258 res ss_id 225

Assigning ss_id attribute to 28 items  

> setattr :107-117 res ss_type 3

Assigning ss_type attribute to 44 items  

> setattr :107-117 res ss_id 226

Assigning ss_id attribute to 44 items  

> setattr :88-101 res ss_type 3

Assigning ss_type attribute to 56 items  

> setattr :88-101 res ss_id 227

Assigning ss_id attribute to 56 items  

> setattr :75-83 res ss_type 3

Assigning ss_type attribute to 36 items  

> setattr :75-83 res ss_id 227

Assigning ss_id attribute to 36 items  

> setattr :40-42 res ss_type 1

Assigning ss_type attribute to 12 items  

> setattr :40-42 res ss_id 228

Assigning ss_id attribute to 12 items  

> setattr :156-158 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :156-158 res ss_id 229

Assigning ss_id attribute to 12 items  

> setattr :439-441 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :439-441 res ss_id 230

Assigning ss_id attribute to 12 items  

> setattr :377-404 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :377-404 res ss_id 231

Assigning ss_id attribute to 112 items  

> set bgColor white

> cartoon style modeHelix default arrows true xsection oval width 1.2
> thickness 0.5

> select clear

> hide atoms

> hide cartoons

> view 1

> select #1/A:162:390:440:160:442

41 atoms, 37 bonds, 5 residues, 1 model selected  

> show sel atoms

> color sel #ffaaff

> color byhetero

> select #1/A:601

Nothing selected  

> setattr b radius 0.3

Assigning radius attribute to 16644 items  

> show sel atoms

> color sel #87ceeb

> color byhetero

> hide H

> select #1/E

1 atom, 1 residue, 1 model selected  

> show sel atoms

> style sel sphere

Changed 1 atom style  

> size sel atomRadius 0.5

Changed 1 atom radii  

> select clear

> hide atoms

> hide cartoons

> view 1

> select #1/A:162:390:440:160:442

41 atoms, 37 bonds, 5 residues, 1 model selected  

> show sel atoms

> color sel #bf70ff

> color byhetero

> select #1/F

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

> setattr b radius 0.3

Assigning radius attribute to 16644 items  

> show sel atoms

> color sel #87ceeb

> color byhetero

> hide H

> select #1/E

1 atom, 1 residue, 1 model selected  

> show sel atoms

> style sel sphere

Changed 1 atom style  

> size sel atomRadius 0.5

Changed 1 atom radii  

> select clear

> hide atoms

> hide cartoons

> view 1

> select #1/A:162:390:440:160:442

41 atoms, 37 bonds, 5 residues, 1 model selected  

> show sel atoms

> color sel #aa55ff

> color byhetero

> select #1/F

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

> setattr b radius 0.3

Assigning radius attribute to 16644 items  

> show sel atoms

> color sel #87ceeb

> color byhetero

> hide H

> select #1/E

1 atom, 1 residue, 1 model selected  

> show sel atoms

> style sel sphere

Changed 1 atom style  

> size sel atomRadius 0.5

Changed 1 atom radii  

> close #1

> close #3

> open "C:/D_disk/new project/AZG1/structure/this work/apo5.5/apo5.5-wat.pdb"

Chain information for apo5.5-wat.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> open "C:/D_disk/new project/AZG1/structure/this work/apo5.5/apo5.5-wat.pdb"

Chain information for apo5.5-wat.pdb #3  
---  
Chain | Description  
A B | No description available  
  

> dssp

> setattr :47-74 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :47-74 res ss_id 200

Assigning ss_id attribute to 112 items  

> setattr :84-87 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :84-87 res ss_id 201

Assigning ss_id attribute to 16 items  

> setattr :102-106 res ss_type 2

Assigning ss_type attribute to 20 items  

> setattr :102-106 res ss_id 202

Assigning ss_id attribute to 20 items  

> setattr :160-171 res ss_type 1

Assigning ss_type attribute to 48 items  

> setattr :160-171 res ss_id 203

Assigning ss_id attribute to 48 items  

> setattr :172-180 res ss_type 3

Assigning ss_type attribute to 36 items  

> setattr :172-180 res ss_id 204

Assigning ss_id attribute to 36 items  

> setattr :181-201 res ss_type 1

Assigning ss_type attribute to 84 items  

> setattr :181-201 res ss_id 228

Assigning ss_id attribute to 84 items  

> setattr :203-209 res ss_type 1

Assigning ss_type attribute to 28 items  

> setattr :203-209 res ss_id 205

Assigning ss_id attribute to 28 items  

> setattr :213-232 res ss_type 1

Assigning ss_type attribute to 80 items  

> setattr :213-232 res ss_id 206

Assigning ss_id attribute to 80 items  

> setattr :241-244 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :241-244 res ss_id 207

