Opened 8 weeks ago

Closed 8 weeks ago

#18614 closed defect (duplicate)

Session restore/reset: 'ClipCap' object has no attribute 'was_deleted'

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

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/wangxuehui/Desktop/figure/figure 1/fig1c 正面pocket.cxs"

Error opening map "/Users/wangxuehui/Desktop/figure/figure 1/fig1c
正面pocket.cxs": File fig1c 正面pocket.cxs, format mrc  
MRC header value nsymbt (15866409) is invalid  
  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Opened 2.mrc zone as #5, grid size 256,256,256, pixel 0.85, shown at level
0.0911, step 1, values float32  
Log from Thu Dec 26 15:59:39 2024UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/wangxuehui/Desktop/figure/figure 1/fig 1c pocket 正面.cxs"

Opened 2.mrc as #3, grid size 256,256,256, pixel 0.85, shown at level 0.0906,
step 1, values float32  
Opened 2.mrc zone as #5, grid size 256,256,256, pixel 0.85, shown at level
0.0911, step 1, values float32  
Log from Mon Dec 16 17:35:49 2024UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/wangxuehui/Desktop/figure/figure 1/fig 1c pocket 正面.cxs"

Opened 2.mrc as #3, grid size 256,256,256, pixel 0.85, shown at level 0.0906,
step 1, values float32  
Opened 2.mrc zone as #5, grid size 256,256,256, pixel 0.85, shown at level
0.0911, step 1, values float32  
Log from Thu Oct 24 09:12:46 2024UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/wangxuehui/Desktop/figure/figure 1/fig 1c pocket 正面.cxs" format
> session

Opened 2.mrc as #3, grid size 256,256,256, pixel 0.85, shown at level 0.0906,
step 1, values float32  
Opened 2.mrc zone as #5, grid size 256,256,256, pixel 0.85, shown at level
0.0911, step 1, values float32  
Log from Thu Oct 24 09:08:51 2024UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/wangxuehui/Desktop/figure/figure 1/fig 1c pocket 正面.cxs" format
> session

Opened 2.mrc as #3, grid size 256,256,256, pixel 0.85, shown at level 0.0906,
step 1, values float32  
Opened 2.mrc zone as #5, grid size 256,256,256, pixel 0.85, shown at level
0.0911, step 1, values float32  
Log from Thu Oct 24 09:06:28 2024UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/wangxuehui/Desktop/figure/figure 1/fig.cxs" format session

Opened 2.mrc as #3, grid size 256,256,256, pixel 0.85, shown at level 0.0906,
step 1, values float32  
Opened 2.mrc zone as #5, grid size 256,256,256, pixel 0.85, shown at level
0.0911, step 1, values float32  
Log from Wed Oct 23 21:56:23 2024UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/wangxuehui/Desktop/figure/figure 1/fig1c-cp55940-map.cxs"
> format session

Opened 2.mrc as #3, grid size 256,256,256, pixel 0.85, shown at level 0.0317,
step 1, values float32  
Opened 2.mrc zone as #5, grid size 256,256,256, pixel 0.85, shown at level
0.0911, step 1, values float32  
Log from Wed Oct 23 17:59:13 2024UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/wangxuehui/Desktop/CB2文章图/cp55940-molecule.pdb

> open /Users/wangxuehui/Desktop/CB2结构/1.pdb

Chain information for 1.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
R | No description available  
  

> open /Users/wangxuehui/Desktop/CB2结构/2.mrc

Opened 2.mrc as #3, grid size 256,256,256, pixel 0.85, shown at level 0.0317,
step 1, values float32  

> volume #3 level 0.03358

> volume #3 level 0.03739

> volume #3 level 0.0393

> volume #3 level 0.04121

> volume #3 level 0.04311

> volume #3 level 0.04502

> hide #1 models

> fitmap #2 inMap #3

Fit molecule 1.pdb (#2) to map 2.mrc (#3) using 7082 atoms  
average map value = 0.1306, steps = 44  
shifted from previous position = 0.0164  
rotated from previous position = 0.00859 degrees  
atoms outside contour = 1337, contour level = 0.045019  
  
Position of 1.pdb (#2) relative to 2.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99999999 -0.00004761 0.00010951 -0.00341177  
0.00004760 0.99999999 0.00009057 0.00294440  
-0.00010951 -0.00009057 0.99999999 0.02230555  
Axis -0.60432270 0.73068845 0.31762945  
Axis point 170.91530182 0.00000000 -31.18268291  
Rotation angle (degrees) 0.00858703  
Shift along axis 0.01129815  
  

> show #1 models

> surface dust #3 size 8.5

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.  

> zone

> volume

> zone #1 [ residueDistance dr ] [ labelDistance dl ] [ surfaceDistance ds ] [
> label true | false ] [ ribbons true | false ]

Expected a keyword  

> zone #1 [ residueDistance 3.5 ] [ labelDistance dl ] [ surfaceDistance 3.5 ]
> [ label true ribbons true

Expected a keyword  

> zone #1 [ residueDistance 3.5 ] [ labelDistance dl ] [ surfaceDistance 3.5 ]
> label true ribbons true

Expected a keyword  

> volume zone #3 nearAtoms #2 range 3.5 newMap true

Opened 2.mrc zone as #4, grid size 256,256,256, pixel 0.85, shown at step 1,
values float32  

> hide #!2 models

> volume zone #3 nearAtoms #1 range 3.5 newMap true

Opened 2.mrc zone as #5, grid size 256,256,256, pixel 0.85, shown at step 1,
values float32  

