Opened 11 months ago

Closed 11 months ago

#16405 closed defect (limitation)

MemoryError saving map in session

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

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open E:\\\DATA\\\IMAGE\\\KCNQ2_Blocker\\\Fig1\\\1104\\\Fig1-1105.cxs

Opened
3_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc as
#3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 2_map_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc
as #4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 1 as
#6.2, grid size 240,240,240, pixel 0.93, shown at level 0.008, step 1, values
float32  
Opened 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 2 as
#6.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 3 as
#6.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 4 as
#6.5, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 1_map_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc as #7,
grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values
float32  
Opened
2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 0
as #5.1, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened
2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 1
as #5.2, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened
2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2
as #5.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened
2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3
as #5.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened 1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1 as
#11.2, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1,
values float32  
Opened 1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 2 as
#11.3, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1,
values float32  
Opened 1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 3 as
#11.4, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1,
values float32  
Log from Tue Nov 5 12:59:07 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open E:\\\DATA\\\IMAGE\\\KCNQ2_Blocker\\\Fig1\\\1104\\\Fig1-1104.cxs

Opened
3_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc as
#3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 2_map_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc
as #4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 1 as
#6.2, grid size 240,240,240, pixel 0.93, shown at level 0.008, step 1, values
float32  
Opened 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 2 as
#6.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 3 as
#6.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 4 as
#6.5, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 1_map_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc as #7,
grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values
float32  
Opened
2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 0
as #5.1, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened
2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 1
as #5.2, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened
2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2
as #5.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened
2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3
as #5.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened 1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1 as
#11.2, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1,
values float32  
Opened 1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 2 as
#11.3, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1,
values float32  
Opened 1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 3 as
#11.4, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1,
values float32  
Log from Mon Nov 4 16:06:22 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open E:\\\DATA\\\IMAGE\\\KCNQ2_Blocker\\\Fig1\\\1031\\\Fig1-1103.cxs

Opened
2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc as
#3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 1_map_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc
as #4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 1 as
#6.2, grid size 240,240,240, pixel 0.93, shown at level 0.008, step 1, values
float32  
Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 2 as
#6.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 3 as
#6.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 4 as
#6.5, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 3_map_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc as #7,
grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values
float32  
Opened
2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 0
as #5.1, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened
2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 1
as #5.2, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened
2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2
as #5.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened
2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3
as #5.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened 3_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1 as
#11.2, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1,
values float32  
Opened 3_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 2 as
#11.3, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1,
values float32  
Opened 3_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 3 as
#11.4, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1,
values float32  
Log from Sun Nov 3 17:25:07 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open E:\\\DATA\\\IMAGE\\\KCNQ2_Blocker\\\Fig1\\\Fig1-1031.cxs

Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
as #3, grid size 240,240,240, pixel 0.93, shown at step 1, values float32  
Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc as
#4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
1 as #5.2, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2 as #5.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
3 as #5.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 1 as
#6.2, grid size 240,240,240, pixel 0.93, shown at level 0.008, step 1, values
float32  
Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 2 as
#6.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 3 as
#6.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 4 as
#6.5, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 3_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc as #7,
grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values
float32  
Log from Fri Nov 1 00:35:11 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open E:\\\DATA\\\IMAGE\\\KCNQ2_Blocker\\\Fig1\\\Fig1.cxs

Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
as #3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc as
#4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
1 as #5.2, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2 as #5.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
3 as #5.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 1 as
#6.2, grid size 240,240,240, pixel 0.93, shown at level 0.008, step 1, values
float32  
Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 2 as
#6.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 3 as
#6.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 4 as
#6.5, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Log from Tue Sep 10 17:05:02 2024 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> E:/DataProcess_MODEL/data/KCNQ2_Blocker_structures_QingDao/0910_KCNQ2_CaM_XE991_closed_real_space_refined_006-1_real_space_refined_007.pdb
> E:/DataProcess_MODEL/data/KCNQ2_Blocker_structures_QingDao/240910_KCNQ2_CaM_PIP2_XE991_open_real_space_refined_012-1.pdb

Chain information for
0910_KCNQ2_CaM_XE991_closed_real_space_refined_006-1_real_space_refined_007.pdb
#1  
---  
Chain | Description  
B C D E | No description available  
  
Chain information for
240910_KCNQ2_CaM_PIP2_XE991_open_real_space_refined_012-1.pdb #2  
---  
Chain | Description  
A B C D | No description available  
  

> ui tool show "Color Actions"

> set bgColor white

> close #1

> open
> E:/DataProcess_MODEL/data/KCNQ2_Blocker_structures_QingDao/0910_KCNQ2_CaM_XE991_closed_real_space_refined_006-1_real_space_refined_007.pdb

Summary of feedback from opening
E:/DataProcess_MODEL/data/KCNQ2_Blocker_structures_QingDao/0910_KCNQ2_CaM_XE991_closed_real_space_refined_006-1_real_space_refined_007.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN E 71
LEU E 85 1 15  
Start residue of secondary structure not found: HELIX 2 2 TRP E 91 THR E 114 5
24  
Start residue of secondary structure not found: HELIX 3 3 GLU E 119 GLY E 149
1 31  
Start residue of secondary structure not found: HELIX 4 4 CYS E 152 TYR E 154
5 3  
Start residue of secondary structure not found: HELIX 5 5 GLY E 156 ALA E 164
1 9  
18 messages similar to the above omitted  
  
Chain information for
0910_KCNQ2_CaM_XE991_closed_real_space_refined_006-1_real_space_refined_007.pdb
#1  
---  
Chain | Description  
A B C D | No description available  
  

> dssp

> cartoon style width 1.15 thickness 0.3

> setattr b radius 0.27

Assigning radius attribute to 43446 items  

> hide #1.1 models

> hide #2.1 models

> hide #!2 models

> show #!2 models

> select #1 /A-D:1042-1148

3396 atoms, 3432 bonds, 428 residues, 1 model selected  

> select #1 /A-D:1006-1148

4504 atoms, 4552 bonds, 572 residues, 1 model selected  

> color sel #b48a76

> select #1 /A-D:1006-1148 #2 /A-D:1006-1148

13020 atoms, 13116 bonds, 1144 residues, 2 models selected  

> select up

13684 atoms, 13776 bonds, 1172 residues, 2 models selected  

> select up

19512 atoms, 19652 bonds, 1640 residues, 2 models selected  

> select down

13684 atoms, 13776 bonds, 1172 residues, 2 models selected  

> select down

13020 atoms, 13116 bonds, 1144 residues, 2 models selected  

> select #1 /A-D:1006-1148 #2 /A-D:1006-1148

13020 atoms, 13116 bonds, 1144 residues, 2 models selected  

> color sel #b48a76

> color sel #a86965

> select clear

> color sel #b48a76

> color sel #a86965

> color sel #b48a76

> color sel #b88884

> color sel #b48a76

[Repeated 1 time(s)]

> color sel #928178

> color sel #a99e93

> select clear

> select #1 /A-D:70-600

10732 atoms, 10996 bonds, 8 pseudobonds, 1316 residues, 2 models selected  

> color sel #00a3af

> select clear

> hide #!2 models

> select #1 /A-D:70-600

10732 atoms, 10996 bonds, 8 pseudobonds, 1316 residues, 2 models selected  

> color sel #83ccd2

> select clear

> lighting soft

> graphics silhouettes true

> graphics silhouettes false

> lighting flat

[Repeated 1 time(s)]

> lighting full

> lighting simple

> lighting soft

> lighting full

> lighting flat

[Repeated 1 time(s)]

> lighting full

> lighting shadows false

> lighting soft

> lighting simple

> graphics silhouettes false

> select #1 /A-D:70-600

10732 atoms, 10996 bonds, 8 pseudobonds, 1316 residues, 2 models selected  

> color sel #7997b4

> select clear

> hide #!1 models

> show #!2 models

> select #2 /A-D:70-600

18576 atoms, 18864 bonds, 8 pseudobonds, 1436 residues, 2 models selected  

> color sel #97b479

> select clear

> show #!1 models

> hide #!1 models

> select #1 /A-D:1006-1148 #2 /A-D:1006-1148

13020 atoms, 13116 bonds, 1144 residues, 2 models selected  

> color sel #b49679

> select clear

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> select clear

[Repeated 1 time(s)]