Assigning ss_id attribute to 16 items  

> setattr :248-251 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :248-251 res ss_id 208

Assigning ss_id attribute to 16 items  

> setattr :259-261 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :259-261 res ss_id 209

Assigning ss_id attribute to 12 items  

> setattr :262-264 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :262-264 res ss_id 210

Assigning ss_id attribute to 12 items  

> setattr :265-268 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :265-268 res ss_id 211

Assigning ss_id attribute to 16 items  

> setattr :271-275 res ss_type 2

Assigning ss_type attribute to 20 items  

> setattr :271-275 res ss_id 212

Assigning ss_id attribute to 20 items  

> setattr :279-282 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :279-282 res ss_id 213

Assigning ss_id attribute to 16 items  

> setattr :285-287 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :285-287 res ss_id 214

Assigning ss_id attribute to 12 items  

> setattr :318-331 res ss_type 1

Assigning ss_type attribute to 56 items  

> setattr :318-331 res ss_id 215

Assigning ss_id attribute to 56 items  

> setattr :344-354 res ss_type 1

Assigning ss_type attribute to 44 items  

> setattr :344-354 res ss_id 216

Assigning ss_id attribute to 44 items  

> setattr :377-403 res ss_type 1

Assigning ss_type attribute to 108 items  

> setattr :377-403 res ss_id 217

Assigning ss_id attribute to 108 items  

> setattr :417-434 res ss_type 1

Assigning ss_type attribute to 72 items  

> setattr :417-434 res ss_id 218

Assigning ss_id attribute to 72 items  

> setattr :443-451 res ss_type 1

Assigning ss_type attribute to 36 items  

> setattr :443-451 res ss_id 219

Assigning ss_id attribute to 36 items  

> setattr :457-469 res ss_type 1

Assigning ss_type attribute to 52 items  

> setattr :457-469 res ss_id 220

Assigning ss_id attribute to 52 items  

> setattr :473-478 res ss_type 1

Assigning ss_type attribute to 24 items  

> setattr :473-478 res ss_id 221

Assigning ss_id attribute to 24 items  

> setattr :481-501 res ss_type 1

Assigning ss_type attribute to 84 items  

> setattr :481-501 res ss_id 222

Assigning ss_id attribute to 84 items  

> setattr :507-522 res ss_type 1

Assigning ss_type attribute to 64 items  

> setattr :507-522 res ss_id 223

Assigning ss_id attribute to 64 items  

> setattr :526-553 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :526-553 res ss_id 224

Assigning ss_id attribute to 112 items  

> setattr :252-258 res ss_type 3

Assigning ss_type attribute to 28 items  

> setattr :252-258 res ss_id 225

Assigning ss_id attribute to 28 items  

> setattr :107-117 res ss_type 3

Assigning ss_type attribute to 44 items  

> setattr :107-117 res ss_id 226

Assigning ss_id attribute to 44 items  

> setattr :88-101 res ss_type 3

Assigning ss_type attribute to 56 items  

> setattr :88-101 res ss_id 227

Assigning ss_id attribute to 56 items  

> setattr :75-83 res ss_type 3

Assigning ss_type attribute to 36 items  

> setattr :75-83 res ss_id 227

Assigning ss_id attribute to 36 items  

> setattr :40-42 res ss_type 1

Assigning ss_type attribute to 12 items  

> setattr :40-42 res ss_id 228

Assigning ss_id attribute to 12 items  

> setattr :156-158 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :156-158 res ss_id 229

Assigning ss_id attribute to 12 items  

> setattr :439-441 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :439-441 res ss_id 230

Assigning ss_id attribute to 12 items  

> setattr :377-404 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :377-404 res ss_id 231

Assigning ss_id attribute to 112 items  

> set bgColor white

> cartoon style modeHelix default arrows true xsection oval width 1.2
> thickness 0.5