> hide #!4 models

> volume zone #3 nearAtoms #1 range 4 newMap true

Opened 2.mrc zone as #6, grid size 256,256,256, pixel 0.85, shown at step 1,
values float32  

> hide #!5 models

> show #!5 models

> select #5

2 models selected  

> close #5

> select #6

2 models selected  

> hide #!6 models

> close #6

> close #4

> volume zone #3 nearAtoms #1 range 4 newMap true

Opened 2.mrc zone as #4, grid size 256,256,256, pixel 0.85, shown at step 1,
values float32  

> volume #4 level 0.04704

> volume #4 level 0.04805

> volume #4 level 0.01572

> surface dust #4 size 8.5

> volume #4 level 0.03795

> volume #4 style mesh

> volume #4 level 0.03896

> volume #4 level 0.03997

> volume #4 level 0.04098

> volume #4 level 0.043

> volume #4 level 0.04401

> volume #4 level 0.04502

> volume #4 level 0.04603

> volume #4 level 0.04704

> volume #4 level 0.04805

> volume #4 level 0.04906

> volume #4 level 0.05007

> volume #4 level 0.05108

> volume #4 level 0.05209

> volume #4 level 0.0531

> volume #4 level 0.05411

> volume #4 level 0.05512

> volume #4 level 0.05613

> volume #4 level 0.05714

> volume #4 level 0.05815

> volume #4 level 0.05916

> volume #4 level 0.05815

> volume #4 level 0.05512

> volume #4 level 0.0531

> volume #4 level 0.05209

> volume #4 level 0.05108

> volume #4 level 0.05007

> volume #4 level 0.04906

> volume #4 level 0.04805

> volume #4 level 0.04704

> volume #4 level 0.04906

> volume #4 level 0.05512

> volume #4 level 0.05815

> volume #4 level 0.05916

> surface dust #4 size 8.5

> volume #4 level 0.07432

> volume #4 level 0.07533

> volume #4 level 0.07937

> volume #4 level 0.08341

> set bgColor white

> select ::name="CP5"

54 atoms, 56 bonds, 2 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel medium purple

> color (#1 & sel) byhetero

> select clear

> volume #4 level 0.0824

> volume #4 level 0.08139

> volume #4 level 0.08038

> volume #4 level 0.07937

> volume #4 level 0.07836

> volume #4 level 0.07735

> volume #4 level 0.07634

> volume #4 level 0.07533

> volume #4 level 0.07432

> volume #4 level 0.07331

> volume #4 level 0.0723

> volume #4 level 0.07129

> volume #4 level 0.07028

> volume #4 level 0.06927

> volume #4 level 0.06826

> volume #4 level 0.06725

> volume #4 level 0.06624

> volume #4 level 0.06523

> volume #4 level 0.06321

> volume #4 level 0.06119

> volume #4 level 0.06017

> volume #4 level 0.05916

> volume #4 level 0.05815

> volume #4 level 0.05714

> volume #4 level 0.05512

> volume #4 level 0.05411

> volume #4 level 0.0531

> volume #4 level 0.05209

> volume #4 level 0.05108

> volume #4 level 0.05007

> volume #4 level 0.04906

> volume #4 level 0.04805

> volume #4 level 0.04704

> volume #4 level 0.04603

> volume #4 level 0.04502

> volume #4 level 0.04401

> volume #4 level 0.043

> volume #4 level 0.04199

> volume #4 level 0.04098

> volume #4 level 0.03997

> volume #4 level 0.03896

> volume #4 level 0.03795

> volume #4 level 0.03593

> volume #4 level 0.03491

> volume #4 level 0.0339

> volume #4 level 0.03289

> volume #4 level 0.03188

> volume #4 level 0.03087

> surface dust #4 size 8.5

> surface dust #4 size 8.5

> volume zone #3 nearAtoms #1 range 3 newMap true

Opened 2.mrc zone as #5, grid size 256,256,256, pixel 0.85, shown at step 1,
values float32  

> hide #!4 models

> hide #4.1 models

> surface dust #5 size 8.5

> close #4

> volume #5 style mesh

> surface dust #5 size 8.5

> volume zone #3 nearAtoms #1 range 3 newMap true

Opened 2.mrc zone as #4, grid size 256,256,256, pixel 0.85, shown at step 1,
values float32  

> hide #!5 models

> close #5

> volume #4 style mesh

> volume #4 level 0.03852

> volume #4 level 0.02552

> volume #4 level 0.01809

> volume #4 level 0.006025

> surface dust #4 size 8.5

> volume #4 level 0.03759

> surface dust #4 size 8.5

> volume #4 level 0.03852

> volume #4 level 0.03945

> volume #4 level 0.04038

> volume #4 level 0.04131

> volume #4 level 0.04223

> volume #4 level 0.04316

> volume #4 level 0.04409

> volume #4 level 0.04502

> volume #4 level 0.04595

> volume #4 level 0.04688

> volume #4 level 0.0478

> volume #4 level 0.04873

> volume #4 level 0.04966

> volume #4 level 0.05059

> volume #4 level 0.05152

> volume #4 level 0.05245

> volume #4 level 0.05337

> volume #4 level 0.0543

> volume #4 level 0.05523

> volume #4 level 0.05616

> volume #4 level 0.05709

> volume #4 level 0.05802

> volume #4 level 0.05895

> volume #4 level 0.05987

> volume #4 level 0.0608

> volume #4 level 0.06173

> volume #4 level 0.06266

> volume #4 level 0.06359

> volume #4 level 0.06452

> volume #4 level 0.0673

> volume #4 level 0.06823

> volume #4 level 0.07009

> volume #4 level 0.07287

> volume #4 level 0.07194

> volume #4 level 0.07009

> volume #4 level 0.06916

> volume #4 level 0.06823

> volume #4 level 0.0673

> volume #4 level 0.06637

> volume #4 level 0.06544

> volume #4 level 0.06452

> volume #4 level 0.06359

> volume #4 level 0.06266

> volume #4 level 0.06173

> volume #4 level 0.06544

> volume zone #3 nearAtoms #1 range 3.5 newMap true

Opened 2.mrc zone as #5, grid size 256,256,256, pixel 0.85, shown at step 1,
values float32  

