MemoryError saving session

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

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

> open X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/240503.cxs

Opened cryosparc_P68_J1072_map_sharp.mrc as #2, grid size 448,448,448, pixel
0.731, shown at level 0.0113, step 1, values float32  
Opened molmap_4A.mrc as #5, grid size 108,91,113, pixel 1.33, shown at level
0.107, step 1, values float32  
Opened molmap_rs.mrc as #6, grid size 448,448,448, pixel 0.731, shown at level
0.107, step 1, values float32  
Opened cryosparc_P68_J1089_map_sharp.mrc as #7.1, grid size 448,448,448, pixel
0.731, shown at level 0.0397, step 1, values float32  
Opened cryosparc_P68_J1090_map_sharp.mrc as #7.2, grid size 448,448,448, pixel
0.731, shown at level 0.0343, step 1, values float32  
Opened cryosparc_P68_J835_008_volume_map_sharp.mrc as #8, grid size
448,448,448, pixel 0.731, shown at level 0.032, step 1, values float32  
Opened cryosparc_P68_J974_map_sharp.mrc as #10, grid size 360,360,360, pixel
0.914, shown at level 0.0484, step 1, values float32  
Opened cryosparc_P68_J974_map_sharp.mrc z flip as #11, grid size 360,360,360,
pixel 0.914, shown at level 0.0484, step 1, values float32  
Log from Fri May 3 11:40:31 2024UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/240502.cxs

Opened cryosparc_P68_J1072_map_sharp.mrc as #2, grid size 448,448,448, pixel
0.731, shown at level 0.0113, step 1, values float32  
Opened molmap_4A.mrc as #5, grid size 108,91,113, pixel 1.33, shown at level
0.107, step 1, values float32  
Opened molmap_rs.mrc as #6, grid size 448,448,448, pixel 0.731, shown at level
0.107, step 1, values float32  
Opened cryosparc_P68_J1089_map_sharp.mrc as #7.1, grid size 448,448,448, pixel
0.731, shown at level 0.0397, step 1, values float32  
Opened cryosparc_P68_J1090_map_sharp.mrc as #7.2, grid size 448,448,448, pixel
0.731, shown at level 0.0343, step 1, values float32  
Log from Thu May 2 09:43:35 2024UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/240430.cxs

Opened cryosparc_P68_J1072_map_sharp.mrc as #2, grid size 448,448,448, pixel
0.731, shown at level 0.0113, step 1, values float32  
Opened molmap_4A.mrc as #5, grid size 108,91,113, pixel 1.33, shown at level
0.107, step 1, values float32  
Opened molmap_rs.mrc as #6, grid size 448,448,448, pixel 0.731, shown at level
0.107, step 1, values float32  
Log from Tue Apr 30 09:49:52 2024UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/7xgd_fit_to_tmb_map_1.pdb
> X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/cryosparc_P68_J1072_map_sharp.mrc

7xgd_fit_to_tmb_map_1.pdb title:  
Cryo-em structure of apo-IGF1R map 1 [more info...]  
  
Chain information for 7xgd_fit_to_tmb_map_1.pdb #1  
---  
Chain | Description | UniProt  
A | insulin-like growth factor 1 receptor | IGF1R_HUMAN  
B | insulin-like growth factor 1 receptor | IGF1R_HUMAN  
  
Opened cryosparc_P68_J1072_map_sharp.mrc as #2, grid size 448,448,448, pixel
0.731, shown at level 0.000155, step 2, values float32  

> set bgColor white

> volume #2 step 1

> volume #2 level 0.01126

> open "G:/Kunden-Projekte/Projekte_22/22-VRA-002/09 Reports,
> Presentations/Structure_delivery/IGF1R-NTD_TMB/Deliverables/IGF1RNTD_TMB_model.pdb"

IGF1RNTD_TMB_model.pdb title:  
Human IGF1R NTD bound to TMB fab [more info...]  
  