> select clear

> hide atoms

> hide cartoons

> view 1

> select #1/A:162:390:440:160:442

41 atoms, 37 bonds, 5 residues, 1 model selected  

> show sel atoms

> color sel #aa55ff

> color byhetero

> select #1/F

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

> setattr b radius 0.3

Assigning radius attribute to 16644 items  

> show sel atoms

> color sel #87ceeb

> color byhetero

> hide H

> select #1/E

1 atom, 1 residue, 1 model selected  

> show sel atoms

> style sel sphere

Changed 1 atom style  

> size sel atomRadius 0.5

Changed 1 atom radii  
Drag select of 4 atoms, 4 bonds  
Drag select of 3 atoms, 3 bonds  
Drag select of 4 atoms, 3 bonds  
Drag select of 3 atoms, 3 bonds  
Drag select of 7 atoms, 8 bonds  
Drag select of 10 atoms, 11 bonds  

> name frozen map sel

> hide sel atoms

[Repeated 1 time(s)]

> show sel atoms

> select map

32 atoms, 33 bonds, 7 residues, 1 model selected  

> surface zone #3 nearAtoms sel

No surfaces specified  

> select map

32 atoms, 33 bonds, 7 residues, 1 model selected  

> surface zone #2 nearAtoms sel

> show #!2 models

> volume #2 style mesh

> color #2 #a8a8a8

> volume #2#3 subdivideSurface true subdivisionLevels 2

> volume #2#3 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.1

> volume #2 level 0.012

> volume #2 level 0.014

> hide #!2 models

> select subtract #1/A:390@OD2

31 atoms, 32 bonds, 7 residues, 1 model selected  

> show #!2 models

> hide #!2 models

> select subtract #1/A:162@CG2

30 atoms, 32 bonds, 7 residues, 1 model selected  

> surface zone #2 nearAtoms sel

> show #!2 models

> volume #2 level 0.015

> hide #!2 models

> select subtract #1/F:1@N06

29 atoms, 31 bonds, 7 residues, 1 model selected  

> surface zone #2 nearAtoms sel

> show #!2 models

> volume #2 level 0.016

> name frozen map sel

> view 1

> select clear

> select #1/F

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

> ui tool show "Color Actions"

> color sel sea green

> color sel olive drab

> color sel gray

> color sel dim gray

> select clear

> color byhetero

> select #1/F

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

> color sel teal

> color sel olive

> color sel midnight blue

> color sel silver

> select clear

> color byhetero

> select clear

> hide cartoons

> select #1/A:434-452:152-168:376-404

500 atoms, 512 bonds, 65 residues, 1 model selected  

> show sel cartoons

> color sel #aa55ff

> color byhetero

> transparency #1 70 cartoons

> select clear

> view 1

> select clear

> ui windowfill toggle

> 1

Unknown command: 1  

> view 1

[Repeated 2 time(s)]

> cd "C:/D_disk/new project/AZG1/paper/Fig/Fig4"

Current working directory is: C:\D_disk\new project\AZG1\paper\Fig\Fig4  

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4g-1.cxs"

——— End of log from Sun Jan 1 23:14:01 2023 ———

opened ChimeraX session  

> view 1

> save C:\Users\xly/Desktop/Fig/Fig4g-1.png width 2000 height 2000
> transparentBackground false

> close #5-6

> open "C:/D_disk/new project/AZG1/paper/Fig/Fig4/1.pb" "C:/D_disk/new
> project/AZG1/paper/Fig/Fig4/2.pb"

Opened Pseudobonds 1.pb, 1 bonds  
Opened Pseudobonds 2.pb, 3 bonds  

> hide #3 models

> show #3 models

> hide #!2 models

> hide #4 atoms

> hide #4 cartoons

> select #4/A:160@ca:442@ca

Nothing selected  

> show sel atoms

> color sel

> style sel sphere

Changed 0 atom styles  

> size sel atomRadius 0.5

Changed 0 atom radii  

> hide #3 atoms

> hide #3 cartoons

> select #3/A:160@ca:442@ca

2 atoms, 2 residues, 1 model selected  

> show sel atoms

> color sel

> style sel sphere

Changed 2 atom styles  

> size sel atomRadius 0.5

Changed 2 atom radii  

> ui tool show "Color Actions"