> close #3

> close #4

> volume #5 style mesh

> volume #5 level 0.03385

> volume #5 level 0.0003617

> surface dust #5 size 8.5

> volume #5 level 0.04502

> volume #5 level 0.05897

> volume #5 level 0.06363

> volume zone #3 nearAtoms #1 range 4 newMap true

> volume zone #3 nearAtoms #1 range 4 newMap true

> open /Users/wangxuehui/Desktop/CB2结构/2.mrc

Opened 2.mrc as #3, grid size 256,256,256, pixel 0.85, shown at level 0.0317,
step 1, values float32  

> volume zone #5 nearAtoms #1 range 4 newMap true

Opened 2.mrc zone zone as #4, grid size 256,256,256, pixel 0.85, shown at step
1, values float32  

> hide #!4 models

> volume zone #3 nearAtoms #1 range 4 newMap true

Opened 2.mrc zone as #6, grid size 256,256,256, pixel 0.85, shown at step 1,
values float32  

> close #5

> close #4

> close #6

> show #!3 models

> volume zone #3 nearAtoms #1 range 4 newMap true

Opened 2.mrc zone as #4, grid size 256,256,256, pixel 0.85, shown at step 1,
values float32  

> volume #4 style mesh

> volume #4 level 0.064

> surface dust #4 size 8.5

> volume zone #3 nearAtoms #1 range 4 newMap true

Opened 2.mrc zone as #5, grid size 256,256,256, pixel 0.85, shown at step 1,
values float32  

> close #4

> volume #5 style mesh

> volume #5 level -0.0006614

> volume #5 level 0.004391

> surface dust #5 size 8.5

> volume #5 level 0.005401

> volume #5 level 0.006411

> volume #5 level 0.007422

> volume #5 level 0.009442

> volume #5 level 0.01045

> volume #5 level 0.01146

> volume #5 level 0.01247

> volume #5 level 0.01348

> volume #5 level 0.01449

> volume #5 level 0.0155

> volume #5 level 0.01652

> volume #5 level 0.01753

> volume #5 level 0.01854

> volume #5 level 0.01955

> volume #5 level 0.02056

> volume #5 level 0.02157

> volume #5 level 0.02258

> volume #5 level 0.02359

> volume #5 level 0.02561

> volume #5 level 0.02662

> volume #5 level 0.02763

> volume #5 level 0.02864

> volume #5 level 0.02965

> volume #5 level 0.03066

> volume #5 level 0.03167

> volume #5 level 0.03268

> volume #5 level 0.0347

> volume #5 level 0.03571

> volume #5 level 0.03672

> volume #5 level 0.03672

> volume #5 level 0.03773

> volume #5 level 0.03874

> volume #5 level 0.03975

> volume #5 level 0.04076

> volume #5 level 0.04177

> volume #5 level 0.04279

> volume #5 level 0.04885

> volume #5 level 0.04986

> volume #5 level 0.05087

> volume #5 level 0.05188

> volume #5 level 0.05289

> volume #5 level 0.0539

> volume #5 level 0.05491

> volume #5 level 0.05491

> volume #5 level 0.05592

> volume #5 level 0.05693

> volume #5 level 0.05794

> volume #5 level 0.05895

> volume #5 level 0.05996

> volume #5 level 0.06097

> volume #5 level 0.06198

> volume #5 level 0.06299

> volume #5 level 0.064

> volume #5 level 0.06501

> volume #5 level 0.06602

> volume #5 level 0.06703

> volume #5 level 0.06602

> volume #5 level 0.07411

> volume #5 level 0.08623

> volume #5 level 0.08219

> volume zone #3 nearAtoms #1 range 3.5 newMap true

Opened 2.mrc zone as #4, grid size 256,256,256, pixel 0.85, shown at step 1,
values float32  