> select #2/X:1201@O08

1 atom, 1 residue, 1 model selected  

> select up

49 atoms, 53 bonds, 1 residue, 1 model selected  

> select up

27505 atoms, 27845 bonds, 2013 residues, 1 model selected  

> select down

49 atoms, 53 bonds, 1 residue, 1 model selected  

> color sel ##b4797a

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

> color sel #b4797a

> color sel orange red

> select clear

> show #!1 models

> hide #!2 models

> select up

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

> select up

49 atoms, 53 bonds, 1 residue, 1 model selected  

> color sel yellow

> color sel orange

> ui tool show "Color Actions"

> set bgColor gold

> set bgColor #ffd70000

> undo

> set bgColor white

> set bgColor #ffffff00

> color sel gold target acspfl

[Repeated 2 time(s)]

> select clear

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> open
> E:/DataProcess_MODEL/data/KCNQ2_Blocker_structures_QingDao/2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc

Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
as #3, grid size 240,240,240, pixel 0.93, shown at level 0.00801, step 1,
values float32  

> open
> E:/DataProcess_MODEL/data/KCNQ2_Blocker_structures_QingDao/1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc

Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc as
#4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!4 models

> volume #3 level 0.0078

> hide #!4 models

> surface dust #3 size 9.3

> show #!4 models

> hide #!3 models

> surface dust #4 size 9.3

> hide #!4 models

> volume #3 level 0.0075

> surface dust #3 size 9.3

> volume #3 level 0.0078

> ui tool show "Color Zone"

> color zone #3 near #1 distance 3.5

> surface dust #3 size 9.3

> surface dust #3 size 5

> surface dust #3 size 3

> surface dust #3 size 2.5

> surface dust #3 size 5

> surface dust #4 size 5

> volume splitbyzone #3

Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
0 as #5.1, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
1 as #5.2, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2 as #5.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
3 as #5.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  

> close #5.1

> surface dust #3 size 4.5

> surface dust #5.3 size 5

> surface dust #5.2 size 9.3

> surface dust #5.3 size 9.3

> surface dust #5.4 size 9.3

> surface dust size 5

Missing or invalid "surfaces" argument: invalid surfaces specifier  

> surface dust #5 size 5

> select clear

> show #!2 models

> hide #!1 models

> show #!4 models

> hide #!5 models

> hide #!2 models

> show #!2 models

> color zone #4 near #2 distance 3.5

> color #4 #bcbcbcff models

> hide #!4 models

> select ::name="PIO"

364 atoms, 364 bonds, 4 residues, 1 model selected  

> show sel atoms

> hide H

[Repeated 1 time(s)]

> color sel hot pink

> color sel #b47997

> color sel hot pink

> ui tool show "Color Actions"

> color sel cornflower blue target acspfl

> color sel dark turquoise target acspfl

> color sel medium aquamarine target acspfl

> color sel medium turquoise target acspfl

> color sel turquoise target acspfl

> color sel cyan target acspfl

> color sel dark orange target acspfl

> color sel orange target acspfl

[Repeated 2 time(s)]

> show #!1 models

> hide #!1 models

> color sel #a69425

> color sel #c3d825

> color sel #d0576b

> color sel #867ba9

> select clear

> select #2/X:1201@C11

1 atom, 1 residue, 1 model selected  

> select up

49 atoms, 53 bonds, 1 residue, 1 model selected  

> select up

27505 atoms, 27845 bonds, 2013 residues, 1 model selected  

> select down

49 atoms, 53 bonds, 1 residue, 1 model selected  

> color sel orange

> color sel orange red

> select clear

> show #!4 models

> color zone #4 near #2 distance 3.5

> volume splitbyzone #4

Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 0 as
#6.1, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 1 as
#6.2, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 2 as
#6.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 3 as
#6.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 4 as
#6.5, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  

> volume splitbyzone #4

Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 0 as
#7.1, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 1 as
#7.2, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 2 as
#7.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 3 as
#7.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  
Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 4 as
#7.5, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values
float32  

> surface dust #6 size 5

> surface dust #7 size 5

> close #7.1

> undo

> hide #!7 models

> show #!7 models

> hide #!6 models

> hide #!7 models

> show #!6 models

> hide #!6 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!7 models

> close #7

> hide #!6.2 models

> show #!6.2 models

> hide #!6.1 models

> close #6.1

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1.cxs

> hide #!6 models

> show #!6 models

> hide #!6 models

> hide #!2 atoms

> show #!1 models

> hide atoms

> select ::name="LIG"

98 atoms, 106 bonds, 2 residues, 2 models selected  

> show sel atoms

> select ::name="PIO"

364 atoms, 364 bonds, 4 residues, 1 model selected  

> show sel atoms

> select clear

> hide H

> select clear

> hide #!2 models

> hide #!1 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!1 models

> view

[Repeated 1 time(s)]

> show #!2 models

> hide #!1 models

> view

> show #!1 models

> hide #!2 models

> view

[Repeated 4 time(s)]

> show #!2 models

> view orient

> hide #!2 models

> turn x 90

[Repeated 2 time(s)]

> turn y 5

[Repeated 10 time(s)]

> view orient

> turn x 90

[Repeated 2 time(s)]

> turn y 5

[Repeated 12 time(s)]

> turn y -5

[Repeated 3 time(s)]

> turn y 5

> view name side1

> show #!2 models

> hide #!1 models

> turn y -5

[Repeated 1 time(s)]

> turn y 5

[Repeated 2 time(s)]

> turn y -5

> view name side1

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> view side1

[Repeated 1 time(s)]

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> ui tool show "Side View"

> view name side1

> view name side2

> viewside2

Unknown command: viewside2  

> view side1

> turn y 5

[Repeated 2 time(s)]

> turn y -5

[Repeated 1 time(s)]

> view name side1

> view name side2

[Repeated 1 time(s)]

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!2 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!5 models

> show #!6 models

> hide #!5 models

> lighting soft

> show #!5 models

> hide #!6 models

> show #!6 models

> lighting simple

> hide #!6 models

> hide #!5 models

> show #!6 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!6 models

> lighting soft

> color #5.2 yellow models

> lighting simple

> lighting soft

> lighting full

> lighting soft

> graphics silhouettes true

> graphics silhouettes false

> lighting simple

[Repeated 1 time(s)]

> lighting soft

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Q2_XE991_C_sideview_map.tif width 3000
> height 3000 transparentBackground true

> view

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Q2_XE991_C_sideview_map.tif width 3000
> height 3000 transparentBackground true

> hide #!5 models

> show #!5 models

> show #!6 models

> hide #!5 models

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> lighting full

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Q2_XE991_O_sideview_map.tif width 3000
> height 3000 transparentBackground true

[Repeated 1 time(s)]

> show #!5 models

> hide #!6 models

> lighting full

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Q2_XE991_C_sideview_map.tif width 3000
> height 3000 transparentBackground true

> hide #!5 models

> show #!1 models

> lighting simple

> view

> show #!2 models

> show #!5 models

> hide #!5 models

> view

> view name side1

> hide #!2 models

> select clear

[Repeated 1 time(s)]

> select up

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

> select up

49 atoms, 53 bonds, 1 residue, 1 model selected  

> color sel byhetero

> select clear

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Q2_XE991_C_sideview_pdb.tif width 3000
> height 3000 transparentBackground true

> hide #!1 models

> show #!2 models

> select ::name="LIG"

98 atoms, 106 bonds, 2 residues, 2 models selected  

> color sel & #!2 byhetero

> select ::name="PIO"

364 atoms, 364 bonds, 4 residues, 1 model selected  

> color sel byhetero

> select clear

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Q2_XE991_PIP2_O_sideview_pdb.tif width
> 3000 height 3000 transparentBackground true

> show #!1 models

> view side2

> hide #!2 models

> hide #!1 models

> show #!2 models

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Q2_XE991_PIP2_O_sideview_pdb.tif width
> 3000 height 3000 transparentBackground true

> hide #!2 models

> combine #1

> combine #2

> rename #7 gate-closed

> rename #8 gate-open

> cartoon style width 1.15 thickness 0.