> color sel dark violet

> color sel dark magenta

> color sel dark violet

> select clear

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4g-2.cxs"

> save C:\Users\xly/Desktop/Fig/Fig4g-2.png width 2000 height 2000
> transparentBackground false

> close #1,3-5#2

> open "C:/D_disk/new project/AZG1/structure/this work/apo7.4/apo7.4-wat.pdb"

Chain information for apo7.4-wat.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> open "C:/D_disk/new project/AZG1/structure/this work/apo7.4/apo7.4-wat.pdb"

Chain information for apo7.4-wat.pdb #2  
---  
Chain | Description  
A B | No description available  
  

> close #2

> open "C:/D_disk/new project/AZG1/structure/this work/apo7.4/apo7.4.mrc"

Opened apo7.4.mrc as #2, grid size 240,240,240, pixel 0.851, shown at level
0.00746, step 1, values float32  

> open "C:/D_disk/new project/AZG1/structure/this work/apo7.4/apo7.4-wat.pdb"

Chain information for apo7.4-wat.pdb #3  
---  
Chain | Description  
A B | No description available  
  

> hide #!2 models

> color #3 tan transparency 0

> dssp

> setattr :47-74 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :47-74 res ss_id 200

Assigning ss_id attribute to 112 items  

> setattr :84-87 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :84-87 res ss_id 201

Assigning ss_id attribute to 16 items  

> setattr :102-106 res ss_type 2

Assigning ss_type attribute to 20 items  

> setattr :102-106 res ss_id 202

Assigning ss_id attribute to 20 items  

> setattr :160-171 res ss_type 1

Assigning ss_type attribute to 48 items  

> setattr :160-171 res ss_id 203

Assigning ss_id attribute to 48 items  

> setattr :172-180 res ss_type 3

Assigning ss_type attribute to 36 items  

> setattr :172-180 res ss_id 204

Assigning ss_id attribute to 36 items  

> setattr :181-201 res ss_type 1

Assigning ss_type attribute to 84 items  

> setattr :181-201 res ss_id 228

Assigning ss_id attribute to 84 items  

> setattr :203-209 res ss_type 1

Assigning ss_type attribute to 28 items  

> setattr :203-209 res ss_id 205

Assigning ss_id attribute to 28 items  

> setattr :213-232 res ss_type 1

Assigning ss_type attribute to 80 items  

> setattr :213-232 res ss_id 206

Assigning ss_id attribute to 80 items  

> setattr :241-244 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :241-244 res ss_id 207

Assigning ss_id attribute to 16 items  

> setattr :248-251 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :248-251 res ss_id 208

Assigning ss_id attribute to 16 items  

> setattr :259-261 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :259-261 res ss_id 209

Assigning ss_id attribute to 12 items  

> setattr :262-264 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :262-264 res ss_id 210

Assigning ss_id attribute to 12 items  

> setattr :265-268 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :265-268 res ss_id 211

Assigning ss_id attribute to 16 items  

> setattr :271-275 res ss_type 2

Assigning ss_type attribute to 20 items  

> setattr :271-275 res ss_id 212

Assigning ss_id attribute to 20 items  

> setattr :279-282 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :279-282 res ss_id 213

Assigning ss_id attribute to 16 items  

> setattr :285-287 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :285-287 res ss_id 214