> hide #!4 models

> show #!4 models

> volume #4 style mesh

> close #5

> volume #4 level 0.07075

> select clear

> select #4

2 models selected  

> select clear

> volume #4 level 0.04004

> surface dust #4 size 8.5

> volume #4 level 0.06702

> volume #4 level 0.06889

> volume #4 level 0.06982

> volume #4 level 0.07075

> volume #4 level 0.06795

> volume #4 level 0.02237

> volume #4 style surface

> volume #4 transparency 0.5

> volume #4 transparency 0.4

> volume #4 transparency 0.1

> volume #4 transparency 0.7

> volume #4 level 0.0233

> volume #4 level 0.0233

> volume #4 level 0.02423

> volume #4 level 0.02516

> volume #4 level 0.02609

> volume #4 level 0.02609

> volume #4 level 0.02702

> volume #4 level 0.02795

> volume #4 level 0.02795

> volume #4 level 0.02888

> volume #4 level 0.02981

> volume #4 level 0.03074

> volume #4 level 0.03167

> volume #4 level 0.0326

> volume #4 level 0.03353

> volume #4 level 0.03353

> volume #4 level 0.03446

> volume #4 level 0.03539

> volume #4 level 0.03632

> volume #4 level 0.03818

> volume #4 level 0.03911

> volume #4 level 0.03911

> volume #4 level 0.04004

> volume #4 level 0.04097

> volume #4 level 0.0419

> volume #4 level 0.04284

> volume #4 level 0.04377

> volume #4 level 0.0447

> volume #4 level 0.04563

> volume #4 level 0.04563

> volume #4 level 0.04656

> volume #4 level 0.04749

> volume #4 level 0.04749

> volume #4 level 0.04842

> volume #4 level 0.04935

> volume #4 level 0.05028

> volume #4 level 0.05121

> volume #4 level 0.05214

> volume #4 level 0.05307

> volume #4 level 0.054

> volume #4 level 0.05493

> volume #4 level 0.05586

> volume #4 level 0.05679

> volume #4 level 0.05772

> volume #4 level 0.05865

> volume #4 level 0.05958

> volume #4 level 0.06051

> volume #4 level 0.06144

> volume #4 level 0.06237

> volume #4 level 0.0633

> volume #4 level 0.06423

> volume #4 level 0.06423

> volume #4 level 0.06516

> volume #4 level 0.06423

> volume #4 level 0.0633

> volume #4 level 0.06237

> volume #4 level 0.06144

> volume #4 level 0.06051

> volume #4 level 0.05586

> volume #4 level 0.05493

> volume #4 level 0.054

> volume #4 level 0.05307

> volume #4 level 0.05214

> volume #4 level 0.05121

> volume #4 level 0.05028

> volume #4 level 0.05307

> volume #4 level 0.05493

> volume #4 level 0.05586

> volume #4 level 0.05679

> volume #4 level 0.05772

> volume #4 level 0.05679

> volume #4 level 0.05586

> volume #4 level 0.05493

> volume #4 level 0.05307

> volume #4 level 0.04842

> volume #4 level 0.04749

> volume #4 level 0.04749

> volume #4 level 0.04656

> volume #4 level 0.04656

> volume #4 level 0.04563

> volume #4 level 0.04563

> volume #4 level 0.0447

> volume #4 level 0.04377

> volume #4 level 0.04284

> volume #4 level 0.0419

> volume #4 level 0.04097

> volume #4 level 0.04097

> volume #4 level 0.04004

> volume #4 level 0.03911

> volume #4 level 0.03911

> volume #4 level 0.03818

> volume #4 level 0.03725

> volume #4 level 0.03632

> volume #4 level 0.03539

> volume #4 level 0.03446

> volume #4 level 0.03353

> volume #4 level 0.0326

> volume #4 level 0.03167

> volume #4 level 0.03074

> volume #4 level 0.02981

> volume #4 level 0.02888

> volume #4 level 0.02795

> volume #4 level 0.02702

> volume #4 level 0.02702

> volume #4 level 0.02609

> volume #4 level 0.02516

> volume #4 level 0.02423

> volume #4 level 0.0233

> volume #4 level 0.02237

> volume #4 level 0.02144

> volume #4 level 0.02237

> volume #4 level 0.0233

> volume #4 level 0.02516

> volume #4 level 0.02609

> volume #4 level 0.02702

> volume #4 level 0.02795

> volume #4 level 0.02888

> volume #4 level 0.02795

> volume #4 level 0.02702

> volume #4 level 0.02609

> volume #4 level 0.0233

> volume #4 level 0.07075

> volume #4 level 0.08098

> volume #4 level 0.06889

> volume #4 level 0.054

> volume #4 level 0.06795

> volume #4 level 0.08191

> volume #4 level 0.08098

> volume #4 level 0.08005

> volume #4 level 0.07912

> volume #4 level 0.07819

> volume #4 level 0.07726

> volume #4 level 0.07633

> volume #4 level 0.0754

> volume #4 level 0.07447

> volume #4 level 0.07354

> volume #4 level 0.07261

> volume #4 level 0.07168

> volume #4 level 0.07075

> volume #4 level 0.06982

> volume #4 level 0.06982

> volume #4 level 0.06889

> volume #4 level 0.06795

> volume #4 level 0.06702

> volume #4 level 0.06609

> volume #4 level 0.06516

> volume #4 level 0.06423

> volume #4 level 0.0633

> volume #4 level 0.06237

> volume #4 level 0.06144

> volume #4 level 0.06051

> volume #4 level 0.05958

> volume #4 level 0.05865

> volume #4 level 0.05865

> volume #4 level 0.05772

> volume #4 level 0.05679

> volume #4 level 0.05586

> volume #4 level 0.05493

> volume #4 level 0.054

> volume #4 level 0.05307

> volume #4 level 0.05307

> volume #4 level 0.05214

> volume #4 level 0.05121

> volume #4 level 0.05028

> volume #4 level 0.04935

> volume #4 level 0.04842

> volume #4 level 0.04656

> volume #4 level 0.04563

> volume #4 level 0.04377

> volume #4 level 0.04284

> volume #4 level 0.04097

> volume #4 level 0.04004

> volume #4 level 0.03818

> volume #4 level 0.03632

> volume #4 level 0.03446

> volume #4 level 0.0326

> volume #4 level 0.03167

> volume #4 level 0.03074

> volume #4 level 0.02981

> volume #4 level 0.02888

> volume #4 level 0.02795

> volume #4 level 0.02702

> volume #4 level 0.02702

> volume #4 level 0.02516

> volume #4 level 0.02423

> volume #4 level 0.0233

> volume #4 level 0.02237

> volume #4 level 0.02144

> volume #4 level 0.01865

> volume #4 level 0.01772

> volume #4 level 0.01772

> volume #4 level 0.01679

> volume #4 level 0.01585

> volume #4 level 0.01492

> volume #4 level 0.01399

> volume #4 level 0.01306

> volume #4 level 0.01213

> volume #4 level 0.01306

> volume #4 level 0.02051

> volume #4 level 0.02516

> volume #4 level 0.02609

> volume #4 level 0.02702

> volume #4 level 0.02795

> volume #4 level 0.02888

> volume #4 level 0.02981

> volume #4 level 0.02888

> volume #4 level 0.02795

> volume #4 level 0.02702

> volume #4 level 0.02609

> volume #4 level 0.02516

> volume #4 level 0.02423

> volume #4 style image

> volume #4 style mesh

> volume #4 style surface

> volume #4 change image level 2.203e-05,0 level 0.02912,0.8 level 0.291,1

> volume #4 level 0.02516

> volume #4 level 0.0633

> volume #4 level 0.0233

> volume zone #3 nearAtoms #1 range 3.5 newMap true

Opened 2.mrc zone as #5, grid size 256,256,256, pixel 0.85, shown at step 1,
values float32  

> volume zone #3 nearAtoms #1 range 4 newMap true

Opened 2.mrc zone as #6, grid size 256,256,256, pixel 0.85, shown at step 1,
values float32  