Invalid "thickness" argument: Must be greater than 0  

> setattr b radius 0.27

Assigning radius attribute to 86892 items  

> setattr b radius 0.27

Assigning radius attribute to 86892 items  

> cartoon style width 1.15 thickness 0.3

> hide #7.1 models

> hide #8.1 models

> select clear

> select ::name="PIO"

728 atoms, 728 bonds, 8 residues, 2 models selected  

> hide sel & #!8 atoms

> select ::name="LIG"

196 atoms, 212 bonds, 4 residues, 4 models selected  

> hide sel & #!7-8 atoms

> select clear

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1.cxs includeMaps true

> select #7 /A:305-325

158 atoms, 161 bonds, 21 residues, 1 model selected  

> select #7 /A:308-325 /C:308-325 #8 /A:308-325 /C:308-325

810 atoms, 818 bonds, 72 residues, 2 models selected  

> select ~sel

84770 atoms, 86066 bonds, 56 pseudobonds, 7732 residues, 28 models selected  

> hide sel & #!7-8 cartoons

> select ~sel

810 atoms, 818 bonds, 72 residues, 2 models selected  

> turn y 5

[Repeated 5 time(s)]

> turn y -5

> hide #!8 models

> select clear

> show #!8 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> select #8/C:310

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

> select #8/A:310

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

> select clear

> hide #!8 models

> show #!8 models

> show #!7 models

> select #8/C:308

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

> hide sel cartoons

> select #7/C:308

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

> hide sel cartoons

> select clear

> select #7 /A:308 /C:308 #8 /A:308 /C:308

42 atoms, 42 bonds, 4 residues, 2 models selected  

> hide sel cartoons

> select clear

> combine #7 #8

Remapping chain ID 'A' in gate-open #8 to 'E'  
Remapping chain ID 'B' in gate-open #8 to 'F'  
Remapping chain ID 'C' in gate-open #8 to 'G'  
Remapping chain ID 'D' in gate-open #8 to 'H'  
Remapping chain ID 'X' in gate-open #8 to 'Y'  

> cartoon style width 1.15 thickness 0.3

> setattr b radius 0.27

Assigning radius attribute to 130338 items  

> select clear

> hide #!9 models

> hide #!7 models

> hide #!8 models

> show #!8 models

> show #!7 models

> hide #!8 models

> select #7/C:314

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

> show sel atoms

> style sel stick

Changed 6 atom styles  

> color sel byhetero

> select #7/A:314

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

> color sel byhetero

> show sel atoms

> style sel stick

Changed 6 atom styles  

> select #7/C:318

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

> show sel atoms

> color sel byhetero

> select #7/A:318

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

> color sel byhetero

> style sel stick

Changed 8 atom styles  

> show sel atoms

> select clear

> view name gate1

> show #!8 models

> hide #!7 models

> view

> show #!7 models

> view name gate1

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!9 models

Drag select of 3 residues  

> select up

346 atoms, 354 bonds, 44 residues, 1 model selected  

> hide #!9 models

> select clear

> show #!9 models

> hide #!9 models

> select #8/C:314

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

> show sel atoms

> style sel stick

Changed 11 atom styles  

> color sel byhetero

> select #8/A:314

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

> show sel atoms

> style sel stick

Changed 11 atom styles  

> select #8/C:318

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

> show sel atoms

> style sel stick

Changed 19 atom styles  

> select #8/A:318

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

> show sel atoms

> style sel stick

Changed 19 atom styles  

> color sel byhetero

[Repeated 1 time(s)]Drag select of 12 atoms, 10 bonds, 12 residues  

> color sel byhetero

> select clear

> hide H

> select clear

> view gate1

> select clear

> select #8/C:310

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

> show #!9 models

> hide #!8 models

Drag select of 3 residues  

> select up

346 atoms, 354 bonds, 44 residues, 1 model selected  

> hide sel cartoons

> select clear

> select #9/G:310

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

> select #9/G:310 /E:310

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

> select ~sel

128356 atoms, 130322 bonds, 84 pseudobonds, 11704 residues, 30 models selected  

> hide sel & #!9 cartoons

> show sel & #!9 atoms

> undo

> select clear

Drag select of 2 residues  

> select clear

Drag select of 2 residues  

> show sel atoms

> hide sel cartoons

> style sel stick

Changed 14 atom styles  

> color sel byhetero

> hide H

> show #!8 models

> select clear

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Q2_XE991_PIP2_O_side-gate.tif width
> 3000 height 3000 transparentBackground true

> show #!7 models

> hide #!8 models

> hide #!9 models

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Q2_XE991_C_side-gate.tif width 3000
> height 3000 transparentBackground true

> show #!8 models

> show #!9 models

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\merge_side-gate-1.tif width 3000
> height 3000 transparentBackground true

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1.cxs

> hide #!7 models

> show #!7 models

> hide #!9 models

> show #!9 models

> combine #7 #8 #9

Remapping chain ID 'A' in gate-open #8 to 'E'  
Remapping chain ID 'B' in gate-open #8 to 'F'  
Remapping chain ID 'C' in gate-open #8 to 'G'  
Remapping chain ID 'D' in gate-open #8 to 'H'  
Remapping chain ID 'X' in gate-open #8 to 'Y'  
Remapping chain ID 'A' in combination #9 to 'I'  
Remapping chain ID 'B' in combination #9 to 'J'  
Remapping chain ID 'C' in combination #9 to 'K'  
Remapping chain ID 'D' in combination #9 to 'L'  
Remapping chain ID 'E' in combination #9 to 'M'  
Remapping chain ID 'F' in combination #9 to 'N'  
Remapping chain ID 'G' in combination #9 to 'O'  
Remapping chain ID 'H' in combination #9 to 'P'  
Remapping chain ID 'X' in combination #9 to 'Z'  
Remapping chain ID 'Y' in combination #9 to 'a'  

> hide #!9 models

> hide #!8 models

> hide #!7 models

> setattr b radius 0.27

Assigning radius attribute to 217230 items  

> cartoon style width 1.15 thickness 0.3

> hide #!10 atoms

> select clear

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\merge_side-gate-1.tif width 3000
> height 3000 transparentBackground true

> hide #!10 models

> show #!9 models

> show #!8 models

> show #!7 models

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\merge_side-gate-2.tif width 3000
> height 3000 transparentBackground true

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1.cxs includeMaps true

> hide #!9 models

> hide #!8 models

> hide #!7 models

> show #!1 models

> hide #!1 models

> show #!6 models

> view side1

> lighting full

> surface dust #6.2 size 9.3

> surface dust #6.3 size 9.3

> surface dust #6.4 size 9.3

> surface dust #6.5 size 9.3

> surface dust #6.2 size 9.3

> surface dust #6.3 size 9.3

> surface dust #6.4 size 9.3

> surface dust #6.5 size 9.3

> surface dust #6.2 size 9.3

> surface dust #6.3 size 9.3

> surface dust #6.4 size 9.3

> surface dust #6.5 size 9.3

> surface dust #6 size 9

> surface dust #6.2 size 9

> surface dust #6.2 size 12

> surface dust #6.2 size 16

> surface dust #6.2 size 19

> surface dust #6.2 size 10

> surface dust #6.2 size 12

> volume #6.2 level 0.008

> volume #6.2 level 0.008996

> volume #6.2 level 0.008

> select clear

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Q2_XE991_PIP2_O_sideview_map.tif width
> 3000 height 3000 transparentBackground true

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1.cxs includeMaps true

> show #!2 models

> show #!1 models

> hide #!6 models

> hide #!2 models

> show #!7 models

> hide #!7 models

> rename #9 gate-open-1

> rename #10 combination-gate

> combine #1

> combine #2

> hide #11.1 models

> hide #12.1 models

> rename #11 vsd-closed

> rename #12 vsd-open

> lighting simple

> hide #!11 models

> hide #!12 models

> show #!5 models

> hide #!1 models

> lighting flat

[Repeated 1 time(s)]

> lighting full

> graphics silhouettes false

> lighting soft

> lighting simple

> graphics silhouettes true

> graphics silhouettes false

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting simple

[Repeated 1 time(s)]

> lighting soft

> lighting full

> lighting soft

> show #!6 models

> hide #!5 models

> view side1

> show #!5 models

> hide #!6 models

> ui mousemode right clip

> select #5.3

3 models selected  

> select clear

> select #5.3

3 models selected  

> select clear

> select #5.3

3 models selected  

> select clear

> hide #!5 models

> show #!5 models

> view side1

> hide #!5.2 models

> show #!5.2 models

> hide #!5 models

> show #!11 models

> show #!12 models

> cartoon style width 1.15 thickness 0.3

> lighting simple

> select clear

> hide #!11 models

> show #!11 models

> show #!11-12 surfaces

> hide #!12 models

> undo

[Repeated 1 time(s)]

> hide #!11-12 surfaces

> select clear

> hide #!12 models

> select clear

> show #!11 surfaces

> hide #!11 surfaces

> hide #!11 models

> show #!11 models

> show #!11 surfaces

[Repeated 1 time(s)]