Assigning ss_id attribute to 12 items  

> setattr :318-331 res ss_type 1

Assigning ss_type attribute to 56 items  

> setattr :318-331 res ss_id 215

Assigning ss_id attribute to 56 items  

> setattr :344-354 res ss_type 1

Assigning ss_type attribute to 44 items  

> setattr :344-354 res ss_id 216

Assigning ss_id attribute to 44 items  

> setattr :377-403 res ss_type 1

Assigning ss_type attribute to 108 items  

> setattr :377-403 res ss_id 217

Assigning ss_id attribute to 108 items  

> setattr :417-434 res ss_type 1

Assigning ss_type attribute to 72 items  

> setattr :417-434 res ss_id 218

Assigning ss_id attribute to 72 items  

> setattr :443-451 res ss_type 1

Assigning ss_type attribute to 36 items  

> setattr :443-451 res ss_id 219

Assigning ss_id attribute to 36 items  

> setattr :457-469 res ss_type 1

Assigning ss_type attribute to 52 items  

> setattr :457-469 res ss_id 220

Assigning ss_id attribute to 52 items  

> setattr :473-478 res ss_type 1

Assigning ss_type attribute to 24 items  

> setattr :473-478 res ss_id 221

Assigning ss_id attribute to 24 items  

> setattr :481-501 res ss_type 1

Assigning ss_type attribute to 84 items  

> setattr :481-501 res ss_id 222

Assigning ss_id attribute to 84 items  

> setattr :507-522 res ss_type 1

Assigning ss_type attribute to 64 items  

> setattr :507-522 res ss_id 223

Assigning ss_id attribute to 64 items  

> setattr :526-553 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :526-553 res ss_id 224

Assigning ss_id attribute to 112 items  

> setattr :252-258 res ss_type 3

Assigning ss_type attribute to 28 items  

> setattr :252-258 res ss_id 225

Assigning ss_id attribute to 28 items  

> setattr :107-117 res ss_type 3

Assigning ss_type attribute to 44 items  

> setattr :107-117 res ss_id 226

Assigning ss_id attribute to 44 items  

> setattr :88-101 res ss_type 3

Assigning ss_type attribute to 56 items  

> setattr :88-101 res ss_id 227

Assigning ss_id attribute to 56 items  

> setattr :75-83 res ss_type 3

Assigning ss_type attribute to 36 items  

> setattr :75-83 res ss_id 227

Assigning ss_id attribute to 36 items  

> setattr :40-42 res ss_type 1

Assigning ss_type attribute to 12 items  

> setattr :40-42 res ss_id 228

Assigning ss_id attribute to 12 items  

> setattr :156-158 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :156-158 res ss_id 229

Assigning ss_id attribute to 12 items  

> setattr :439-441 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :439-441 res ss_id 230

Assigning ss_id attribute to 12 items  

> setattr :377-404 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :377-404 res ss_id 231

Assigning ss_id attribute to 112 items  

> set bgColor white

> cartoon style modeHelix default arrows true xsection oval width 1.2
> thickness 0.5

> select clear

> hide atoms

> hide cartoons

> view 1

> select #1/A:162:390:440:160:442

41 atoms, 37 bonds, 5 residues, 1 model selected  

> show sel atoms

> color sel #d2b48c

> color byhetero

> select #1/A:162:390:440:160:442

41 atoms, 37 bonds, 5 residues, 1 model selected  

> show sel atoms

> color sel #d2b48c

> color byhetero

> setattr b radius 0.3

Assigning radius attribute to 16612 items  

> select clear

> select #1/A:162:390:440:160:442/E

42 atoms, 37 bonds, 6 residues, 1 model selected  

> show sel atoms

> color sel #d2b48c

> color byhetero

> setattr b radius 0.3

Assigning radius attribute to 16612 items  

> select clear

Drag select of 5 atoms, 7 bonds  

> select add #1/A:442@CD1

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

> select add #1/A:442@CE1

7 atoms, 8 bonds, 1 residue, 1 model selected  
Drag select of 1 atoms  
Drag select of 3 atoms, 3 bonds  
Drag select of 4 atoms, 3 bonds  
Drag select of 3 atoms, 3 bonds  
Drag select of 4 atoms, 4 bonds  

> hide sel atoms

[Repeated 1 time(s)]

> show sel atoms

> hide sel atoms

> show sel atoms

> name frozen map sel

> surface zone #2 nearAtoms sel

> volume #2 style mesh

> color #2 #a8a8a8

> volume #2#3 subdivideSurface true subdivisionLevels 2

> volume #2#3 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.1

> show #!2 models

> volume #2 level 0.006283

> volume #2 level 0.003

> volume #2 level 0.02

> volume #2 level 0.01

> close #1,3

> open "C:/D_disk/new project/AZG1/structure/this work/apo7.4/apo7.4-ade.pdb"

Chain information for apo7.4-ade.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> open "C:/D_disk/new project/AZG1/structure/this work/apo7.4/apo7.4-ade.pdb"

Chain information for apo7.4-ade.pdb #3  
---  
Chain | Description  
A B | No description available  
  

> dssp

> setattr :47-74 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :47-74 res ss_id 200

Assigning ss_id attribute to 112 items  

> setattr :84-87 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :84-87 res ss_id 201