> volume #6 level 0.03369

> volume #6 level 0.03571

> volume #6 level 0.03773

> volume #6 level 0.03773

> volume #6 level 0.03874

> volume #6 level 0.03975

> volume #6 level 0.04076

> volume #6 level 0.04076

> volume #6 level 0.04177

> volume #6 level 0.04279

> volume #6 level 0.0438

> volume #6 level 0.04481

> volume #6 level 0.04683

> volume #6 level 0.04885

> volume #6 level 0.05087

> volume #6 level 0.05188

> volume #6 level 0.05491

> volume #6 level 0.05592

> volume #6 level 0.05794

> volume #6 level 0.05895

> volume #6 level 0.05996

> volume #6 level 0.06097

> volume #6 level 0.06198

> volume #6 level 0.06299

> volume #6 level 0.06501

> volume #6 level 0.06906

> volume #6 level 0.07007

> volume #6 level 0.07209

> volume #6 level 0.0731

> volume #6 level 0.07613

> volume #6 level 0.07714

> volume #6 level 0.07916

> volume #6 level 0.08118

> volume #6 level 0.08219

> volume #6 level 0.0832

> volume #6 level 0.08421

> volume #6 level 0.08522

> volume #6 level 0.08623

> volume #6 level 0.08724

> volume #6 level 0.08825

> volume #6 level 0.08724

> volume #6 level 0.08421

> volume #6 level 0.0832

> volume #6 level 0.07815

> volume #6 level 0.07714

> volume #6 style mesh

> volume #6 level 0.1105

> surface dust #6 size 8.5

> volume #6 level 0.07714

> volume #6 level 0.08421

> close #5

> volume #6 step 4

> volume #6 step 2

> volume #6 step 8

> volume #6 step 1

> volume #4 step 2

> volume #4 step 1

> volume #4

> volume #6 style surface

> volume #4 level 0.05865

> volume #4 level 0.06051

> volume #4 level 0.06237

> volume #4 level 0.0633

> volume #4 level 0.06423

> volume #4 level 0.0633

> volume #4 level 0.06237

> volume #4 level 0.06144

> volume #4 level 0.06051

> volume #4 level 0.05958

> volume #4 level 0.05865

> volume #4 level 0.05772

> volume #4 level 0.05679

> volume #4 level 0.05772

> volume #4 level 0.05865

> volume #4 level 0.05958

> volume #4 level 0.06051

> volume #4 level 0.06144

> volume #4 level 0.06237

> volume #4 level 0.0633

> volume #4 style mesh

> volume #4 level 0.07075

> volume #4 level 0.0847

> volume #4 level 0.02795

> volume #4 style surface

> volume #4 level 0.02888

> volume #4 level 0.02981

> volume #4 level 0.03074

> volume #4 level 0.03167

> volume #4 level 0.0326

> volume #4 level 0.03353

> volume #4 level 0.03446

> volume #4 level 0.03446

> volume #4 level 0.03539

> volume #4 level 0.03632

> volume #4 level 0.03632

> volume #4 level 0.03725

> volume #4 level 0.03818

> volume #4 level 0.03911

> volume #4 level 0.04004

> volume #4 level 0.04097

> volume #4 level 0.0419

> volume #4 level 0.04284

> volume #4 level 0.04377

> volume #4 level 0.0447

> volume #4 level 0.04563

> volume #4 level 0.04656

> volume #4 level 0.04656

> volume #4 level 0.04749

> volume #4 level 0.04842

> volume #4 level 0.04935

> volume #4 level 0.05028

> volume #4 level 0.05121

> volume #4 level 0.05028

> volume #4 level 0.05121

> volume #4 level 0.05214

> volume #4 level 0.05307

> volume #4 level 0.05307

> volume #4 level 0.054

> volume #4 level 0.05493

> volume #4 level 0.05493

> volume #4 level 0.05586

> volume #4 level 0.05679

> volume #4 level 0.05772

> volume #4 level 0.05865

> volume #4 level 0.05958

> volume #4 level 0.06051

> volume #4 level 0.06144

> volume #4 level 0.06237

> volume #4 level 0.0633

> volume #4 level 0.06423

> volume #4 level 0.06516

> volume #4 level 0.06609

> volume #4 level 0.06702

> volume #4 level 0.06795

> volume #4 level 0.06889

> volume #4 level 0.06982

> volume #4 level 0.07075

> volume #4 level 0.07168

> volume #4 level 0.07261

> volume #4 level 0.07354

> volume #4 level 0.07447

> volume #4 level 0.0754

> volume #4 level 0.07633

> volume #4 level 0.07726

> volume #4 level 0.07819

> volume #4 level 0.07912

> volume #4 level 0.07912

> volume #4 level 0.08005

> volume #4 level 0.08098

> volume #4 level 0.08191

> volume #4 level 0.08284

> volume #4 level 0.08377

> volume #4 level 0.08284

> volume #4 level 0.08191

> volume #4 level 0.08098

> volume #4 level 0.08005

> volume #4 level 0.07912

> volume #4 level 0.07819

> volume #4 level 0.07726

> volume #4 level 0.07633

> volume #4 level 0.0754

> volume #4 level 0.07447

> volume #4 level 0.07354

> volume #4 level 0.07261

> volume #4 level 0.07168

> volume #4 level 0.07075

> volume #4 level 0.06982

> volume #4 level 0.06889

> volume #4 level 0.06795

> volume #4 level 0.06702

> volume #4 level 0.06609

> volume #4 level 0.06516

> volume #4 level 0.06423

> volume #4 level 0.0633

> volume #4 level 0.06237

> volume #4 level 0.0633

> volume #4 level 0.06516

> volume #4 level 0.06609

> volume #4 level 0.06516

> volume #4 level 0.06423

> volume #4 level 0.0633

> volume #4 level 0.06423

> volume #4 level 0.08005

> volume zone #3 nearAtoms #1 range 3 newMap true

Opened 2.mrc zone as #5, grid size 256,256,256, pixel 0.85, shown at step 1,
values float32  