Chain information for IGF1RNTD_TMB_model.pdb #3  
---  
Chain | Description  
A | No description available  
H | No description available  
L | No description available  
  
Non-standard residues in IGF1RNTD_TMB_model.pdb #3  
---  
NAG — (NAG)  
  

> select add #3

5585 atoms, 5734 bonds, 2 pseudobonds, 715 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,54.336,0,1,0,40.882,0,0,1,52.236

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.75506,-0.070699,-0.65183,159.69,0.4964,-0.58785,0.63877,92.591,-0.42834,-0.80587,-0.40877,340.99

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.75506,-0.070699,-0.65183,184.86,0.4964,-0.58785,0.63877,61.443,-0.42834,-0.80587,-0.40877,380.34

> hide #!2 models

> view matrix models
> #3,0.75506,-0.070699,-0.65183,187.63,0.4964,-0.58785,0.63877,69.287,-0.42834,-0.80587,-0.40877,378.16

> dssp #3

> view matrix models
> #3,0.75506,-0.070699,-0.65183,189.56,0.4964,-0.58785,0.63877,71.431,-0.42834,-0.80587,-0.40877,378

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.99679,-0.067568,0.042989,87.385,-0.064136,-0.99499,-0.076751,255.87,0.047959,0.073747,-0.99612,291.32

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.99679,-0.067568,0.042989,69.977,-0.064136,-0.99499,-0.076751,267.43,0.047959,0.073747,-0.99612,283.36

> view matrix models
> #3,0.99679,-0.067568,0.042989,60.878,-0.064136,-0.99499,-0.076751,283.52,0.047959,0.073747,-0.99612,315.78

> view matrix models
> #3,0.99679,-0.067568,0.042989,62.574,-0.064136,-0.99499,-0.076751,280.2,0.047959,0.073747,-0.99612,315.36

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.88539,-0.050232,0.46213,27.735,-0.13638,-0.97847,0.15493,261.36,0.4444,-0.2002,-0.87317,288.46

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.88539,-0.050232,0.46213,29.28,-0.13638,-0.97847,0.15493,260.03,0.4444,-0.2002,-0.87317,285.02

> view matrix models
> #3,0.88539,-0.050232,0.46213,25.211,-0.13638,-0.97847,0.15493,250.71,0.4444,-0.2002,-0.87317,281.87

> view matrix models
> #3,0.88539,-0.050232,0.46213,22.3,-0.13638,-0.97847,0.15493,255.6,0.4444,-0.2002,-0.87317,287.98

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.73414,-0.076853,0.67464,19.057,-0.23107,-0.96255,0.1418,265.75,0.63847,-0.25999,-0.7244,257.02

> view matrix models
> #3,0.69646,0.12577,0.70649,-2.6273,-0.082991,-0.9638,0.25338,237.42,0.71278,-0.23511,-0.66081,239.16

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.69646,0.12577,0.70649,-11.536,-0.082991,-0.9638,0.25338,230.62,0.71278,-0.23511,-0.66081,231.87

> view matrix models
> #3,0.69646,0.12577,0.70649,-10.195,-0.082991,-0.9638,0.25338,236.7,0.71278,-0.23511,-0.66081,229.1

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.66761,0.0011792,0.74451,2.6808,-0.29288,-0.91895,0.26409,253.84,0.68448,-0.39437,-0.61316,244.72

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.66761,0.0011792,0.74451,2.1535,-0.29288,-0.91895,0.26409,251.61,0.68448,-0.39437,-0.61316,241.22

> view matrix models
> #3,0.66761,0.0011792,0.74451,-3.7204,-0.29288,-0.91895,0.26409,249.43,0.68448,-0.39437,-0.61316,244.48

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.52326,0.097993,0.84652,-9.4525,-0.24245,-0.93519,0.25812,246.28,0.81696,-0.34031,-0.46559,207.88

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.52326,0.097993,0.84652,-10.904,-0.24245,-0.93519,0.25812,246.84,0.81696,-0.34031,-0.46559,203.62

> view matrix models
> #3,0.52326,0.097993,0.84652,-13.069,-0.24245,-0.93519,0.25812,249.39,0.81696,-0.34031,-0.46559,203.63

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.55006,-0.030594,0.83457,-0.5201,-0.30548,-0.93744,0.16697,266.46,0.77725,-0.34679,-0.52499,215.17

> select subtract #3

Nothing selected  

> show #!2 models

> ui tool show "Fit in Map"

> fitmap #3 inMap #2

Fit molecule IGF1RNTD_TMB_model.pdb (#3) to map
cryosparc_P68_J1072_map_sharp.mrc (#2) using 5585 atoms  
average map value = 0.04506, steps = 112  
shifted from previous position = 2.65  
rotated from previous position = 2.57 degrees  
atoms outside contour = 4312, contour level = 0.011255  
  
Position of IGF1RNTD_TMB_model.pdb (#3) relative to
cryosparc_P68_J1072_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.56827748 -0.06024340 0.82062869 3.32063719  
-0.33520039 -0.92776063 0.16401496 271.43672499  
0.75146617 -0.36828107 -0.54741908 222.67509857  
Axis -0.88260692 0.11467926 -0.45590975  
Axis point 0.00000000 152.48357186 86.00765603  
Rotation angle (degrees) 162.44941937  
Shift along axis -73.32240141  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/B