> hide #!11 surfaces

> show #!11 atoms

> hide #!11 atoms

> select ::name="LIG"

588 atoms, 636 bonds, 12 residues, 8 models selected  

> show sel & #!11 atoms

> select clear

> hide H

> select clear

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> select #11 /A:119-212 #12 /A:119-212

1386 atoms, 1409 bonds, 2 pseudobonds, 173 residues, 4 models selected  

> show #!12 models

> select #11 /A:119-212 #12 /A:119-212

1386 atoms, 1409 bonds, 2 pseudobonds, 173 residues, 4 models selected  

> select ~sel

255354 atoms, 259263 bonds, 166 pseudobonds, 23239 residues, 36 models
selected  

> hide sel & #!11-12 cartoons

> hide sel & #!11-12 atoms

> select clear

> matchmaker #11 #12

Missing required "to" argument  

> matchmaker #11 to #12

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker vsd-open, chain B (#12) with vsd-closed, chain D (#11), sequence
alignment score = 2358.4  
RMSD between 235 pruned atom pairs is 0.622 angstroms; (across all 472 pairs:
23.501)  
  
Drag select of 3 residues  

> undo

[Repeated 3 time(s)]

> close #11

> hide #!12 models

> show #!12 models

> close #12

> combine #1 #2

Remapping chain ID 'A' in
240910_KCNQ2_CaM_PIP2_XE991_open_real_space_refined_012-1.pdb #2 to 'E'  
Remapping chain ID 'B' in
240910_KCNQ2_CaM_PIP2_XE991_open_real_space_refined_012-1.pdb #2 to 'F'  
Remapping chain ID 'C' in
240910_KCNQ2_CaM_PIP2_XE991_open_real_space_refined_012-1.pdb #2 to 'G'  
Remapping chain ID 'D' in
240910_KCNQ2_CaM_PIP2_XE991_open_real_space_refined_012-1.pdb #2 to 'H'  
Remapping chain ID 'X' in
240910_KCNQ2_CaM_PIP2_XE991_open_real_space_refined_012-1.pdb #2 to 'Y'  

> select #10 /A:119-212 /E:119-212

1386 atoms, 1409 bonds, 2 pseudobonds, 173 residues, 2 models selected  

> select #11 /A:119-212 /E:119-212

1386 atoms, 1409 bonds, 2 pseudobonds, 173 residues, 2 models selected  

> select ~sel

255354 atoms, 259263 bonds, 166 pseudobonds, 23239 residues, 34 models
selected  

> hide sel & #!11 cartoons

> hide sel & #!11 atoms

> cartoon style width 1.15 thickness 0.3

> setattr b radius 0.27

Assigning radius attribute to 260676 items  

> select clear

> hide #11.1 models

> rename #11 VSD

> select #11/E:192

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

> hide sel cartoons

> select #11 /A:195-211

145 atoms, 145 bonds, 17 residues, 1 model selected  

> setattr sel res ss_id 999

Assigning ss_id attribute to 17 items  

> setattr sel res ss_type 1

Assigning ss_type attribute to 17 items  

> select clear

> select #11 /A:198 201

Expected a keyword  

> select #11/E:200

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

> select add #11/E:204

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

> select #11 /A:198 /A:201 /A:204 /A:207 /A:210 #11 /E:198 /A:201 /E:204
> /E:207 /E:210

95 atoms, 86 bonds, 9 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 95 atom styles  

> color sel byhetero

> select clear

> select #11 /A:137 /A:140 /A:172 #11 /E:137 /E:140 /E:172

56 atoms, 52 bonds, 6 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 56 atom styles  

> color sel byhetero

> select clear

> select #11/E:201

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

> show sel atoms

> style sel stick

Changed 11 atom styles  

> color sel byhetero

> select clear

> view side1

> view

> select clear

> select #11/E:193

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

> hide sel cartoons

> select #11/E:194

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

> hide sel cartoons

> select clear

> view VSD1

Expected an objects specifier or a view name or a keyword  

> view name VSD1

[Repeated 1 time(s)]

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\VSD.tif width 3000 height 3000
> transparentBackground true

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1.cxs includeMaps true

——— End of log from Tue Sep 10 17:05:02 2024 ———

opened ChimeraX session  

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> rename #1 KCNQ2_XE991_closed

> rename #2 KCNQ2_P_XE991_open

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!5 models

> hide #!5 models

> show #!6 models

> show #!2 models

> hide #!2 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> close #7-9

> show #!10 models

> hide #!10 models

> hide #!11 models

> close #10-11

> show #!1 models

> hide #!1 models

> rename #1 KCNQ2_XE991_PLL_closed

> show #!2 models

> view side1

> show #!1 models

> hide #!2 models

> hide #!1 models

> show #!4 models

> hide #!4 models

> show #!3 models

> hide #3.1 models

> show #3.1 models

> hide #3.1 models

> rename #1 2_KCNQ2_XE991_PLL_closed

> rename #2 1_KCNQ2_P_XE991_open

> show #!5 models

> hide #!5 models

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1-1031.cxs includeMaps true

> open
> E:/DataProcess_MODEL/data/KCNQ2_Blocker_structures_QingDao/KCNQ2_Blocker_summary_0928/structures/XE991/3_KCNQ2_XE991_close/3_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc
> E:/DataProcess_MODEL/data/KCNQ2_Blocker_structures_QingDao/KCNQ2_Blocker_summary_0928/structures/XE991/3_KCNQ2_XE991_close/KCNQ2_XE991_closed_real_space_refined_001.pdb

Opened 3_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc as #7,
grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values
float32  
Chain information for KCNQ2_XE991_closed_real_space_refined_001.pdb #8  
---  
Chain | Description  
A C D | No description available  
B | No description available  
  

> hide #!3 models

> hide #!7 models

> hide #!8 models

> show #!8 models

> close #1

> open
> E:/DataProcess_MODEL/data/KCNQ2_Blocker_structures_QingDao/KCNQ2_Blocker_summary_0928/structures/XE991/2_KCNQ2_PIP2_XE991_PLL_close/2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc

Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
as #1, grid size 240,240,240, pixel 0.93, shown at level 0.00801, step 1,
values float32  

> color #1 #779999ff models

> color #1 #7997b4ff models

> hide #!1 models

> show #!1 models

> close #1

> open
> E:/DataProcess_MODEL/data/KCNQ2_Blocker_structures_QingDao/KCNQ2_Blocker_summary_0928/structures/XE991/2_KCNQ2_PIP2_XE991_PLL_close/KCNQ2_CaM_XE991_closed_real_space_refined_006-1.pdb

Chain information for KCNQ2_CaM_XE991_closed_real_space_refined_006-1.pdb #1  
---  
Chain | Description  
B C D E | No description available  
  

> rename #1 KCNQ2_P_XE991_PLL_closed

> hide #!8 models

> hide #!1 models

> close #1

> open
> E:/DataProcess_MODEL/data/Q2_P_XE991_PLL/RealSpaceRefine_9/1020_KCNQ2_CaM_XE991_closed-1_real_space_refined_009.pdb

Chain information for 1020_KCNQ2_CaM_XE991_closed-1_real_space_refined_009.pdb
#1  
---  
Chain | Description  
A B C D | No description available  
  

> color #1 #779999ff

> color #1 #7997b4ff

> select up

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

> select up

49 atoms, 53 bonds, 1 residue, 1 model selected  

> color sel orange

> select clear

[Repeated 2 time(s)]

> select #1/C:1201@O08

1 atom, 1 residue, 1 model selected  

> select up

49 atoms, 53 bonds, 1 residue, 1 model selected  

> color sel orange red

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!8 models

> hide #!8 models

> rename #1 2_KCNQ2_p_XE991_PLL_closed

> rename #8 3_KCNQ2_XE991_closed

> hide #!1 models

> show #!1 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> color #8 #bb4477ff

> color #8 #b4797aff

> show #!8 models

> select #8 /A-D:1006-1149

1126 atoms, 1138 bonds, 143 residues, 1 model selected  

> select clear

> show #!8 atoms

> undo

> show #!8 cartoons

[Repeated 1 time(s)]

> show #!7 models

> hide #!7 models

> select #8 /A-D:1006-1149

1126 atoms, 1138 bonds, 143 residues, 1 model selected  

> color sel #b49679

> select clear

> close #8

> show #!1 models

> show #!2 models

> hide #!2 models

> hide #1.1 models

> select #1 /A-D:1006-1149

4504 atoms, 4552 bonds, 572 residues, 1 model selected  

> color

> color sel #b49679

> select clear

> hide #!1 atoms

> select ::name="LIG"