> volume #5 level 0.03167

> volume #5 level 0.0326

> volume #5 level 0.03353

> volume #5 level 0.03446

> volume #5 level 0.03538

> volume #5 level 0.03631

> volume #5 level 0.03724

> volume #5 level 0.03817

> volume #5 level 0.0391

> volume #5 level 0.04003

> volume #5 level 0.04003

> volume #5 level 0.04096

> volume #5 level 0.04188

> volume #5 level 0.04188

> volume #5 level 0.04281

> volume #5 level 0.04374

> volume #5 level 0.0456

> volume #5 level 0.04653

> volume #5 level 0.04745

> volume #5 level 0.04838

> volume #5 level 0.04838

> volume #5 level 0.04931

> volume #5 level 0.05024

> volume #5 level 0.05117

> volume #5 level 0.0521

> volume #5 level 0.05302

> volume #5 level 0.05395

> volume #5 level 0.05488

> volume #5 level 0.05581

> volume #5 level 0.05674

> volume #5 level 0.05767

> volume #5 level 0.0586

> volume #5 level 0.05952

> volume #5 level 0.06138

> volume #5 level 0.06417

> volume #5 level 0.06509

> volume #5 level 0.06602

> volume #5 level 0.06695

> volume #5 level 0.06788

> volume #5 level 0.06974

> volume #5 level 0.07067

> volume #5 level 0.07159

> volume #5 level 0.07252

> volume #5 level 0.07345

> volume #5 level 0.07438

> volume #5 level 0.07531

> volume #5 level 0.07624

> volume #5 level 0.07624

> volume #5 level 0.07716

> volume #5 level 0.07809

> volume #5 level 0.07902

> volume #5 level 0.07995

> volume #5 level 0.08088

> volume #5 level 0.08181

> volume #5 level 0.08366

> volume #5 level 0.08459

> volume #5 level 0.08552

> volume #5 level 0.08645

> volume #5 level 0.08738

> volume #5 level 0.08831

> volume #5 level 0.08923

> volume #5 level 0.09016

> volume #5 level 0.09109

> volume #5 level 0.09202

> volume #5 level 0.09295

> volume #5 level 0.09388

> volume #5 level 0.0948

> volume #5 level 0.09573

> volume #5 level 0.09666

> volume #5 level 0.09759

> volume #5 level 0.09852

> volume #5 level 0.09945

> volume #5 level 0.1004

> volume #5 level 0.1013

> volume #5 level 0.1022

> volume #5 level 0.1032

> volume #5 level 0.1041

> volume #5 level 0.105

> volume #5 level 0.1059

> volume #5 level 0.1069

> volume #5 level 0.1078

> volume #5 level 0.1115

> volume #5 level 0.1124

> volume #5 level 0.1134

> volume #5 level 0.1143

> volume #5 level 0.1152

> volume #5 level 0.1162

> volume #5 level 0.1171

> volume #5 level 0.118

> volume #5 level 0.1189

> volume #5 level 0.118

> volume #5 level 0.1162

> volume #5 level 0.1143

> volume #5 level 0.105

> volume #5 level 0.1041

> volume #5 level 0.1004

> volume #5 level 0.09666

> volume #5 level 0.09573

> volume #5 level 0.0948

> volume #5 level 0.09388

> volume #5 level 0.09388

> volume #5 level 0.09295

> volume #5 level 0.09388

> volume #5 level 0.09759

> volume #5 level 0.09852

> volume #5 level 0.1013

> volume #5 level 0.1087

> volume #5 level 0.1134

> volume #5 level 0.1152

> volume #5 level 0.1171

> volume #5 level 0.1189

> volume #5 level 0.1199

> volume #5 level 0.1208

> volume #5 level 0.1199

> volume #5 level 0.1189

> volume #5 level 0.1171

> volume #5 level 0.1162

> volume #5 level 0.1152

> volume #5 level 0.1134

> volume #5 level 0.1124

> volume #5 level 0.1106

> volume #5 level 0.1097

> volume #5 level 0.1059

> volume #5 level 0.105

> volume #5 level 0.1041

> volume #5 level 0.1032

> volume #5 level 0.1022

> volume #5 level 0.1013

> volume #5 level 0.1004

> volume #5 level 0.1004

> volume #5 level 0.09945

> volume #5 level 0.09759

> volume #5 level 0.09573

> volume #5

> volume #5 style mesh

> volume #5 level 0.105

> volume #5 level 0.1041

> volume #5 level 0.1032

> volume #5 level 0.1022

> volume #5 level 0.1013

> volume #5 level 0.1004

> volume #5 level 0.09945

> volume #5 level 0.09852

> volume #5 level 0.09759

> volume #5 level 0.09666

> volume #5 level 0.09573

> volume #5 level 0.0948

> volume #5 level 0.09388

> volume #5 level 0.09388

> volume #5 level 0.09388

> volume #5 level 0.09295

> volume #5 level 0.09202

> volume #5 level 0.09202

> volume #5 level 0.09109

> volume #5 level 0.09016

> volume #5 level 0.09016

> volume #5 level 0.08923

> volume #5 level 0.09016