Alignment identifier is 1/B  

> hide #!2 models

> select #1/B:1

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

> select #1/B:1-328

4950 atoms, 5019 bonds, 328 residues, 1 model selected  

> select #1/B:1

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

> select #1/B:1-323

4868 atoms, 4936 bonds, 323 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show "Fit in Map"

> fitmap #3 inMap #2

Fit molecule IGF1RNTD_TMB_model.pdb (#3) to map
cryosparc_P68_J1072_map_sharp.mrc (#2) using 5585 atoms  
average map value = 0.04506, steps = 64  
shifted from previous position = 0.00925  
rotated from previous position = 0.00616 degrees  
atoms outside contour = 4312, contour level = 0.011255  
  
Position of IGF1RNTD_TMB_model.pdb (#3) relative to
cryosparc_P68_J1072_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.56826330 -0.06015245 0.82064518 3.31757027  
-0.33519643 -0.92774578 0.16410704 271.42224031  
0.75147866 -0.36833334 -0.54736676 222.66818050  
Axis -0.88260111 0.11465405 -0.45592734  
Axis point 0.00000000 152.48003544 85.99902338  
Rotation angle (degrees) 162.44438631  
Shift along axis -73.32894316  
  

> show #!2 models

> fitmap #3 inMap #2

Fit molecule IGF1RNTD_TMB_model.pdb (#3) to map
cryosparc_P68_J1072_map_sharp.mrc (#2) using 5585 atoms  
average map value = 0.04506, steps = 60  
shifted from previous position = 0.00924  
rotated from previous position = 0.0071 degrees  
atoms outside contour = 4317, contour level = 0.011255  
  
Position of IGF1RNTD_TMB_model.pdb (#3) relative to
cryosparc_P68_J1072_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.56836209 -0.06014835 0.82057706 3.31139090  
-0.33519227 -0.92773732 0.16416338 271.41149908  
0.75140580 -0.36835533 -0.54745198 222.69638739  
Axis -0.88262905 0.11464867 -0.45587459  
Axis point 0.00000000 152.47859532 86.01364913  
Rotation angle (degrees) 162.44229321  
Shift along axis -73.32738691  
  

> fitmap #3 inMap #2

Fit molecule IGF1RNTD_TMB_model.pdb (#3) to map
cryosparc_P68_J1072_map_sharp.mrc (#2) using 5585 atoms  
average map value = 0.04506, steps = 92  
shifted from previous position = 0.00956  
rotated from previous position = 0.0121 degrees  
atoms outside contour = 4312, contour level = 0.011255  
  
Position of IGF1RNTD_TMB_model.pdb (#3) relative to
cryosparc_P68_J1072_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.56827888 -0.06029833 0.82062368 3.32538020  
-0.33520694 -0.92776826 0.16395841 271.44576592  
0.75146219 -0.36825286 -0.54744353 222.67670269  
Axis -0.88260831 0.11469601 -0.45590284  
Axis point 0.00000000 152.48588626 86.01053802  
Rotation angle (degrees) 162.45233365  
Shift along axis -73.32020329  
  

> hide #!2 models

> select add #1

7880 atoms, 7989 bonds, 2 pseudobonds, 517 residues, 2 models selected  

> select add #3

13465 atoms, 13723 bonds, 4 pseudobonds, 1232 residues, 4 models selected  

> show #!2 models

> transparency 50

> color #2 #55aaff models transparency 0

> transparency 50

> save X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/pdb-for-
> mask.pdb selectedOnly true relModel #2

> open X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/pdb-for-
> mask.pdb

Summary of feedback from opening
X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/pdb-for-mask.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 506
GLY A 510 1 5  
Start residue of secondary structure not found: HELIX 2 2 ASP A 512 SER A 516
1 5  
Start residue of secondary structure not found: HELIX 3 3 GLU A 560 ILE A 564
1 5  
Start residue of secondary structure not found: HELIX 4 4 ASP A 624 ARG A 629
1 6  
Start residue of secondary structure not found: HELIX 5 5 GLY A 667 CYS A 672
1 6  
34 messages similar to the above omitted  
  
pdb-for-mask.pdb title:  
Cryo-em structure of apo-IGF1R map 1 [more info...]  
  