98 atoms, 106 bonds, 2 residues, 2 models selected  

> show sel & #!1 atoms

> hide H

> select clear

> select #1/B:564

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

> select clear

> select #1/C:1201@C16

1 atom, 1 residue, 1 model selected  

> select up

49 atoms, 53 bonds, 1 residue, 1 model selected  

> color sel byhetero

> select clear

> cartoon style width 1.15 thickness 0.3

> sdd

Unknown command: sdd  

> setattr b radius 0.27

Assigning radius attribute to 43446 items  

> select clear

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> show #!1 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> select up

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

> select up

49 atoms, 53 bonds, 1 residue, 1 model selected  

> color sel yellow

> color sel byhetero

> select clear

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> view side2

> view side1

> turn x 90

> ui tool show "Side View"

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!1 models

> combine #1

> hide #!1 models

> combine #2

> cartoon style width 1.15 thickness 0.3

> setattr b radius 0.27

Assigning radius attribute to 86892 items  

> hide #!8 models

> hide #!9 models

> show #!8 models

> select #8/B

3809 atoms, 3887 bonds, 3 pseudobonds, 472 residues, 2 models selected  

> select ~sel

81771 atoms, 83005 bonds, 53 pseudobonds, 7332 residues, 30 models selected  

> undo

[Repeated 1 time(s)]

> select clear

[Repeated 1 time(s)]

> select #1 /B-D:70-700

8049 atoms, 8247 bonds, 6 pseudobonds, 987 residues, 2 models selected  

> select #8 /B-D:70-700

8049 atoms, 8247 bonds, 6 pseudobonds, 987 residues, 2 models selected  

> color (#!8 & sel) dark gray

> select clear

> select #8 /A

3809 atoms, 3887 bonds, 3 pseudobonds, 472 residues, 2 models selected  

> select ~sel

81771 atoms, 83005 bonds, 53 pseudobonds, 7332 residues, 30 models selected  

> color (#!8 & sel) light gray

> select clear

> select up

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

> select up

49 atoms, 53 bonds, 1 residue, 1 model selected  

> color sel yellow

> color sel byhetero

> select clear

> select #8 /A-D:1006-1149

4504 atoms, 4552 bonds, 572 residues, 1 model selected  

> hide sel cartoons

> select clear

[Repeated 1 time(s)]

> view name top1

> show #!9 models

> hide #!8 models

> select #9 /A-D:1006-1149

8516 atoms, 8564 bonds, 572 residues, 1 model selected  

> hide sel cartoons

[Repeated 1 time(s)]

> select #9 /A-

Expected a keyword  

> select #9 /A

6864 atoms, 6948 bonds, 4 pseudobonds, 503 residues, 2 models selected  

> select ~sel

78716 atoms, 79944 bonds, 52 pseudobonds, 7301 residues, 30 models selected  

> color (#!9 & sel) light gray

> select clear

> show #!8 models

> hide #!8 models

> select clear

[Repeated 1 time(s)]

> hide #!9 atoms

> undo

> select ::name="PIO"

728 atoms, 728 bonds, 8 residues, 2 models selected  

> hide sel & #!9 atoms

> select clear

[Repeated 1 time(s)]

> select #9/X:1201@C15

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

49 atoms, 53 bonds, 1 residue, 1 model selected  

> color sel orange red

> color sel byhetero

> select clear

> show #!8 models

> hide #!9 models

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1031\2_Q2_P_XE991_PLL_top.tif width
> 3000 height 3000 transparentBackground true

> show #!9 models

> hide #!8 models

> rename #8 top_2_KCNQ2_p_XE991_PLL_closed

> rename #9 top_1_KCNQ2_P_XE991_open

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1031\2_Q2_P_XE991_top.tif width 3000
> height 3000 transparentBackground true

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1031\1_Q2_P_XE991_top.tif width 3000
> height 3000 transparentBackground true

> show #!1 models

> hide #!9 models

> view side1

> view side2

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1031\2_Q2_P_XE991_PLL_side.tif width
> 3000 height 3000 transparentBackground true

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1-1031.cxs includeMaps true

——— End of log from Fri Nov 1 00:35:11 2024 ———

opened ChimeraX session  

> show #!7 models

> hide #!7 models

> show #!6 models

> hide #!6 models

> show #!4 models

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #3.1 models

> hide #3.1 models

> show #3.1 models

> hide #!3.1 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> hide #!3 models

> show #!3 models

> show #3.1 models

> hide #!3.1 models

> show #3.1 models

> color #3.1 #bcbcbcff

> color #3.1 #b2b2b2ff

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!5 models

> hide #!5 models

> hide #!5.3 models

> show #!5.3 models

> hide #!3.1 models

> hide #!5 models

> hide #!3 models

> rename #3
> 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc

> rename #4
> 1_mapKCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc

> rename #4
> 1_map_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc

> show #!7 models

> hide #!7 models

> hide #!1 models

> show #!7 models

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1-1103.cxs includeMaps true

[Repeated 1 time(s)]

> show #!4 models

> hide #!4 models

> surface dust #7 size 9.3

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!7 models

> show #3.1 models

> show #!1 models

> ui tool show "Color Zone"

> color zone #3 near #1 distance 3.5

> show #!5 models

> hide #!5 models

> hide #!3 models

> show #!5 models

> close #5

> hide #3.1 models

> select up

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

> select up

49 atoms, 53 bonds, 1 residue, 1 model selected  

> color sel yellow

> show #!4 models

> hide #!4 models

> show #!3 models

> show #3.1 models

> color zone #3 near #1 distance 3.5

> color #3 #bcbcbcff models

> color zone #3 near #1 distance 3.5

> volume splitbyzone #3

Opened
2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 0
as #5.1, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened
2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 1
as #5.2, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened
2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2
as #5.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened
2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3
as #5.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  

> hide #!5.1 models

> surface dust #5.2 size 9.3

> surface dust #5.3 size 9.3

> surface dust #5.4 size 9.3

> hide #!5 models

> show #!5 models

> select clear

> close #5

> hide #!1 models

> show #!1 models

> show #!3 models

> color zone #3 near #1 distance 3.5

> volume splitbyzone #3

Opened
2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 0
as #5.1, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened
2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 1
as #5.2, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened
2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2
as #5.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  
Opened
2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3
as #5.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1,
values float32  

> hide #!5.1 models

> hide #!1 models

> surface dust #5.2 size 9.3

> surface dust #5.3 size 9.3

> surface dust #5.4 size 9.3

> surface dust #5 size 5

> show #!6 models

> hide #!6 models

> hide #!5 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> rename #6
> "1_KCNQ2_PIP2_XE991_map_open_3.14A_job119_B65_postprocess_resampled.mrc
> split"

> rename #6
> "1_map_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc
> split"

> open
> E:/DataProcess_MODEL/data/Q2_XE991/RealSpaceRefine_6/KCNQ2_XE991_close_real_space_refined_002-ABCD_real_space_refined_006.pdb

Chain information for
KCNQ2_XE991_close_real_space_refined_002-ABCD_real_space_refined_006.pdb #10  
---  
Chain | Description  
A B C D | No description available  
  

> cartoon style width 1.15 thickness 0.3

> setattr b radius 0.27

Assigning radius attribute to 102629 items  

> select clear

> hide #10.1 models

> hide #!10 atoms

> select ::name="LIG"

245 atoms, 265 bonds, 5 residues, 5 models selected  

> show sel & #!10 atoms

> select #10/C:151

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

> hide H

> select #10/C:1145

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

> color #10 #B4797a

> select clear

> select #10 /A-D:1006-1149

4504 atoms, 4552 bonds, 572 residues, 1 model selected  

> color

> color sel #b49679

> select #10 /A-D:1006-1149

4504 atoms, 4552 bonds, 572 residues, 1 model selected  

> color sel #b49679

> select clear

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> color sel tan

> select #10 /A-D:1006-1149

4504 atoms, 4552 bonds, 572 residues, 1 model selected  

> color sel tan

> show #!2 models

> hide #!2 models

> combine #1

> hide #!10 models

> select #11/A:1018

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

> select up

119 atoms, 121 bonds, 14 residues, 1 model selected  

> select up

1126 atoms, 1138 bonds, 143 residues, 1 model selected  

> select ~sel

115160 atoms, 117092 bonds, 79 pseudobonds, 11459 residues, 36 models selected  

> delete atoms (#!11 & sel)