> volume #5 level 0.09202

> volume #5 level 0.09295

> volume #5 level 0.09388

> volume #5 level 0.09295

> volume #5 level 0.09202

> volume #5 level 0.09109

> volume #5 level 0.1041

> volume #5 style surface

> close #6

> volume #5 transparency 0.8

> volume #5 level 0.1032

> volume #5 level 0.1022

> volume #5 level 0.09388

> surface dust #5 size 8.5

> surface dust #5 size 8.5

> surface dust #5 size 8.5

> surface dust #5 size 3

> volume #5 style mesh

> volume #5 color #b2ffb233

> close #4

> volume #5 level 0.09109

> save "/Users/wangxuehui/Desktop/figure/figure 1/fig1c-cp55940-map.cxs"

> save "/Users/wangxuehui/Desktop/figure/figure 1/fig1c-cp55940-map.png" width
> 864 height 723 supersample 3 transparentBackground true

> volume #5 surfaceSmoothing true

> volume #5 surfaceSmoothing false

> volume #5 meshLighting false

> volume #5 meshLighting true

> volume #5 dimTransparency false

> volume #5 dimTransparency false

> volume #5 squareMesh false

> volume #5 squareMesh false dimTransparency false

> volume #5 squareMesh false dimTransparency false meshLighting true

> volume #5 dimTransparency false

> volume #5 meshLighting true

> volume #5 level 0.07995

> surface dust #5 size 8.5

> surface dust #5 size 8.5

> surface dust #5 size 7

> surface dust #5 size 6

> surface dust #5 size 5

> surface dust #5 size 3

> surface dust #5 size 3.5

> volume #5 level 0.07716

> volume #5 style surface

> volume #5 style mesh

> save "/Users/wangxuehui/Desktop/figure/figure 1/fig1c-cp55940-map.png" width
> 864 height 723 supersample 3 transparentBackground true

> volume #5 level 0.07809

> volume #5 level 0.07902

> volume #5 level 0.07995

> volume #5 level 0.08088

> volume #5 level 0.08088

> volume #5 level 0.08181

> volume #5 level 0.08273

> volume #5 level 0.08366

> volume #5 level 0.08459

> volume #5 level 0.08552

> volume #5 level 0.08645

> volume #5 level 0.08738

> volume #5 level 0.08552

> surface dust #5 size 3

> surface dust #5 size 3

> volume #5 level 0.09109

> volune

Unknown command: volune  

> volume

> volume

> volume #5 meshLighting false

> volume #5 meshLighting true

> volume #5 squareMesh false

> volume #5 squareMesh true

> volume #5 squareMesh false

> volume #5 twoSidedLighting false

> volume #5 capFaces false

> volume #5 flipNormals false

> volume #5 subdivisionLevels 3

> volume #5 subdivideSurface true

> volume #5 subdivisionLevels 1

> save "/Users/wangxuehui/Desktop/figure/figure 1/fig1c-cp55940-map.png" width
> 864 height 723 supersample 3 transparentBackground true

> save "/Users/wangxuehui/Desktop/figure/figure 1/fig1c-cp55940-map.cxs"

——— End of log from Wed Oct 23 17:59:13 2024 ———

opened ChimeraX session  

> hide #!5 models

> hide #1 models

> show #!2 models

> show #!3 models

> volume #3 level 0.08271

> ui tool show Clashes

> clashes

179 clashes  

> hide #!3 models

> ui tool show H-Bonds

> hbonds reveal true

698 hydrogen bonds found  

> ui tool show Contacts

> ui tool show "Hide Dust"

> ui tool show "Show Volume Menu"

> ui tool show "Measure Volume and Area"

> select clear

> toolshed show

> close #6

> close #4

> hide #!2 atoms

> hide #!2 atoms

> select ::name="CP5"

54 atoms, 56 bonds, 2 residues, 2 models selected  

> show sel & #!2 atoms

> select ::name="ECL"

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

> show sel atoms

> color sel hot pink

> color sel byhetero

> select #2/R:401@C17

1 atom, 1 residue, 1 model selected  

> select #2/R:401@C19

1 atom, 1 residue, 1 model selected  

> select ::name="CP5"

54 atoms, 56 bonds, 2 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel medium purple

> color (#!2 & sel) byhetero

> show #!3 models

> volume #3 level 0.09057

> hide #!3 models

> show sel & #!2 surfaces

> show sel & #!2 surfaces

> hide sel & #!2 surfaces

> hide sel & #!2 surfaces

> select clear

> select #2/R

2367 atoms, 2431 bonds, 300 residues, 1 model selected  

> show sel surfaces

> select #2/A

1687 atoms, 1716 bonds, 2 pseudobonds, 215 residues, 2 models selected  

> hide sel cartoons

Drag select of 341 residues  
Drag select of 61 residues  
Drag select of 394 residues  