Chain information for pdb-for-mask.pdb  
---  
Chain | Description | UniProt  
4.1/A | insulin-like growth factor 1 receptor | IGF1R_HUMAN  
4.2/A | insulin-like growth factor 1 receptor | IGF1R_HUMAN  
4.1/B | insulin-like growth factor 1 receptor | IGF1R_HUMAN  
4.2/H | No description available |  
4.2/L | No description available |  
  

> hide #!3 models

> select subtract #3

7880 atoms, 7989 bonds, 2 pseudobonds, 517 residues, 2 models selected  

> select subtract #1

Nothing selected  

> hide #!1 models

> molmap #4

Missing or invalid "resolution" argument: Expected a number  

> molmap #4 4

Opened map 4 as #5, grid size 108,91,113, pixel 1.33, shown at level 0.107,
step 1, values float32  

> volume #5 color #00aa7f

> save X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/molmap_4A.mrc
> models #5

> volume resample #5 onGrid #2

Opened molmap_4A.mrc resampled as #6, grid size 448,448,448, pixel 0.731,
shown at step 1, values float32  

> volume #6 color #00aa7f

> volume #5 color #ffaaff

> save X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/molmap_rs.mrc
> models #6

> save X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/240530.cxs
> includeMaps true

——— End of log from Tue Apr 30 09:49:52 2024 ———

opened ChimeraX session  

> hide #!6 models

> hide #!2 models

> color #4 #00aa7f models transparency 0

> open
> X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/cryosparc_P68_J1089_map_sharp.mrc
> X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/cryosparc_P68_J1090_map_sharp.mrc

Opened cryosparc_P68_J1089_map_sharp.mrc as #7.1, grid size 448,448,448, pixel
0.731, shown at level 0.000175, step 2, values float32  
Opened cryosparc_P68_J1090_map_sharp.mrc as #7.2, grid size 448,448,448, pixel
0.731, shown at level 3.98e-05, step 2, values float32  

> volume #7.1 step 1

> volume #7.2 step 1

> hide #!4 models

> volume #7.1 level 0.03974

> volume #7.2 level 0.03426

> volume #7.2 color #ffaaff

> lighting soft

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\jeyasankar\Desktop\movie3.mp4

Movie saved to \C:Users\\...\Desktop\movie3.mp4  
  

> show #!4 models

> ui tool show "Fit in Map"

> fitmap #1 inMap #7.2

Fit molecule 7xgd_fit_to_tmb_map_1.pdb (#1) to map
cryosparc_P68_J1090_map_sharp.mrc (#7.2) using 7880 atoms  
average map value = 0.07775, steps = 172  
shifted from previous position = 1.98  
rotated from previous position = 2.8 degrees  
atoms outside contour = 5457, contour level = 0.034259  
  
Position of 7xgd_fit_to_tmb_map_1.pdb (#1) relative to
cryosparc_P68_J1090_map_sharp.mrc (#7.2) coordinates:  
Matrix rotation and translation  
0.99980766 -0.01656087 0.01050626 2.79376402  
0.01701526 0.99885350 -0.04474552 4.99006302  
-0.00975319 0.04491568 0.99894317 -5.16273657  
Axis 0.91620223 0.20702098 0.34309734  
Axis point 0.00000000 131.20244663 99.73235387  
Rotation angle (degrees) 2.80465400  
Shift along axis 1.82137934  
  

> fitmap #4.1 inMap #7.2

Fit molecule pdb-for-mask.pdb (#4.1) to map cryosparc_P68_J1090_map_sharp.mrc
(#7.2) using 7880 atoms  
average map value = 0.07775, steps = 172  
shifted from previous position = 1.98  
rotated from previous position = 2.8 degrees  
atoms outside contour = 5457, contour level = 0.034259  
  
Position of pdb-for-mask.pdb (#4.1) relative to
cryosparc_P68_J1090_map_sharp.mrc (#7.2) coordinates:  
Matrix rotation and translation  
0.99980766 -0.01656087 0.01050626 2.79376402  
0.01701526 0.99885350 -0.04474552 4.99006302  
-0.00975319 0.04491568 0.99894317 -5.16273657  
Axis 0.91620223 0.20702098 0.34309734  
Axis point 0.00000000 131.20244663 99.73235387  
Rotation angle (degrees) 2.80465400  
Shift along axis 1.82137934  
  

> fitmap #4.2 inMap #7.2

Fit molecule pdb-for-mask.pdb (#4.2) to map cryosparc_P68_J1090_map_sharp.mrc
(#7.2) using 5585 atoms  
average map value = 0.07511, steps = 140  
shifted from previous position = 4.64  
rotated from previous position = 3.19 degrees  
atoms outside contour = 3904, contour level = 0.034259  
  