Assigning ss_id attribute to 16 items  

> setattr :102-106 res ss_type 2

Assigning ss_type attribute to 20 items  

> setattr :102-106 res ss_id 202

Assigning ss_id attribute to 20 items  

> setattr :160-171 res ss_type 1

Assigning ss_type attribute to 48 items  

> setattr :160-171 res ss_id 203

Assigning ss_id attribute to 48 items  

> setattr :172-180 res ss_type 3

Assigning ss_type attribute to 36 items  

> setattr :172-180 res ss_id 204

Assigning ss_id attribute to 36 items  

> setattr :181-201 res ss_type 1

Assigning ss_type attribute to 84 items  

> setattr :181-201 res ss_id 228

Assigning ss_id attribute to 84 items  

> setattr :203-209 res ss_type 1

Assigning ss_type attribute to 28 items  

> setattr :203-209 res ss_id 205

Assigning ss_id attribute to 28 items  

> setattr :213-232 res ss_type 1

Assigning ss_type attribute to 80 items  

> setattr :213-232 res ss_id 206

Assigning ss_id attribute to 80 items  

> setattr :241-244 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :241-244 res ss_id 207

Assigning ss_id attribute to 16 items  

> setattr :248-251 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :248-251 res ss_id 208

Assigning ss_id attribute to 16 items  

> setattr :259-261 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :259-261 res ss_id 209

Assigning ss_id attribute to 12 items  

> setattr :262-264 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :262-264 res ss_id 210

Assigning ss_id attribute to 12 items  

> setattr :265-268 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :265-268 res ss_id 211

Assigning ss_id attribute to 16 items  

> setattr :271-275 res ss_type 2

Assigning ss_type attribute to 20 items  

> setattr :271-275 res ss_id 212

Assigning ss_id attribute to 20 items  

> setattr :279-282 res ss_type 2

Assigning ss_type attribute to 16 items  

> setattr :279-282 res ss_id 213

Assigning ss_id attribute to 16 items  

> setattr :285-287 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :285-287 res ss_id 214

Assigning ss_id attribute to 12 items  

> setattr :318-331 res ss_type 1

Assigning ss_type attribute to 56 items  

> setattr :318-331 res ss_id 215

Assigning ss_id attribute to 56 items  

> setattr :344-354 res ss_type 1

Assigning ss_type attribute to 44 items  

> setattr :344-354 res ss_id 216

Assigning ss_id attribute to 44 items  

> setattr :377-403 res ss_type 1

Assigning ss_type attribute to 108 items  

> setattr :377-403 res ss_id 217

Assigning ss_id attribute to 108 items  

> setattr :417-434 res ss_type 1

Assigning ss_type attribute to 72 items  

> setattr :417-434 res ss_id 218

Assigning ss_id attribute to 72 items  

> setattr :443-451 res ss_type 1

Assigning ss_type attribute to 36 items  

> setattr :443-451 res ss_id 219

Assigning ss_id attribute to 36 items  

> setattr :457-469 res ss_type 1

Assigning ss_type attribute to 52 items  

> setattr :457-469 res ss_id 220

Assigning ss_id attribute to 52 items  

> setattr :473-478 res ss_type 1

Assigning ss_type attribute to 24 items  

> setattr :473-478 res ss_id 221

Assigning ss_id attribute to 24 items  

> setattr :481-501 res ss_type 1

Assigning ss_type attribute to 84 items  

> setattr :481-501 res ss_id 222

Assigning ss_id attribute to 84 items  

> setattr :507-522 res ss_type 1

Assigning ss_type attribute to 64 items  

> setattr :507-522 res ss_id 223

Assigning ss_id attribute to 64 items  

> setattr :526-553 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :526-553 res ss_id 224

Assigning ss_id attribute to 112 items  

> setattr :252-258 res ss_type 3

Assigning ss_type attribute to 28 items  

> setattr :252-258 res ss_id 225

Assigning ss_id attribute to 28 items  

> setattr :107-117 res ss_type 3

Assigning ss_type attribute to 44 items  

> setattr :107-117 res ss_id 226

Assigning ss_id attribute to 44 items  

> setattr :88-101 res ss_type 3

Assigning ss_type attribute to 56 items  

> setattr :88-101 res ss_id 227

Assigning ss_id attribute to 56 items  

> setattr :75-83 res ss_type 3

Assigning ss_type attribute to 36 items  

> setattr :75-83 res ss_id 227

Assigning ss_id attribute to 36 items  

> setattr :40-42 res ss_type 1

Assigning ss_type attribute to 12 items  

> setattr :40-42 res ss_id 228

Assigning ss_id attribute to 12 items  

> setattr :156-158 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :156-158 res ss_id 229