> hide sel cartoons

Drag select of 1 residues  

> hide sel cartoons

> clip

> clip model #!2 false

> hide #!2 models

> show #!2 models

> hide sel cartoons

> hide ~:ecl cp5 targ ar

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

> hide sel cartoons

> hide sel cartoons

> hide #!2 models

> show #!2 models

> select #2/R

2367 atoms, 2431 bonds, 300 residues, 1 model selected  

> hide sel cartoons

> hide sel cartoons

> select clear

> hide ~:ecl & cp5 targ ar

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

> hide ~:ecl target ar

> hide ~:cp5 target ar

> ui tool show "Color Actions"

> color :ecl & C hot pink

> color :cp5 & C mediumblue purpule

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

> color :cp5 & C medium purple

> ui mousemode right clip

> ui mousemode right "clip rotate"

> ui mousemode right clip

> ui mousemode right "clip rotate"

> clip model #!2 false

> select ::name="CP5"

54 atoms, 56 bonds, 2 residues, 2 models selected  

> hide sel & #!2 surfaces

> show sel & #!2 atoms

> select ::name="ECL"

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

> show sel atoms

> show sel atoms

> select clear

> lighting soft

> transparency #2.3 30

> transparency #2.3 70

> transparency #2.3 10

> transparency #2.3 0

> save "/Users/wangxuehui/Desktop/figure/figure 1/fig.cxs"

——— End of log from Wed Oct 23 21:56:23 2024 ———

opened ChimeraX session  

> save "/Users/wangxuehui/Desktop/figure/figure 1/fig1c 正面pocket.png" width
> 864 height 723 supersample 3 transparentBackground true

> save "/Users/wangxuehui/Desktop/figure/figure 1/fig 1c pocket 正面.cxs"

——— End of log from Thu Oct 24 09:06:28 2024 ———

opened ChimeraX session  

> graphics silhouettes false

> save "/Users/wangxuehui/Desktop/figure/figure 1/fig 1c pocket 正面.cxs"

——— End of log from Thu Oct 24 09:08:51 2024 ———

opened ChimeraX session  

> save "/Users/wangxuehui/Desktop/figure/figure 1/fig1c 正面pocket.png" width
> 804 height 670 supersample 3 transparentBackground true

> save "/Users/wangxuehui/Desktop/figure/figure 1/fig 1c pocket 正面.cxs"

——— End of log from Thu Oct 24 09:12:46 2024 ———

opened ChimeraX session  

> graphics silhouettes false

> hide #2.1 models

> hide #2.2 models

> hide #!2.3 models

> show #!2.3 models

> hide #!2.3 models

> show #!2.3 models

> hide #!2.3 models

> show #!2.3 models

> ui mousemode right clip

> ui mousemode right "clip rotate"

> save "/Users/wangxuehui/Desktop/figure/figure 1/fig 1c pocket 正面.cxs"

——— End of log from Mon Dec 16 17:35:49 2024 ———

opened ChimeraX session  

> ui mousemode right "clip rotate"

> show #!2 cartoons

> hide #!2 surfaces

> show #!2 surfaces

> hide #!2 cartoons

> close #2.6

> close #2.2

> close #2.5

> close #2.4

> ui mousemode right clip

> ui mousemode right "clip rotate"

> ui mousemode right clip

> show #!2 cartoons

> ui mousemode right "clip rotate"

> hide #!2 cartoons

> ui mousemode right clip

> ui mousemode right "clip rotate"

> ui mousemode right clip

> save "/Users/wangxuehui/Desktop/figure/figure 1/fig1c 正面pocket.png" width
> 808 height 670 supersample 3 transparentBackground true

> save "/Users/wangxuehui/Desktop/figure/figure 1/fig1c 正面pocket.cxs"

——— End of log from Thu Dec 26 15:59:39 2024 ———

opened ChimeraX session  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Users/wangxuehui/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 713, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Users/wangxuehui/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/surface/cap.py", line 231, in restore_snapshot  
c = ClipCap(data['clip_plane_name'], data['clip_cap_owner'])  
File
"/Users/wangxuehui/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/surface/cap.py", line 210, in __init__  
Surface.__init__(self, 'cap ' + plane_name, drawing.session)  
AttributeError: 'NoneType' object has no attribute 'session'  
  
Exception ignored in: <function Drawing.__del__ at 0x7fbe907db4c0>  
Traceback (most recent call last):  
File
"/Users/wangxuehui/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 1182, in __del__  
if not self.was_deleted:  
AttributeError: 'ClipCap' object has no attribute 'was_deleted'  
opened ChimeraX session  




OpenGL version: 4.1 Metal - 71.7.1
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 4 MB
      Memory: 8 GB

Software:

    System Software Overview:

      System Version: macOS 11.7.10 (20G1427)
      Kernel Version: Darwin 20.6.0
      Time since boot: 27 days 33 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Resolution: 2880 x 1800
          UI Looks like: 1440 x 900 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by pett, 8 weeks ago

Component: Unassigned → Sessions
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Session restore/reset: 'ClipCap' object has no attribute 'was_deleted'

comment:2 by Tom Goddard, 8 weeks ago

Resolution: → duplicate
Status: assigned → closed

Restoring session where a clipped volume was missing and was not replaced and the clip cap restore code gave an error because it was expecting the volume surface to exist. No longer happens in ChimeraX daily build, probably fixed long ago. Bug was reported in ChimeraX 1.2.

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