Position of pdb-for-mask.pdb (#4.2) relative to
cryosparc_P68_J1090_map_sharp.mrc (#7.2) coordinates:  
Matrix rotation and translation  
0.99851361 0.03293892 0.04342340 -9.46125373  
-0.03344317 0.99938077 0.01093739 4.65428868  
-0.04303624 -0.01237335 0.99899689 8.74390562  
Axis -0.20912394 0.77564145 -0.59552290  
Axis point 203.25571349 0.00000000 223.00425409  
Rotation angle (degrees) 3.19499481  
Shift along axis 0.38143785  
  

> transparency #7.2.1 50

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\jeyasankar\Desktop\movie4.mp4

Movie saved to \C:Users\\...\Desktop\movie4.mp4  
  

> save X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/240502.cxs
> includeMaps true

——— End of log from Thu May 2 09:43:35 2024 ———

opened ChimeraX session  

> open
> X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/cryosparc_P68_J835_008_volume_map_sharp.mrc

Opened cryosparc_P68_J835_008_volume_map_sharp.mrc as #8, grid size
448,448,448, pixel 0.731, shown at level 0.017, step 2, values float32  

> color #8 #55aaff models transparency 0

> volume #8 step 1

> volume #8 level 0.03197

> open
> X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/7xgd_fit_to_tmb_map_1.pdb

7xgd_fit_to_tmb_map_1.pdb title:  
Cryo-em structure of apo-IGF1R map 1 [more info...]  
  
Chain information for 7xgd_fit_to_tmb_map_1.pdb #9  
---  
Chain | Description | UniProt  
A | insulin-like growth factor 1 receptor | IGF1R_HUMAN  
B | insulin-like growth factor 1 receptor | IGF1R_HUMAN  
  

> transparency #8.1#7.2.1 0

> transparency #8.1#7.2.1 50

> color #9 #ff5500 transparency 0

> select add #9

12748 atoms, 12926 bonds, 2 pseudobonds, 840 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #9,0.21227,0.7324,0.64694,-107.7,0.95667,-0.02072,-0.29045,64.363,-0.19932,0.68056,-0.70506,223.42

> view matrix models
> #9,0.84215,0.056247,0.5363,-79.049,0.19009,-0.96167,-0.19764,335.43,0.50462,0.26839,-0.82056,195.86

> hide #!7 models

> hide #!4 models

> transparency #8.1 0

> ui mousemode right "translate selected models"

> view matrix models
> #9,0.84215,0.056247,0.5363,-66.963,0.19009,-0.96167,-0.19764,342.56,0.50462,0.26839,-0.82056,152.48

> show #!4 models

> view matrix models
> #9,0.84215,0.056247,0.5363,-60.635,0.19009,-0.96167,-0.19764,345.45,0.50462,0.26839,-0.82056,135.08

> view matrix models
> #9,0.84215,0.056247,0.5363,-62.734,0.19009,-0.96167,-0.19764,332.02,0.50462,0.26839,-0.82056,137.33

> ui mousemode right "rotate selected models"

> view matrix models
> #9,0.19271,0.099039,0.97625,-39.877,0.16069,-0.98465,0.068173,293.26,0.96801,0.14373,-0.20566,-29.287

> view matrix models
> #9,0.51915,-0.11124,0.84741,-35.948,0.12401,-0.9712,-0.20346,345.75,0.84564,0.21071,-0.49041,30.85

> ui tool show "Fit in Map"

> fitmap #9 inMap #8

Fit molecule 7xgd_fit_to_tmb_map_1.pdb (#9) to map
cryosparc_P68_J835_008_volume_map_sharp.mrc (#8) using 12748 atoms  
average map value = 0.01561, steps = 116  
shifted from previous position = 1.96  
rotated from previous position = 4.31 degrees  
atoms outside contour = 10298, contour level = 0.031973  
  
Position of 7xgd_fit_to_tmb_map_1.pdb (#9) relative to
cryosparc_P68_J835_008_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
0.57863625 -0.08897674 0.81071769 -43.95662777  
0.11464932 -0.97528693 -0.18886734 343.78351446  
0.80748720 0.20223372 -0.55413526 49.75389094  
Axis 0.88695756 0.00732626 0.46179283  
Axis point 0.00000000 168.55088291 57.95605197  
Rotation angle (degrees) 167.26316127  
Shift along axis -13.49302488  
  