Assigning ss_id attribute to 12 items  

> setattr :439-441 res ss_type 2

Assigning ss_type attribute to 12 items  

> setattr :439-441 res ss_id 230

Assigning ss_id attribute to 12 items  

> setattr :377-404 res ss_type 1

Assigning ss_type attribute to 112 items  

> setattr :377-404 res ss_id 231

Assigning ss_id attribute to 112 items  

> set bgColor white

> cartoon style modeHelix default arrows true xsection oval width 1.2
> thickness 0.5

> select clear

> hide atoms

> hide cartoons

> view 1

> select #1/A:162:390:440:160:442/E

56 atoms, 53 bonds, 6 residues, 1 model selected  

> show sel atoms

> color sel #d2b48c

> color byhetero

> setattr b radius 0.3

Assigning radius attribute to 16644 items  

> hide #!2 models

> hide H

> select clear

Drag select of 5 atoms, 7 bonds  

> select add #1/A:442@CD1

6 atoms, 8 bonds, 1 residue, 1 model selected  
Drag select of 1 bonds  

> select clear

Drag select of 8 atoms, 11 bonds  

> select clear

Drag select of 4 atoms, 4 bonds  
Drag select of 3 atoms, 3 bonds  
Drag select of 4 atoms, 4 bonds  
Drag select of 3 atoms, 3 bonds  
Drag select of 10 atoms, 11 bonds  
Drag select of 7 atoms, 7 bonds  

> hide sel atoms

> show sel atoms

> name frozen map sel

> surface zone #2 nearAtoms sel

> show #!2 models

> volume #2 level 0.015

> volume #2 level 0.012

> volume #2 level 0.013

> volume #2 level 0.01

> volume #2 level 0.012

> hide cartoons

> select #1/A:434-452:152-168:376-404

500 atoms, 512 bonds, 65 residues, 1 model selected  

> show sel cartoons

> color sel #d2b48c

> color byhetero

> transparency #1 70 cartoons

> view 1

> select clear

> hide #!2 models

> select map

31 atoms, 33 bonds, 6 residues, 1 model selected  
Drag select of 1 bonds  

> select subtract #1/E:1@N10

30 atoms, 32 bonds, 6 residues, 1 model selected  

> surface zone #2 nearAtoms sel

> show #!2 models

> hide #!2 models

> select subtract #1/E:1@C07

29 atoms, 30 bonds, 6 residues, 1 model selected  

> surface zone #2 nearAtoms sel

> show #!2 models

> select clear

> view 1

> save C:\Users\xly/Desktop/Fig/Fig4f-1.png width 2000 height 2000
> transparentBackground false

> cd "C:/D_disk/new project/AZG1/paper/Fig/Fig4"

Current working directory is: C:\D_disk\new project\AZG1\paper\Fig\Fig4  

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4f-1.cxs"

> hide #!2 models

> hide #3 models

> show #3 models

> hide #3 atoms

> hide #3 cartoons

> select #3/A:160@ca:442@ca

2 atoms, 2 residues, 1 model selected  

> show sel atoms

> color sel

> style sel sphere

Changed 2 atom styles  

> size sel atomRadius 0.5

Changed 2 atom radii  

> ui tool show "Color Actions"