> delete bonds (#!11 & sel)

> select clear

> close #11

> show #!10 models

> select #10 /A-D:1006-1149

4504 atoms, 4552 bonds, 572 residues, 1 model selected  

> color sel #b49679

> select clear

> select #10/A:1201@O08

1 atom, 1 residue, 1 model selected  

> select up

49 atoms, 53 bonds, 1 residue, 1 model selected  

> select up

3892 atoms, 3974 bonds, 478 residues, 1 model selected  

> select down

49 atoms, 53 bonds, 1 residue, 1 model selected  

> color sel yellow

> select clear

> show #!7 models

> hide #!7 models

> color zone #7 near #10 distance 3.5

> show #!7 models

> volume splitbyzone #7

Opened 3_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 0 as
#11.1, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1,
values float32  
Opened 3_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1 as
#11.2, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1,
values float32  
Opened 3_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 2 as
#11.3, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1,
values float32  
Opened 3_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 3 as
#11.4, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1,
values float32  

> rename #10
> 3_KCNQ2_XE991_close_real_space_refined_002-ABCD_real_space_refined_006.pdb

> close #11.1

> select clear

> rename #5
> "2_splitmap_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
> split"

> rename #6
> "1_splitmap_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc
> split"

> rename #11
> "3_splitmapQ2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc split"

> rename #11
> "3_splitmap_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc
> split"

> rename #7 3_map_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc

> hide #!10 models

> surface dust #11.2 size 9.3

> surface dust #11.3 size 9.3

> surface dust #11.4 size 9.3

> surface dust #11 size 5

> lighting soft

> view side2

> ui tool show "Side View"

> lighting soft

> view side2

[Repeated 1 time(s)]

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1031\3_Q2_XE991_sideview_map.tif width
> 3000 height 3000 transparentBackground true

> view side1

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1031\3_Q2_XE991_sideview_map.tif width
> 3000 height 3000 transparentBackground true

> show #!10 models

> hide #!11 models

> lighting simple

> select #10/A:1201@C15

1 atom, 1 residue, 1 model selected  

> select #10/A:1201@C15

1 atom, 1 residue, 1 model selected  

> select up

49 atoms, 53 bonds, 1 residue, 1 model selected  

> color sel byhetero

> select clear

> view side2

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1031\3_Q2_XE991_sideview_pdb.tif width
> 3000 height 3000 transparentBackground true

> view top1

> select #10 /A-D:1006-1149

4504 atoms, 4552 bonds, 572 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select clear

> select #10/C:157

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

> select up

88 atoms, 90 bonds, 10 residues, 1 model selected  

> select up

951 atoms, 977 bonds, 115 residues, 1 model selected  

> select up

957 atoms, 982 bonds, 116 residues, 1 model selected  

> select up

2225 atoms, 2286 bonds, 273 residues, 1 model selected  

> select up

2229 atoms, 2289 bonds, 274 residues, 1 model selected  

> select up

2717 atoms, 2783 bonds, 334 residues, 1 model selected  

> select up

2724 atoms, 2789 bonds, 335 residues, 1 model selected  

> select up

3843 atoms, 3921 bonds, 477 residues, 1 model selected  

> select down

2724 atoms, 2789 bonds, 335 residues, 1 model selected  

> select down

2717 atoms, 2783 bonds, 334 residues, 1 model selected  

> select down

2229 atoms, 2289 bonds, 274 residues, 1 model selected  

> select up

2717 atoms, 2783 bonds, 334 residues, 1 model selected  

> select ~sel

98284 atoms, 99846 bonds, 65 pseudobonds, 9379 residues, 41 models selected  

> color (#!10 & sel) light gray

> select clear

> select #10/A:1201@C15

1 atom, 1 residue, 1 model selected  

> select up

49 atoms, 53 bonds, 1 residue, 1 model selected  

> color sel yellow

> color sel byhetero

> select clear

> view top1

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1031\3_Q2_XE991_top.tif width 3000
> height 3000 transparentBackground true

> show #!11 models

> hide #!10 models

> view side1

> lighting soft

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1-1103.cxs includeMaps true

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/1031/Fig1-1103.cxs includeMaps true

——— End of log from Sun Nov 3 17:25:07 2024 ———

opened ChimeraX session  

> rename #1 3_KCNQ2_p_XE991_PLL_closed

> rename #2 2_KCNQ2_P_XE991_open

> rename #3
> 3_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc

> rename #5
> "3_splitmap_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
> split"

> rename #4
> 2_map_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc

> rename #6
> "2_splitmap_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc
> split"

> rename #7 1_map_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc

> rename #8 top_3_KCNQ2_p_XE991_PLL_closed

> rename #9 top_2_KCNQ2_P_XE991_open

> rename #10
> 1_KCNQ2_XE991_close_real_space_refined_002-ABCD_real_space_refined_006.pdb

> rename #11
> "1_splitmap_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc
> split"

> rename #11.2 "1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc
> 1"

> rename #11.3 "1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc
> 2"

> rename #11.4 "1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc
> 3"

> rename #6.2
> "2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 1"

> rename #6.3
> "2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 2"

> rename #6.4
> "2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 3"

> rename #6.5
> "2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 4"

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/1104/Fig1-1104.cxs includeMaps true

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!2 models

> hide #!11 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!10 models

> color #10 #7997b4ff

> show #!10 atoms

> hide #!10 atoms

> show #!10 cartoons

> select clear

Drag select of 6 residues  

> select clear

> select #10 /A-D 1006-1149

Expected a keyword  

> select #10 /A-D 1006-1149

Expected a keyword  

> select #10 /A-D：1006-1149

Expected a keyword  

> select #10 /A-D:1006-1149

4504 atoms, 4552 bonds, 572 residues, 1 model selected  

> color sel #b49679

> select clear

> select ::name="LIG"

245 atoms, 265 bonds, 5 residues, 5 models selected  

> show sel & #!10 atoms

> color (#!10 & sel) yellow

> hide H

> select clear

> show #!11 models

> color #11.2 #7997b4ff models

> select clear

> view side1

[Repeated 1 time(s)]

> color #1 #55557fff

> color #5.2 #55557fff models

> hide #!11 models

> show #!11 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> view side1

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> lighting soft

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1104\1_Q2_XE991_map.tif width 3000
> height 3000 transparentBackground true

> show #!10 models

> hide #!11 models

> lighting simple

> select #10/A:1201@C17

1 atom, 1 residue, 1 model selected  

> select up

49 atoms, 53 bonds, 1 residue, 1 model selected  

> select up

3892 atoms, 3974 bonds, 478 residues, 1 model selected  

> select down

49 atoms, 53 bonds, 1 residue, 1 model selected  

> color sel byhetero

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1104\1_Q2_XE991_side.tif width 3000
> height 3000 transparentBackground true

> select clear

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1104\1_Q2_XE991_side.tif width 3000
> height 3000 transparentBackground true

> view top1

> combine #10

> hide #!10 models

> rename #12
> top_1_KCNQ2_XE991_close_real_space_refined_002-ABCD_real_space_refined_006.pdb

> cartoon style width 1.15 thickness 0.3

> setattr b radius 0.27

Assigning radius attribute to 118366 items  

> select clear

> select #12 /A-D:1006-1149

4504 atoms, 4552 bonds, 572 residues, 1 model selected  

> hide sel cartoons

> select clear

> hide #12.1 models

> select #12/C:157

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

> select up

88 atoms, 90 bonds, 10 residues, 1 model selected  

> select up

951 atoms, 977 bonds, 115 residues, 1 model selected  

> select up

957 atoms, 982 bonds, 116 residues, 1 model selected  

> select up

2225 atoms, 2286 bonds, 273 residues, 1 model selected  

> select up

2229 atoms, 2289 bonds, 274 residues, 1 model selected  

> select up

2717 atoms, 2783 bonds, 334 residues, 1 model selected  

> select ~sel

113705 atoms, 115583 bonds, 77 pseudobonds, 11288 residues, 43 models selected  

> color (#!12 & sel) light gray

> select clear

> select up

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

> select up

49 atoms, 53 bonds, 1 residue, 1 model selected  

> color sel yellow

> color sel byhetero

> select clear

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1104\1_Q2_XE991_top.tif width 3000
> height 3000 transparentBackground true

> color #1 #bb4477ff

> color #1 #b4797aff

> hide #!12 models

> show #!1 models

> show #!8 models

> hide #!1 models

> hide #8.1 models

> select clear

> select #8/A:156

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

> select up

88 atoms, 90 bonds, 10 residues, 1 model selected  

> select up

951 atoms, 977 bonds, 115 residues, 1 model selected  

> select up

957 atoms, 982 bonds, 116 residues, 1 model selected  

> select up

2219 atoms, 2280 bonds, 272 residues, 1 model selected  

> select up

2225 atoms, 2285 bonds, 273 residues, 1 model selected  

> select up

2683 atoms, 2749 bonds, 329 residues, 1 model selected  

> color sel #b4797a

> select clear

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1104\3_Q2_XE991_top.tif width 3000
> height 3000 transparentBackground true

> hide #!8 models

> show #!3 models

> show #!5 models

> color #5.2 #bb4477ff models

> color #5.2 #b4797aff models

> hide #!3 models

> view side1

> lighting soft

> hide #!5.4 models

> show #!5.4 models

> select clear

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1104\3_Q2_XE991_map.tif width 3000
> height 3000 transparentBackground true

> show #!1 models

> hide #!5.2 models

> show #!5.2 models

> hide #!5 models

> select #1 /A-D:1006-1149

4504 atoms, 4552 bonds, 572 residues, 1 model selected  

> color sel #b49679

> select clear

> select up

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

> select up

49 atoms, 53 bonds, 1 residue, 1 model selected  

> color sel yellow

> color sel byhetero

> select clear

> lighting simple

> select clear

> view side2

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1104\3_Q2_XE991_side.tif width 3000
> height 3000 transparentBackground true

> hide #!1 models

> show #!12 models

> show #!11 models

> hide #!11 models

> hide #!12 models

> show #!10 models

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1104\1_Q2_XE991_side.tif width 3000
> height 3000 transparentBackground true

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/1104/Fig1-1104.cxs includeMaps true

——— End of log from Mon Nov 4 16:06:22 2024 ———

opened ChimeraX session  

> show #!5 models

> show #!6 models

> hide #!6 models

> hide #!10 models

> hide #!5 models

> show #!11 models

> lighting soft

> lighting simple

> lighting soft

> lighting full

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1104\1.tif width 3000 height 3000
> transparentBackground true

> hide #!11 models

> show #!5 models

> view side1

> ui tool show "Side View"

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1104\3.tif width 3000 height 3000
> transparentBackground true

> show #!11 models

> hide #!5 models

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1104\1.tif width 3000 height 3000
> transparentBackground true

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/1104/Fig1-1105.cxs includeMaps true

——— End of log from Tue Nov 5 12:59:07 2024 ———

opened ChimeraX session  

> color #11.4 #55ffffff models

> color #11.4 lime models

> color #11.4 #55ffffff models

> color #11.4 #fdb604ff models

> color #11.4 #e17f00ff models

> color #11.4 #00b7b7ff models

> color #11.4 #55ffffff models

> color #11.4 #ffaaffff models

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-Q2X-.tif width
> 3000 height 3000 transparentBackground true

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-Q2X-1.tif width
> 3000 height 3000 transparentBackground true

> show #!6 models

> hide #!6 models

> show #!10 models

> hide #!10 models

> hide #!11 models

> show #!12 models

> hide #!12 models

> show #!4 models

> hide #!4 models

> show #!5 models

> color #5.4 magenta models

> color #5.4 #ffaaffff models

> color #5.4 magenta models

> color #5.4 #ffaaffff models

> color #5.4 magenta models

> color #5.4 #ff007fff models

> color #5.4 magenta models

> color #5.4 #38b48bff models

> color #11.4 #38b48bff models

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-Q2X-3.tif width
> 3000 height 3000 transparentBackground true

> hide #!5 models

> show #!7 models

> hide #!7 models

> show #!11 models

> color #11.4 #83ccd2ff models

> color #11.4 #a22041ff models

> color #5.4 #a22041ff models

> show #!5 models

> hide #!11 models

> color #5.4 #f08300ff models

> color #11.4 #f08300ff models

> hide #!5 models

> show #!11 models

> color #11.4 red models

> color #11.4 #fdb604ff models

> color #5.4 #fdb604ff models

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-1-Q2X-1.tif width
> 3000 height 3000 transparentBackground true

> show #!5 models

> hide #!11 models

> color #5.4 #00a497ff models

> color #5.4 #00b9aaff models

> color #5.4 #00c3b3ff models

> color #5.4 #00c1b1ff models

> color #11.4 #00c1b1ff models

> show #!10 models

> hide #!10 models

> show #!11 models

> hide #!5 models

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-1-Q2X-1.tif width
> 3000 height 3000 transparentBackground true

> ui tool show "Side View"

> lighting simple

> lighting soft

> lighting simple

> lighting full

> lighting soft

> lighting simple

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-1-Q2X-2.tif width
> 3000 height 3000 transparentBackground true

> hide #!11 models

> show #!5 models

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-3-Q2X-1.tif width
> 3000 height 3000 transparentBackground true

> color #11.4 #00a497ff models

> color #5.4 #00a497ff models

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-3-Q2X-1.tif width
> 3000 height 3000 transparentBackground true

> hide #!5 models

> show #!11 models

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-1-Q2X-1.tif width
> 3000 height 3000 transparentBackground true

> hide #!11 models

> show #!6 models

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-2-Q2X-1.tif width
> 3000 height 3000 transparentBackground true

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1-maps-1204/Fig1-1204.cxs

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
310, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5EB0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9C670> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9C1F0>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2' -> <chimerax.map.session.GridDataState object at 0x0000017882428130>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5EB0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9C670> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9C1F0>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2' -> <chimerax.map.session.GridDataState object at 0x0000017882428130>: Error
while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5EB0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9C670> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9C1F0>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2' -> <chimerax.map.session.GridDataState object at 0x0000017882428130>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2' -> : Error while saving session data for '_surface_updaters' -> -> ->
'surface' ->
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2' ->  
  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
310, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5EB0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9C670> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9C1F0>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2' -> <chimerax.map.session.GridDataState object at 0x0000017882428130>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5EB0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9C670> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9C1F0>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2' -> <chimerax.map.session.GridDataState object at 0x0000017882428130>: Error
while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5EB0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9C670> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9C1F0>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2' -> <chimerax.map.session.GridDataState object at 0x0000017882428130>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2' -> : Error while saving session data for '_surface_updaters' -> -> ->
'surface' ->
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2' ->  
  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1-maps-1204/fig1-1204.cxs
> includeMaps true

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
310, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF550> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9CFA0> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9CB20>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
3' -> <chimerax.map.session.GridDataState object at 0x0000017882428040>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF550> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9CFA0> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9CB20>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
3' -> <chimerax.map.session.GridDataState object at 0x0000017882428040>: Error
while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF550> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9CFA0> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9CB20>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
3' -> <chimerax.map.session.GridDataState object at 0x0000017882428040>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
3' -> : Error while saving session data for '_surface_updaters' -> -> ->
'surface' ->
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
3' ->  
  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
310, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF550> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9CFA0> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9CB20>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
3' -> <chimerax.map.session.GridDataState object at 0x0000017882428040>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF550> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9CFA0> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9CB20>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
3' -> <chimerax.map.session.GridDataState object at 0x0000017882428040>: Error
while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF550> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9CFA0> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9CB20>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
3' -> <chimerax.map.session.GridDataState object at 0x0000017882428040>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
3' -> : Error while saving session data for '_surface_updaters' -> -> ->
'surface' ->
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
3' ->  
  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/fig1-1204/fig1204-A.cxs includeMaps
> true

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
310, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A964B0D0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D98820> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D98250>
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1' ->
<chimerax.map.session.GridDataState object at 0x000001788245C370>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A964B0D0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D98820> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D98250>
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1' ->
<chimerax.map.session.GridDataState object at 0x000001788245C370>: Error while
saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A964B0D0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D98820> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D98250>
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1' ->
<chimerax.map.session.GridDataState object at 0x000001788245C370>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1' -> : Error
while saving session data for '_surface_updaters' -> -> -> 'surface' ->
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1' ->  
  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
310, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A964B0D0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D98820> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D98250>
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1' ->
<chimerax.map.session.GridDataState object at 0x000001788245C370>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A964B0D0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D98820> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D98250>
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1' ->
<chimerax.map.session.GridDataState object at 0x000001788245C370>: Error while
saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A964B0D0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D98820> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D98250>
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1' ->
<chimerax.map.session.GridDataState object at 0x000001788245C370>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1' -> : Error
while saving session data for '_surface_updaters' -> -> -> 'surface' ->
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1' ->  
  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> rename #11.2 1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc

> rename #11.3 1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc

> rename #11.4 1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/fig1-1204/1204.cxs includeMaps true

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
310, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5EB0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9C670> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9C1F0>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2' -> <chimerax.map.session.GridDataState object at 0x00000178823F6940>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5EB0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9C670> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9C1F0>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2' -> <chimerax.map.session.GridDataState object at 0x00000178823F6940>: Error
while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5EB0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9C670> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9C1F0>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2' -> <chimerax.map.session.GridDataState object at 0x00000178823F6940>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2' -> : Error while saving session data for '_surface_updaters' -> -> ->
'surface' ->
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2' ->  
  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
310, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5EB0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9C670> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9C1F0>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2' -> <chimerax.map.session.GridDataState object at 0x00000178823F6940>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5EB0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9C670> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9C1F0>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2' -> <chimerax.map.session.GridDataState object at 0x00000178823F6940>: Error
while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5EB0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9C670> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9C1F0>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2' -> <chimerax.map.session.GridDataState object at 0x00000178823F6940>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2' -> : Error while saving session data for '_surface_updaters' -> -> ->
'surface' ->
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc
2' ->  
  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> rename #6.2
> 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc

> rename #6.3
> 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc

> rename #6.4
> 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc

> rename #6.5
> 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc

> rename #5.1
> 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc

> rename #5.2
> 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc

> rename #5.3
> 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc

> rename #5.4
> 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/fig1-1204/1.cxs includeMaps true

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
310, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5EB0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9C670> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9C1F0>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc'
-> <chimerax.map.session.GridDataState object at 0x00000178AD549C10>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5EB0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9C670> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9C1F0>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc'
-> <chimerax.map.session.GridDataState object at 0x00000178AD549C10>: Error
while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5EB0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9C670> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9C1F0>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc'
-> <chimerax.map.session.GridDataState object at 0x00000178AD549C10>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc'
-> : Error while saving session data for '_surface_updaters' -> -> ->
'surface' ->
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc'
->  
  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
310, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5EB0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9C670> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9C1F0>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc'
-> <chimerax.map.session.GridDataState object at 0x00000178AD549C10>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5EB0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9C670> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9C1F0>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc'
-> <chimerax.map.session.GridDataState object at 0x00000178AD549C10>: Error
while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5EB0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D9C670> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D9C1F0>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc'
-> <chimerax.map.session.GridDataState object at 0x00000178AD549C10>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc'
-> : Error while saving session data for '_surface_updaters' -> -> ->
'surface' ->
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc'
->  
  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/fig1-1204/1204.cxs

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
310, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF2B0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D93D00> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D93880>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc'
-> <chimerax.map.session.GridDataState object at 0x0000017880A0C700>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF2B0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D93D00> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D93880>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc'
-> <chimerax.map.session.GridDataState object at 0x0000017880A0C700>: Error
while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF2B0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D93D00> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D93880>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc'
-> <chimerax.map.session.GridDataState object at 0x0000017880A0C700>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc'
-> : Error while saving session data for '_surface_updaters' -> -> ->
'surface' ->
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc'
->  
  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
310, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF2B0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D93D00> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D93880>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc'
-> <chimerax.map.session.GridDataState object at 0x0000017880A0C700>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF2B0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D93D00> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D93880>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc'
-> <chimerax.map.session.GridDataState object at 0x0000017880A0C700>: Error
while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF2B0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D93D00> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D93880>
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc'
-> <chimerax.map.session.GridDataState object at 0x0000017880A0C700>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc'
-> : Error while saving session data for '_surface_updaters' -> -> ->
'surface' ->
'2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc'
->  
  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> show #!5 models

> hide #!6 models

> rename #5.1 1.mrc

> rename #5.2 Q2.mrc

> rename #5.3 CAM.mrc

> rename #5.4 XE991.mrc

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/fig1-1204/fig1-1204.cxs includeMaps
> true

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
310, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF2B0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D93D00> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D93880> 'Q2.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000017880A16BE0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF2B0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D93D00> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D93880> 'Q2.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000017880A16BE0>: Error while
saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF2B0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D93D00> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D93880> 'Q2.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000017880A16BE0>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'Q2.mrc' -> : Error while saving session data for '_surface_updaters' -> -> ->
'surface' -> 'Q2.mrc' ->  
  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
310, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF2B0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D93D00> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D93880> 'Q2.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000017880A16BE0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF2B0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D93D00> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D93880> 'Q2.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000017880A16BE0>: Error while
saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF2B0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D93D00> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D93880> 'Q2.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000017880A16BE0>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'Q2.mrc' -> : Error while saving session data for '_surface_updaters' -> -> ->
'surface' -> 'Q2.mrc' ->  
  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> rename #5.2 Q2-1.mrc

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/fig1-1204/fig1-1204.cxs includeMaps
> true

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
310, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF2B0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D93D00> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D93880> 'Q2-1.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000017880A16D30>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF2B0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D93D00> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D93880> 'Q2-1.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000017880A16D30>: Error while
saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF2B0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D93D00> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D93880> 'Q2-1.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000017880A16D30>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'Q2-1.mrc' -> : Error while saving session data for '_surface_updaters' -> ->
-> 'surface' -> 'Q2-1.mrc' ->  
  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
310, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF2B0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D93D00> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D93880> 'Q2-1.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000017880A16D30>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF2B0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D93D00> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D93880> 'Q2-1.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000017880A16D30>: Error while
saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91BF2B0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7D93D00> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D93880> 'Q2-1.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000017880A16D30>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'Q2-1.mrc' -> : Error while saving session data for '_surface_updaters' -> ->
-> 'surface' -> 'Q2-1.mrc' ->  
  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> hide #!5.2 models

> show #!5.2 models

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-3-Q2PXL-1.tif
> width 3000 height 3000 transparentBackground true

> hide #!5 models

> show #!6 models

> save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-2-Q2PX-1.tif width
> 3000 height 3000 transparentBackground true

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/fig1-1204/1204.cxs includeMaps true

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
310, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5D60> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7DA6190> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D98CD0>
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001788243FF40>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5D60> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7DA6190> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D98CD0>
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001788243FF40>: Error while
saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5D60> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7DA6190> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D98CD0>
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001788243FF40>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> : Error
while saving session data for '_surface_updaters' -> -> -> 'surface' ->
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' ->  
  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
310, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5D60> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7DA6190> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D98CD0>
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001788243FF40>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5D60> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7DA6190> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D98CD0>
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001788243FF40>: Error while
saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5D60> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7DA6190> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D98CD0>
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001788243FF40>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> : Error
while saving session data for '_surface_updaters' -> -> -> 'surface' ->
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' ->  
  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> lighting simple

> save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/fig1-1204/111.cxs

Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
310, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5D60> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7DA6190> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D98CD0>
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000017882485190>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5D60> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7DA6190> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D98CD0>
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000017882485190>: Error while
saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5D60> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7DA6190> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D98CD0>
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000017882485190>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> : Error
while saving session data for '_surface_updaters' -> -> -> 'surface' ->
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' ->  
  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py", line
310, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5D60> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7DA6190> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D98CD0>
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000017882485190>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5D60> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7DA6190> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D98CD0>
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000017882485190>: Error while
saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x00000178A91BF700> ->
<chimerax.surface.dust.Redust object at 0x00000178A91B5D60> ->
<chimerax.map.volume.VolumeSurface object at 0x00000178A7DA6190> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000178A7D98CD0>
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000017882485190>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> : Error
while saving session data for '_surface_updaters' -> -> -> 'surface' ->
'1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' ->  
  
File "D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 425.45
OpenGL renderer: Quadro K1100M/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: Dell Precision M3800
OS: Microsoft Windows 10 专业版 (Build 19045)
Memory: 17,078,124,544
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-4712HQ CPU @ 2.30GHz
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0

Change History (2)

comment:1 by pett, 11 months ago

Cc: Greg Couch added
Component: Unassigned → Sessions
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → MemoryError saving map in session

comment:2 by Tom Goddard, 11 months ago

Resolution: → limitation
Status: assigned → closed

The user ran out of memory. It happened to be while saving a session where it was allocating 55 Mbytes for a volume that was created in ChimeraX. The user had lots of these volumes (tens?). They have 16 Gbytes of memory. These out of memory errors always happen on Windows 10. It is in old ChimeraX 1.6 and maybe it is related to that long ago bug where opening mmCIF files sometimes ran out of memory.

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