> transparency #8.1 50

> select subtract #9

Nothing selected  

> select add #9

12748 atoms, 12926 bonds, 2 pseudobonds, 840 residues, 2 models selected  

> view matrix models
> #9,0.58673,0.11347,0.8018,-77.968,0.2256,-0.97384,-0.027274,296.02,0.77773,0.19689,-0.59697,63.313

> ui mousemode right "translate selected models"

> view matrix models
> #9,0.58673,0.11347,0.8018,-73.106,0.2256,-0.97384,-0.027274,289.58,0.77773,0.19689,-0.59697,73.51

> fitmap #9 inMap #8

Fit molecule 7xgd_fit_to_tmb_map_1.pdb (#9) to map
cryosparc_P68_J835_008_volume_map_sharp.mrc (#8) using 12748 atoms  
average map value = 0.01566, steps = 156  
shifted from previous position = 12.6  
rotated from previous position = 9.1 degrees  
atoms outside contour = 10145, contour level = 0.031973  
  
Position of 7xgd_fit_to_tmb_map_1.pdb (#9) relative to
cryosparc_P68_J835_008_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
0.62966375 -0.03131144 0.77623649 -55.70116899  
0.10132242 -0.98734265 -0.12201715 336.09863864  
0.77023196 0.15547994 -0.61852134 75.99878929  
Axis 0.90206627 0.01951907 0.43115595  
Axis point 0.00000000 165.19103922 65.73299054  
Rotation angle (degrees) 171.15210163  
Shift along axis -10.91848161  
  

> select subtract #9

Nothing selected  

> color #8 #55aa0080 models

> color #8 #00aa7f80 models

> open
> X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/cryosparc_P68_J974_map_sharp.mrc

Opened cryosparc_P68_J974_map_sharp.mrc as #10, grid size 360,360,360, pixel
0.914, shown at level 0.000137, step 2, values float32  

> color #10 #00aa7f models transparency 0

> volume #10 step 1

> volume #10 level 0.04839

> hide #!8 models

> select add #4

13465 atoms, 13723 bonds, 4 pseudobonds, 1232 residues, 5 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.087885,0.98981,0.11201,-6.8316,-0.37434,-0.13702,0.91711,73.054,0.92312,0.038673,0.38257,-37.125

> view matrix models
> #4,-0.065857,0.15147,-0.98627,338.56,0.72952,0.68166,0.055978,-77.684,0.68078,-0.71581,-0.15539,230.27

> volume flip #10

Opened cryosparc_P68_J974_map_sharp.mrc z flip as #11, grid size 360,360,360,
pixel 0.914, shown at step 1, values float32  

> view matrix models
> #4,0.31094,0.88877,0.33674,-101,0.065142,0.33354,-0.94048,277.95,-0.94819,0.31437,0.045816,282.59

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.31094,0.88877,0.33674,-95.773,0.065142,0.33354,-0.94048,240.38,-0.94819,0.31437,0.045816,271.25

> view matrix models
> #4,0.31094,0.88877,0.33674,-97.638,0.065142,0.33354,-0.94048,236.23,-0.94819,0.31437,0.045816,268.26

> fitmap #4.1 inMap #11

Fit molecule pdb-for-mask.pdb (#4.1) to map cryosparc_P68_J974_map_sharp.mrc z
flip (#11) using 7880 atoms  
average map value = 0.05451, steps = 360  
shifted from previous position = 8.74  
rotated from previous position = 26.8 degrees  
atoms outside contour = 6276, contour level = 0.048391  
  
Position of pdb-for-mask.pdb (#4.1) relative to
cryosparc_P68_J974_map_sharp.mrc z flip (#11) coordinates:  
Matrix rotation and translation  
0.89900357 0.42085130 0.12114770 -74.04776112  
-0.41717643 0.90712941 -0.05549831 84.49662589  
-0.13325317 -0.00064679 0.99108182 26.49571510  
Axis 0.06250834 0.28991313 -0.95500947  
Axis point 158.84612695 213.26032200 0.00000000  
Rotation angle (degrees) 26.02438437  
Shift along axis -5.43558053  
  

> fitmap #4.2 inMap #11

Fit molecule pdb-for-mask.pdb (#4.2) to map cryosparc_P68_J974_map_sharp.mrc z
flip (#11) using 5585 atoms  
average map value = 0.04511, steps = 168  
shifted from previous position = 5.01  
rotated from previous position = 6.91 degrees  
atoms outside contour = 4571, contour level = 0.048391  
  
Position of pdb-for-mask.pdb (#4.2) relative to
cryosparc_P68_J974_map_sharp.mrc z flip (#11) coordinates:  
Matrix rotation and translation  
0.99797836 -0.02306791 -0.05922047 22.41017825  
0.02199149 0.99958205 -0.01876440 3.93477093  
0.05962857 0.01742412 0.99806855 -15.21993725  
Axis 0.27383306 -0.89931270 0.34095765  
Axis point 252.79471662 0.00000000 381.77174712  
Rotation angle (degrees) 3.78873407  
Shift along axis -2.59129575  
  

> select add #9

26213 atoms, 26649 bonds, 6 pseudobonds, 2072 residues, 7 models selected  

> select subtract #4

12748 atoms, 12926 bonds, 2 pseudobonds, 840 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #9,0.064284,-0.89945,0.43228,247.49,-0.42988,0.36597,0.82539,26.579,-0.9006,-0.23889,-0.36312,377.02

> ui mousemode right "translate selected models"

> view matrix models
> #9,0.064284,-0.89945,0.43228,229.63,-0.42988,0.36597,0.82539,68.382,-0.9006,-0.23889,-0.36312,409.33

> fitmap #9 inMap #11

Fit molecule 7xgd_fit_to_tmb_map_1.pdb (#9) to map
cryosparc_P68_J974_map_sharp.mrc z flip (#11) using 12748 atoms  
average map value = 0.07069, steps = 200  
shifted from previous position = 13.1  
rotated from previous position = 23.6 degrees  
atoms outside contour = 9251, contour level = 0.048391  
  
Position of 7xgd_fit_to_tmb_map_1.pdb (#9) relative to
cryosparc_P68_J974_map_sharp.mrc z flip (#11) coordinates:  
Matrix rotation and translation  
0.13438194 -0.98804945 0.07549634 297.86449630  
-0.23454726 0.04230749 0.97118360 53.67511157  
-0.96277153 -0.14821699 -0.22605894 386.54904864  
Axis -0.65746805 0.60981560 0.44256151  
Axis point -0.00000000 327.61303334 272.79701682  
Rotation angle (degrees) 121.64702478  
Shift along axis 7.96726087  
  

> select subtract #9

Nothing selected  

> save X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/240503.cxs
> includeMaps true

——— End of log from Fri May 3 11:40:31 2024 ———

opened ChimeraX session  

> show #!3 models

> select add #3

5585 atoms, 5734 bonds, 2 pseudobonds, 715 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.56828,-0.060298,0.82062,20.381,-0.33521,-0.92777,0.16396,361.62,0.75146,-0.36825,-0.54744,206.35

> hide #!11 models

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.31693,-0.39909,0.8604,81.428,-0.22408,-0.91299,-0.34095,402.2,0.9216,-0.084738,-0.37878,137.91

> view matrix models
> #3,0.75651,0.64327,-0.11792,23.035,0.11037,-0.3033,-0.94648,363.07,-0.6446,0.703,-0.30045,215.86

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.75651,0.64327,-0.11792,40.522,0.11037,-0.3033,-0.94648,369.52,-0.6446,0.703,-0.30045,198.33

> view matrix models
> #3,0.75651,0.64327,-0.11792,45.925,0.11037,-0.3033,-0.94648,356.16,-0.6446,0.703,-0.30045,197.3

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.55893,0.80952,-0.17966,56.094,0.29931,-0.39902,-0.86672,337.19,-0.77331,0.43066,-0.46532,259.5

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.55893,0.80952,-0.17966,56.099,0.29931,-0.39902,-0.86672,336.02,-0.77331,0.43066,-0.46532,257.72

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.56264,0.80849,-0.17255,55.032,0.32864,-0.41027,-0.85069,332.28,-0.75857,0.42193,-0.49654,260.43

> view matrix models
> #3,0.27843,0.96042,0.008604,50.154,0.47547,-0.13005,-0.87007,287.1,-0.83451,0.24634,-0.49286,287.87

> view matrix models
> #3,0.55896,0.82677,-0.063323,41.621,0.52926,-0.41452,-0.74031,298.6,-0.63831,0.38029,-0.66928,270.36

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.55896,0.82677,-0.063323,38.791,0.52926,-0.41452,-0.74031,294.29,-0.63831,0.38029,-0.66928,276.81

> select subtract #3

Nothing selected  

> select add #3

5585 atoms, 5734 bonds, 2 pseudobonds, 715 residues, 2 models selected  

> view matrix models
> #3,0.55896,0.82677,-0.063323,39.208,0.52926,-0.41452,-0.74031,294.64,-0.63831,0.38029,-0.66928,277.71

> select subtract #3

Nothing selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #4.1/A #9/A

Alignment identifier is 1  

> hide #!9 models

> show #!9 models

> ui tool show "Show Sequence Viewer"

> sequence chain #1/B #9/B

Alignment identifier is 1  

> ui tool show "Show Sequence Viewer"

> sequence chain #4.1/B

Alignment identifier is 4.1/B  

> select #9/B:1

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

> select #9/B:1-323

4868 atoms, 4936 bonds, 323 residues, 1 model selected  

> select #9/B:310

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #9/B:1-310

4688 atoms, 4755 bonds, 310 residues, 1 model selected  

> select #9/B:302

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

> select #9/B:1-302

4549 atoms, 4616 bonds, 302 residues, 1 model selected  

> select #9/B:1

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

> select #9/B:1-323

4868 atoms, 4936 bonds, 323 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> show #!11 models

> save
> X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/cryosparc_P68_J974_map_sharp_flipped.mrc
> models #11

> select add #9

7880 atoms, 7989 bonds, 2 pseudobonds, 517 residues, 2 models selected  

> select add #4

21345 atoms, 21712 bonds, 6 pseudobonds, 1749 residues, 7 models selected  

> select add #3

26930 atoms, 27446 bonds, 8 pseudobonds, 2464 residues, 9 models selected  

> save X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/pdb-for-mask-
> both-monomers.pdb models #3-4,9 selectedOnly true relModel #11

> open X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/pdb-for-mask-
> both-monomers.pdb

Summary of feedback from opening
X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/pdb-for-mask-both-
monomers.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLN A 44
LEU A 49 1 6  
Start residue of secondary structure not found: HELIX 2 2 LEU A 96 LEU A 99 1
4  
Start residue of secondary structure not found: HELIX 3 3 TRP A 157 LEU A 159
1 3  
Start residue of secondary structure not found: HELIX 4 4 ARG A 279 ALA A 283
1 5  
Start residue of secondary structure not found: HELIX 5 5 PHE H 29 SER H 31 1
3  
115 messages similar to the above omitted  
  
pdb-for-mask-both-monomers.pdb title:  
Human IGF1R NTD bound to TMB fab [more info...]  
  
Chain information for pdb-for-mask-both-monomers.pdb  
---  
Chain | Description  
12.1/A 12.3/A | No description available  
12.2/A 12.4/A | No description available  
12.2/B 12.4/B | No description available  
12.1/H 12.3/H | No description available  
12.1/L 12.3/L | No description available  
  

> select subtract #3

21345 atoms, 21712 bonds, 6 pseudobonds, 1749 residues, 7 models selected  

> select subtract #4

7880 atoms, 7989 bonds, 2 pseudobonds, 517 residues, 2 models selected  

> select subtract #9

Nothing selected  

> hide #!9 models

> hide #!4.2 models

> hide #!4.1 models

> hide #!4 models

> hide #!3 models

> save X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/240506.cxs
> includeMaps true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save  
fserialize(stream, data)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\safesave.py", line 136, in write  
self._f.write(buf)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\lz4\frame\\__init__.py", line 718, in write  
compressed = self._compressor.compress(data)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
MemoryError  
  
MemoryError  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 165, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider  
providers.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 45, in run_provider  
what(session)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save  
fserialize(stream, data)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\safesave.py", line 136, in write  
self._f.write(buf)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\lz4\frame\\__init__.py", line 718, in write  
compressed = self._compressor.compress(data)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
MemoryError  
  
MemoryError  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
  
See log for complete Python traceback.  
  

> save X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/240506.cxs
> includeMaps true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save  
fserialize(stream, data)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 165, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider  
providers.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 45, in run_provider  
what(session)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save  
fserialize(stream, data)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  

> save X:/gayathri/22-VRA-002_23-VRA-008/FL_IGF1R_TMBFab/Latest/240506.cxs

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save  
fserialize(stream, data)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\safesave.py", line 136, in write  
self._f.write(buf)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\lz4\frame\\__init__.py", line 718, in write  
compressed = self._compressor.compress(data)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
MemoryError  
  
MemoryError  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 165, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider  
providers.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 45, in run_provider  
what(session)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save  
fserialize(stream, data)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\safesave.py", line 136, in write  
self._f.write(buf)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\lz4\frame\\__init__.py", line 718, in write  
compressed = self._compressor.compress(data)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
MemoryError  
  
MemoryError  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.4953
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_GB.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: LENOVO
Model: 20TD00GNGE
OS: Microsoft Windows 11 Enterprise (Build 22631)
Memory: 8,277,577,728
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz
OSLanguage: de-DE

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