> color sel rosy brown

> color sel tan

> color sel #d7eaf8ff

> color sel #f0f0f0ff

> color sel #000000ff

> color sel #e1e1e1ff

> color sel #7f3300ff

> color sel #e1e1e1ff

> color sel #a0e1e1ff

> color sel #e1e1a0ff

> color sel #e1e1e1ff

> color sel #d2b48cff

> color sel #968064ff

> color sel #a28b6cff

> color sel #8a765cff

> color sel #7d6b53ff

> color sel #7d7853ff

> color sel #7d7c54ff

> color sel #7d7c56ff

> color sel #7d7c57ff

> color sel #7d7b58ff

> color sel #7d7257ff

> color sel #7d6c57ff

> color sel #7d6a57ff

> color sel #aa557fff

> color sel #aaaa61ff

> color sel #aaa86fff

> color sel #aaa671ff

> color sel #aaa572ff

> color sel #aaa173ff

> color sel #aa9474ff

> color sel #aa8b74ff

> color sel #aa8a74ff

> color sel #d4e4f2ff

> color sel #f0f0f0ff

> color sel #f0ab60ff

> color sel #e1e1e1ff

> color sel #f0f0f0ff

> color sel #f08080ff

> color sel #e1e1e1ff

> color sel #adadadff

> color sel #e1e1e1ff

> color sel #deb887ff

> color sel #e1e1e1ff

> color sel #deb887ff

> color sel #e1e1e1ff

> color sel #f0f0f0ff

> color sel #d2b48cff

> color sel #988265ff

> color sel #867359ff

> select clear

> open "C:/D_disk/new project/AZG1/paper/Fig/Fig4/2.pb"

Line 4 "#1/E:1@O #1/A:440@OG1  
", got 0 atoms for spec "#1/E:1@O", require exactly 1  

> open "C:/D_disk/new project/AZG1/paper/Fig/Fig4/1.pb"

Opened Pseudobonds 1.pb, 1 bonds  

> select clear

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4f-2.cxs"

> save C:\Users\xly/Desktop/Fig/Fig4f-2.png width 2000 height 2000
> transparentBackground false

> hide #1/E

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4f-2.cxs"

> save C:\Users\xly/Desktop/Fig/Fig4f-2.png width 2000 height 2000
> transparentBackground false

> hide #4 models

> show #!2 models

> hide #3 models

> save "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4f-1.cxs"

——— End of log from Sun Jan 1 23:38:00 2023 ———

opened ChimeraX session  

> close #2

> open "C:/D_disk/new project/AZG1/paper/Fig/Fig4/Fig4f-1.cxs"

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 697, in restore  
self.reset()  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 588, in reset_state  
for pbg in list(self.group_map.values()):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 536, in group_map  
f = c_function('set_pbgroup_py_instance',  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molc.py", line 31, in c_function  
f = getattr(self._c_lib, func_name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\ctypes\\__init__.py", line 387, in
__getattr__  
func = self.__getitem__(name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\ctypes\\__init__.py", line 392, in
__getitem__  
func = self._FuncPtr((name_or_ordinal, self))  
AttributeError: function 'set_pbgroup_py_instance' not found  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 697, in restore  
self.reset()  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 588, in reset_state  
for pbg in list(self.group_map.values()):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 536, in group_map  
f = c_function('set_pbgroup_py_instance',  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molc.py", line 31, in c_function  
f = getattr(self._c_lib, func_name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\ctypes\\__init__.py", line 387, in
__getattr__  
func = self.__getitem__(name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\ctypes\\__init__.py", line 392, in
__getitem__  
func = self._FuncPtr((name_or_ordinal, self))  
AttributeError: function 'set_pbgroup_py_instance' not found  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 458, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 1001, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 739, in restore  
self.reset()  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 588, in reset_state  
for pbg in list(self.group_map.values()):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 536, in group_map  
f = c_function('set_pbgroup_py_instance',  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molc.py", line 31, in c_function  
f = getattr(self._c_lib, func_name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\ctypes\\__init__.py", line 387, in
__getattr__  
func = self.__getitem__(name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\ctypes\\__init__.py", line 392, in
__getitem__  
func = self._FuncPtr((name_or_ordinal, self))  
AttributeError: function 'set_pbgroup_py_instance' not found  
  
AttributeError: function 'set_pbgroup_py_instance' not found  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\ctypes\\__init__.py", line 392, in
__getitem__  
func = self._FuncPtr((name_or_ordinal, self))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 22.20.16.4749
OpenGL renderer: Intel(R) HD Graphics 620
OpenGL vendor: Intel

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

Manufacturer: HP
Model: HP Pavilion x360 Convertible
OS: Microsoft Windows 10 家庭中文版 (Build 19044)
Memory: 8,456,323,072
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-7200U CPU @ 2.50GHz
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pywin32: 303
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

[pett]

Hi Lingyi,

Thanks for reporting this problem. It has been fixed in the latest release, so if you upgrade to ChimeraX 1.5 it won't happen again.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab