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Opened 4 years ago
Closed 4 years ago
#5883 closed defect (limitation)
MemoryError saving map in session
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19042
ChimeraX Version: 1.3.dev202109140730 (2021-09-14 07:30:30 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3.dev202109140730 (2021-09-14)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/SF_Localres_filtered.mrc
> F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/SG_Localres_filtered.mrc
> F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/SH_Localres_filtered.mrc
Opened SF_Localres_filtered.mrc as #1.1, grid size 448,448,448, pixel 1.33,
shown at level 0.0323, step 2, values float32
Opened SG_Localres_filtered.mrc as #1.2, grid size 448,448,448, pixel 1.33,
shown at level 0.0341, step 2, values float32
Opened SH_Localres_filtered.mrc as #1.3, grid size 448,448,448, pixel 1.33,
shown at level 0.0338, step 2, values float32
> volume #1.1 level 0.01573
> volume #1.2 level 0.01299
> volume #1.3 level 0.01856
> volume #1.1 level 0.01149
> close #1
> open F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/K420A-SF-07-refined-
> align.pdb
Summary of feedback from opening
F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/K420A-SF-07-refined-align.pdb
---
warnings | Ignored bad PDB record found on line 20
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 21
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 22
BOND : 0.009 2.636 224391
Ignored bad PDB record found on line 23
ANGLE : 1.054 19.023 312585
Ignored bad PDB record found on line 24
CHIRALITY : 0.057 0.489 37384
16 messages similar to the above omitted
Chain information for K420A-SF-07-refined-align.pdb #1
---
Chain | Description
3A | No description available
3B | No description available
3C | No description available
3D | No description available
3E | No description available
3F | No description available
3G 3H | No description available
5A | No description available
5B | No description available
5C | No description available
5D | No description available
5E | No description available
5F | No description available
5G | No description available
5H | No description available
5I | No description available
5J | No description available
5K | No description available
A4 | No description available
A5 | No description available
A8 | No description available
A9 | No description available
AE | No description available
AF | No description available
AG | No description available
B1 | No description available
B2 | No description available
B3 | No description available
B6 | No description available
B8 | No description available
BE | No description available
RD | No description available
RE | No description available
RF | No description available
RG | No description available
RH | No description available
RJ | No description available
RK | No description available
RN | No description available
RO | No description available
RP | No description available
RQ | No description available
RS | No description available
RT | No description available
RW | No description available
SA | No description available
SC | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SM | No description available
SO | No description available
SP | No description available
SR | No description available
ST | No description available
SU | No description available
SX | No description available
SY | No description available
SZ | No description available
Sc | No description available
Sd | No description available
X1 | No description available
X2 | No description available
> open F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/K420A-SG-07-refined-
> align.pdb
Summary of feedback from opening
F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/K420A-SG-07-refined-align.pdb
---
warnings | Ignored bad PDB record found on line 20
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 21
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 22
BOND : 0.007 0.139 229760
Ignored bad PDB record found on line 23
ANGLE : 1.019 16.616 319746
Ignored bad PDB record found on line 24
CHIRALITY : 0.058 0.451 38145
16 messages similar to the above omitted
Chain information for K420A-SG-07-refined-align.pdb #2
---
Chain | Description
3A | No description available
3B | No description available
3C | No description available
3D | No description available
3E | No description available
3F | No description available
3G 3H | No description available
5A | No description available
5B | No description available
5C | No description available
5D | No description available
5E | No description available
5F | No description available
5G | No description available
5H | No description available
5I | No description available
5J | No description available
5K | No description available
A4 | No description available
A5 | No description available
A8 | No description available
A9 | No description available
AE | No description available
AF | No description available
AG | No description available
B1 | No description available
B2 | No description available
B3 | No description available
B6 | No description available
B8 | No description available
BE | No description available
RD | No description available
RE | No description available
RF | No description available
RG | No description available
RH | No description available
RJ | No description available
RK | No description available
RN | No description available
RO | No description available
RP | No description available
RQ | No description available
RS | No description available
RT | No description available
RW | No description available
SA | No description available
SC | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SM | No description available
SO | No description available
SP | No description available
SR | No description available
ST | No description available
SU | No description available
SX | No description available
SY | No description available
SZ | No description available
Sc | No description available
Sd | No description available
X1 | No description available
X2 | No description available
> open F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/K420A-SH-07-refined-
> align.pdb
Summary of feedback from opening
F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/K420A-SH-07-refined-align.pdb
---
warnings | Ignored bad PDB record found on line 20
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 21
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 22
BOND : 0.011 0.214 231980
Ignored bad PDB record found on line 23
ANGLE : 1.146 17.704 322748
Ignored bad PDB record found on line 24
CHIRALITY : 0.064 0.607 38488
16 messages similar to the above omitted
Chain information for K420A-SH-07-refined-align.pdb #3
---
Chain | Description
3A | No description available
3B | No description available
3C | No description available
3D | No description available
3E | No description available
3F | No description available
3G 3H | No description available
5A | No description available
5B | No description available
5C | No description available
5D | No description available
5E | No description available
5F | No description available
5G | No description available
5H | No description available
5I | No description available
5J | No description available
5K | No description available
A4 | No description available
A5 | No description available
A8 | No description available
A9 | No description available
AE | No description available
AF | No description available
AG | No description available
B1 | No description available
B2 | No description available
B3 | No description available
B6 | No description available
B8 | No description available
BE | No description available
RD | No description available
RE | No description available
RF | No description available
RG | No description available
RH | No description available
RJ | No description available
RK | No description available
RN | No description available
RO | No description available
RP | No description available
RQ | No description available
RS | No description available
RT | No description available
RU | No description available
RW | No description available
SA | No description available
SC | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SM | No description available
SO | No description available
SP | No description available
SR | No description available
ST | No description available
SU | No description available
SX | No description available
SY | No description available
SZ | No description available
Sc | No description available
Sd | No description available
X1 | No description available
X2 | No description available
> open F:/data/paper/Dhr1_K420A_paper/K420A/postprocess_mrc/GH-SG.mrc
> F:/data/paper/Dhr1_K420A_paper/K420A/postprocess_mrc/GH-SH.mrc
> F:/data/paper/Dhr1_K420A_paper/K420A/postprocess_mrc/SI-A1cleaved.mrc
Opened GH-SG.mrc as #4.1, grid size 448,448,448, pixel 1.33, shown at level
0.0194, step 2, values float32
Opened GH-SH.mrc as #4.2, grid size 448,448,448, pixel 1.33, shown at level
0.0207, step 2, values float32
Opened SI-A1cleaved.mrc as #4.3, grid size 448,448,448, pixel 1.33, shown at
level 0.0207, step 2, values float32
> select #1
216553 atoms, 224395 bonds, 191 pseudobonds, 24724 residues, 3 models selected
> select #2
221784 atoms, 229760 bonds, 173 pseudobonds, 25192 residues, 3 models selected
> select #1
216553 atoms, 224395 bonds, 191 pseudobonds, 24724 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> select #2
221784 atoms, 229760 bonds, 173 pseudobonds, 25192 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> select #3
223963 atoms, 231980 bonds, 174 pseudobonds, 25464 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> hide #!4.3 models
> hide #!4.2 models
> hide #!4.1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> select #1
216553 atoms, 224395 bonds, 191 pseudobonds, 24724 residues, 3 models selected
> color #1 #f5f2f1
> select clear
> ui tool show "Color Actions"
> set bgColor white
> select #1 /SA :1-608 :609-1144
22054 atoms, 24663 bonds, 10 pseudobonds, 1035 residues, 2 models selected
> color #1 /SA :1-608 forest green color #1 /SA :609-1144 gold
Invalid "color" argument: Expected a color or one of 'byatom', 'bychain',
'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer',
'fromatoms', or 'random'
> color #1 /SA :1-608 forest green
> color #1 /SA :609-1144 gold
> show #!4.1 models
> hide #!4.1 models
> color #4.1 #bb22bb models
> color #4.1 #ff55ff models
> color #4.1 #f5f2f1 models
> select #2
221784 atoms, 229760 bonds, 173 pseudobonds, 25192 residues, 3 models selected
> show #!2 models
> color #4.1 #f5f1ef models
> color #4.1 #f5f3ef models
> color #4.1 #b5b5b5 models
> color #2 #f5e9dd
> color #2 #f5efea
> color #2 #f5f0e9
> color #2 #ff55ff
> color #2 #f5f2f1
> select #3
223963 atoms, 231980 bonds, 174 pseudobonds, 25464 residues, 3 models selected
> show #!3 models
> color #2 #f5f0ee
> color #2 #f5f1ea
> color #2 #f5efec
> color #2 #ff55ee
> color #2 #ff55ff
> color #2 #f5f2f1
> color #1 /SA :609-1144 gold
> color #3 #f5f0ec
> color #3 #ff55ff
> color #3 #f5f2f1
> select clear
> color #1 /SA :1-608 forest green
> color #1 /SA :609-1144 gold
> color #2 /SA :1-608 forest green
> color #2 /SA :609-1144 gold
> color #3 /SA :1-608 forest green
> color #3 /SA :609-1144 gold
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> select #1 /SA :1-608:609-1144
22054 atoms, 24663 bonds, 10 pseudobonds, 1035 residues, 2 models selected
> show #!1 models
> hide #!2 models
> close #4.3
> open F:/data/paper/Dhr1_K420A_paper/K420A/postprocess_mrc/SF.mrc
Opened SF.mrc as #5, grid size 448,448,448, pixel 1.33, shown at level 0.0181,
step 2, values float32
> volume #5 level 0.01157
> volume #5 level 0.009273
> hide #!4.1 models
> hide #!4 models
> ui tool show "Surface Color"
> ui tool show "Color Zone"
> color zone #5 near sel distance 8
> color zone #5 near sel distance 10
[Repeated 1 time(s)]
> volume splitbyzone #5
Opened SF.mrc 0 as #6.1, grid size 448,448,448, pixel 1.33, shown at level
0.00927, step 1, values float32
Opened SF.mrc 1 as #6.2, grid size 448,448,448, pixel 1.33, shown at level
0.00927, step 1, values float32
Opened SF.mrc 2 as #6.3, grid size 448,448,448, pixel 1.33, shown at level
0.00927, step 1, values float32
> hide #!6 models
> show #!6 models
> hide #!6.1 models
> hide #!6.3 models
> show #!6.3 models
> hide #!6.2 models
> show #!6.2 models
> hide #!1 models
> show #!6.1 models
> hide #!6.1 models
> hide #!6.2 models
> color zone #5 near sel distance 18
> color zone #5 near sel distance 8
> show #!5 models
> color zone #5 near sel distance 5
> volume splitbyzone #5
Opened SF.mrc 0 as #7.1, grid size 448,448,448, pixel 1.33, shown at level
0.00927, step 1, values float32
Opened SF.mrc 1 as #7.2, grid size 448,448,448, pixel 1.33, shown at level
0.00927, step 1, values float32
Opened SF.mrc 2 as #7.3, grid size 448,448,448, pixel 1.33, shown at level
0.00927, step 1, values float32
> hide #!7.1 models
> hide #!7.2 models
> show #!7.2 models
> hide #!7.3 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!7.2 models
> hide #!6.3 models
> show #!7.2 models
> show #!7.3 models
> show #!1 models
> hide #!1 models
> hide #!6 models
> show #!2 models
> hide #!7.2 models
> hide #!7.3 models
> hide #!7 models
> show #!4.1 models
> select #2 /SA :1-608:609-1144
23117 atoms, 25848 bonds, 12 pseudobonds, 1085 residues, 2 models selected
> volume #4.1 level 0.0091
> color zone #4.1 near sel distance 5
> volume splitbyzone #4.1
Opened GH-SG.mrc 0 as #8.1, grid size 448,448,448, pixel 1.33, shown at level
0.0091, step 1, values float32
Opened GH-SG.mrc 1 as #8.2, grid size 448,448,448, pixel 1.33, shown at level
0.0091, step 1, values float32
Opened GH-SG.mrc 2 as #8.3, grid size 448,448,448, pixel 1.33, shown at level
0.0091, step 1, values float32
> hide #!8.1 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!7.2 models
> show #!7.3 models
> hide #!7.2 models
> show #!7.2 models
> hide #!7.2 models
> show #!7.2 models
> hide #!7.2 models
> show #!7.2 models
> hide #!7.2 models
> show #!7.2 models
> hide #!7.2 models
> show #!7.2 models
> hide #!7.2 models
> show #!7.2 models
> hide #!7.2 models
> show #!7.2 models
> hide #!7.3 models
> show #!7.3 models
> hide #!7.3 models
> show #!7.3 models
> hide #!7.3 models
> show #!7.3 models
> hide #!7.3 models
> show #!7.3 models
> hide #!7.3 models
> show #!7.3 models
> hide #!7.3 models
> show #!7.3 models
> hide #!7.3 models
> show #!7.3 models
> hide #!7.3 models
> show #!7.3 models
> hide #!7.3 models
> show #!7.3 models
> hide #!7.3 models
> show #!7.3 models
> hide #!7.3 models
> show #!7.3 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!8.1 models
> hide #!8.1 models
> hide #!7.2 models
> show #!7.2 models
> hide #!7.2 models
> show #!7.2 models
> hide #!7.2 models
> hide #!7.3 models
> show #!7.3 models
> show #!7.2 models
> hide #!8.2 models
> hide #!8.3 models
> show #!8.2 models
> hide #!8.2 models
> show #!8.2 models
> hide #!8.2 models
> show #!8.2 models
> hide #!8.2 models
> show #!8.2 models
> hide #!8.2 models
> show #!8.2 models
> hide #!8.2 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select #3/RU
2179 atoms, 2220 bonds, 1 pseudobond, 272 residues, 2 models selected
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!7.3 models
> show #!7.3 models
> hide #!7.3 models
> show #!7.3 models
> hide #!7.3 models
> show #!7.3 models
> hide #!7.3 models
> show #!7.3 models
> hide #!7.3 models
> show #!8.1 models
> hide #!8.1 models
> show #!8.3 models
> hide #!8.3 models
> show #!8.3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> open F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/K420A-SI-07-refined-
> align.pdb
Summary of feedback from opening
F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/K420A-SI-07-refined-align.pdb
---
warnings | Ignored bad PDB record found on line 20
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 21
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 22
BOND : 0.009 0.207 239586
Ignored bad PDB record found on line 23
ANGLE : 1.093 18.055 333032
Ignored bad PDB record found on line 24
CHIRALITY : 0.061 0.815 39672
16 messages similar to the above omitted
End residue of secondary structure not found: HELIX 15 15 ALASF 247 ALASF 255
1 9
Chain information for K420A-SI-07-refined-align.pdb #9
---
Chain | Description
3A | No description available
3B | No description available
3C | No description available
3D | No description available
3E | No description available
3F | No description available
3G 3H | No description available
5A | No description available
5B | No description available
5C | No description available
5D | No description available
5E | No description available
5F | No description available
5G | No description available
5H | No description available
5I | No description available
5J | No description available
5K | No description available
A4 | No description available
A5 | No description available
A8 | No description available
A9 | No description available
AE | No description available
AF | No description available
AG | No description available
B1 | No description available
B2 | No description available
B3 | No description available
B6 | No description available
B8 | No description available
BE | No description available
RD | No description available
RE | No description available
RF | No description available
RG | No description available
RH | No description available
RJ | No description available
RK | No description available
RN | No description available
RO | No description available
RP | No description available
RQ | No description available
RS | No description available
RT | No description available
RU | No description available
RW | No description available
RZ | No description available
SA | No description available
SC | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SM | No description available
SO | No description available
SP | No description available
SR | No description available
ST | No description available
SU | No description available
SX | No description available
SY | No description available
SZ | No description available
Sc | No description available
Sd | No description available
X1 | No description available
X2 | No description available
> open F:/data/paper/Dhr1_K420A_paper/K420A/postprocess_mrc/SI-A1cleaved.mrc
Opened SI-A1cleaved.mrc as #10, grid size 448,448,448, pixel 1.33, shown at
level 0.0207, step 2, values float32
> color #10 /SA :1-608 forest green
> color #10 /SA :609-1144 gold
> hide #!10 models
> show #!10 models
> select #10
2 models selected
> hide #!2-3,9 atoms
> show #!2-3,9 cartoons
> hide #!8.3 models
> hide #!8.2 models
> color #9 /SA :609-1144 gold
> color #9 /SA :1-608 forest green
> hide #!7.2 models
> show #!10 models
> color #10 #fffaf8 models
> color #9 #fff7f2
> color #9 #fff7f4
> color #9 #fffcf7
> color #9 white
> color #9 #ff55ff
> color #9 #f5f2f1
> hide #!10 models
> hide #!9 models
> hide #!7 models
> hide #!2 models
> hide #!3 models
> show #!9 models
> color #9 /SA :1-608 forest green
> color #9 /SA :609-1144 gold
> show #!10 models
> color #9 /SA :609-1144 gold color #9 /SA :1-608 forest green
Invalid "color" argument: Expected a color or one of 'byatom', 'bychain',
'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer',
'fromatoms', or 'random'
> color #9 /SA :609-1144 gold color #9 /SA :1-608 forest green
Invalid "color" argument: Expected a color or one of 'byatom', 'bychain',
'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer',
'fromatoms', or 'random'
> color #9 /SA :609-1144 gold color #9 /SA :1-608 forest green
Invalid "color" argument: Expected a color or one of 'byatom', 'bychain',
'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer',
'fromatoms', or 'random'
> color #9 /SA :1-608 forest green
> color #9 /SA :609-1144 gold
No atoms selected for color zoning
> select #9
231406 atoms, 239557 bonds, 184 pseudobonds, 26440 residues, 3 models selected
> hide #!10 models
> color #9 /SA :1-608 forest green
> color #9 /SA :609-1144 gold
> ~select #9
Nothing selected
> color #9 /SA :609-1144 gold
[Repeated 1 time(s)]
> color #9 /SA :1-608 forest green
> color #9 /SA :609-1144 gold
> select #9 /SA :1-608 :609-1144
23252 atoms, 26002 bonds, 11 pseudobonds, 1091 residues, 2 models selected
> color zone #10 near sel distance 8
> show #!10 models
> volume splitbyzone #10
Opened SI-A1cleaved.mrc 0 as #11.1, grid size 448,448,448, pixel 1.33, shown
at level 0.0207, step 1, values float32
Opened SI-A1cleaved.mrc 1 as #11.2, grid size 448,448,448, pixel 1.33, shown
at level 0.0207, step 1, values float32
Opened SI-A1cleaved.mrc 2 as #11.3, grid size 448,448,448, pixel 1.33, shown
at level 0.0207, step 1, values float32
> hide #!11.1 models
> hide #!9 models
> show #!8.2 models
> hide #!8.2 models
> show #!8.2 models
> hide #!8.2 models
> show #!8.2 models
> hide #!8.2 models
> show #!8.2 models
> hide #!8.2 models
> show #!8.2 models
> show #!8.3 models
> hide #!8.3 models
> show #!8.3 models
> hide #!8.3 models
> show #!8.3 models
> hide #!8.3 models
> show #!8.3 models
> hide #!8.3 models
> show #!8.3 models
> hide #!8.3 models
> show #!8.3 models
> hide #!8.3 models
> show #!8.3 models
> hide #!8.2 models
> hide #!8.3 models
> hide #!11.3 models
> hide #!11.2 models
> show #!3 models
> select #3 /SA :11-15 :1139-1144
234 atoms, 260 bonds, 11 residues, 1 model selected
> show #!2 models
> hide #!3 models
> select #2 /SA :11-15 :1139-1144
234 atoms, 260 bonds, 11 residues, 1 model selected
> show #!1 models
> select #1 /SA :11-15 :1139-1144
234 atoms, 260 bonds, 11 residues, 1 model selected
> show #!3 models
> hide #!2 models
> hide #!3 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> open F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/K420A-SM-07-refined-
> align.pdb
Summary of feedback from opening
F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/K420A-SM-07-refined-align.pdb
---
warnings | Ignored bad PDB record found on line 20
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 21
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 22
BOND : 0.012 0.156 95003
Ignored bad PDB record found on line 23
ANGLE : 1.151 20.369 135622
Ignored bad PDB record found on line 24
CHIRALITY : 0.064 0.491 16561
16 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 69 69 ASNST 103 ILEST
119 1 17
Start residue of secondary structure not found: HELIX 109 109 GLYRG 75 METRG
80 1 6
Start residue of secondary structure not found: HELIX 110 110 ASPRG 90 THRRG
98 1 9
Start residue of secondary structure not found: HELIX 111 111 PHERG 134 PHERG
137 1 4
Start residue of secondary structure not found: HELIX 112 112 VALRG 142 LEURG
145 1 4
71 messages similar to the above omitted
Chain information for K420A-SM-07-refined-align.pdb #12
---
Chain | Description
3A | No description available
5E | No description available
5G | No description available
5H | No description available
5K | No description available
RJ | No description available
RK | No description available
RQ | No description available
RT | No description available
RU | No description available
RZ | No description available
SA | No description available
SC | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SM | No description available
SO | No description available
SP | No description available
SR | No description available
ST | No description available
SU | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sc | No description available
Sd | No description available
X1 | No description available
X2 | No description available
> select #12
76905 atoms, 81345 bonds, 28 pseudobonds, 7271 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> color #12 #b5b5b5
> select #12 /SA :11-15 :1139-1144
234 atoms, 260 bonds, 11 residues, 1 model selected
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> hide #!4 models
> hide #!8 models
> show #!8.2 models
> hide #!8.2 models
> hide #!12 models
> show #!11.2 models
> show #!11.3 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select #3/RU
2179 atoms, 2220 bonds, 1 pseudobond, 272 residues, 2 models selected
> hide #!3 models
> show #!3 models
> select #3
223963 atoms, 231980 bonds, 174 pseudobonds, 25464 residues, 3 models selected
> select #2
221784 atoms, 229760 bonds, 173 pseudobonds, 25192 residues, 3 models selected
> select #3
223963 atoms, 231980 bonds, 174 pseudobonds, 25464 residues, 3 models selected
> hide #!1 models
> hide #!3 models
> show #!11.1 models
> hide #!11.3 models
> hide #!11.2 models
> show #!11.3 models
> show #!11.2 models
> select #11.1
2 models selected
> transparency sel 50
> select clear
> hide #!11.1 models
> show #!11.1 models
> hide #!11.1 models
> show #!11.1 models
> hide #!11.2 models
> hide #!11.3 models
> show #!11.2 models
> show #!11.3 models
> hide #!11.3 models
> hide #!11.2 models
> hide #!11.1 models
> show #!8.2 models
> show #!8.3 models
> show #!8.1 models
> show #!11.3 models
> hide #!11.3 models
> show #!11.3 models
> hide #!11.3 models
> show #!11.3 models
> hide #!11.3 models
> show #!11.3 models
> hide #!11.3 models
> show #!11.2 models
> hide #!11.2 models
> hide #!11 models
> show #!11 models
> hide #!8 models
> show #!8 models
> hide #!8.1 models
> show #!8.1 models
> hide #!8.1 models
> show #!8.1 models
> hide #!8.1 models
> show #!8.1 models
> hide #!8.1 models
> show #!8.1 models
> hide #!8.1 models
> show #!8.1 models
> hide #!8.1 models
> show #!8.1 models
> show #!2 models
> hide #!8.1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!8.1 models
> select #8.1
2 models selected
> transparency sel 50
> volume #4.1 level 0.02074
> volume #4.1 level 0.03238
> volume #4.1 level 0.008238
> volume #4.1 level 0.01039
> volume #4.1 level 0.006944
> hide #!8 models
> show #!8 models
> hide #!8.1 models
> show #!8.1 models
> hide #!8.1 models
> show #!8.1 models
> hide #!8.1 models
> show #!8.1 models
> hide #!8.1 models
> save "F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central
> domain/SG_3central.png" width 861 height 657 supersample 3
> transparentBackground true
> show #!8.1 models
> hide #!8.2 models
> hide #!8.3 models
> select clear
> save "F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central
> domain/SG_all.png" width 861 height 657 supersample 3
> save "F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central
> domain/SG_all.png" width 861 height 657 supersample 3 transparentBackground
> true
> hide #!8 models
> hide #!8.1 models
> show #!8.1 models
> transparency #8.1.1 0
> transparency #8.1.1 50
> show #!8.2 models
> show #!8.3 models
> show #!3 models
> volume #!8.1-3 showOutlineBox true
> hide #!8.3 models
> hide #!8.2 models
> hide #!8.1 models
> hide #!8 models
> hide #!3 models
> show #!3 models
> hide #!4.1 models
> show #!4.2 models
> color #4.2 #fffaf8 models
> select #3/RU
2179 atoms, 2220 bonds, 1 pseudobond, 272 residues, 2 models selected
> color (#!3 & sel) cyan
> volume #4.1 level 0.006513
> volume #4.2 level 0.0101
> color #3 /RU cyan
> select #3 /RU/SA:1-608:609-1144
25296 atoms, 28068 bonds, 13 pseudobonds, 1357 residues, 2 models selected
> color zone #4.2 near sel distance 8
> volume splitbyzone #4.2
Opened GH-SH.mrc 0 as #13.1, grid size 448,448,448, pixel 1.33, shown at level
0.0101, step 1, values float32
Opened GH-SH.mrc 1 as #13.2, grid size 448,448,448, pixel 1.33, shown at level
0.0101, step 1, values float32
Opened GH-SH.mrc 2 as #13.3, grid size 448,448,448, pixel 1.33, shown at level
0.0101, step 1, values float32
Opened GH-SH.mrc 3 as #13.4, grid size 448,448,448, pixel 1.33, shown at level
0.0101, step 1, values float32
> hide #!13.1 models
> show #!13.1 models
> hide #!13.1 models
> show #!13.1 models
> hide #!13.1 models
> hide #!3 models
> show #!13.1 models
> select #13.1
2 models selected
> transparency sel 50
> hide #!13.4 models
> hide #!13.3 models
> hide #!13.2 models
> select clear
> save "F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central
> domain/SH_all.png" width 861 height 657 supersample 3
> hide #!13.1 models
> show #!13.2 models
> show #!13.3 models
> show #!13.4 models
> save "F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central
> domain/SH_3central.png" width 861 height 657 supersample 3
> show #!11.1 models
> hide #!11.1 models
> show #!9 models
> hide #!13.2 models
> hide #!13.3 models
> hide #!13.4 models
> hide #!13 models
> hide #!9 models
> show #!9 models
> color #9 /RU cyan /RZ red
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #9 /RU cyan
> color #9 /RZ red
> undo
> color #9 /RZ:90-136 red
> show #!10 models
> volume #11.1 level 0.01579
> volume #10 level 0.007355
> volume #10 level 0.01329
> volume #10 level 0.009828
No atoms selected for color zoning
> select #9 /RZ:90-136/SA:1-608:609-1144/RU
25868 atoms, 28663 bonds, 11 pseudobonds, 1421 residues, 2 models selected
> color zone #10 near sel distance 8
> volume splitbyzone #10
Opened SI-A1cleaved.mrc 0 as #14.1, grid size 448,448,448, pixel 1.33, shown
at level 0.00983, step 1, values float32
Opened SI-A1cleaved.mrc 1 as #14.2, grid size 448,448,448, pixel 1.33, shown
at level 0.00983, step 1, values float32
Opened SI-A1cleaved.mrc 2 as #14.3, grid size 448,448,448, pixel 1.33, shown
at level 0.00983, step 1, values float32
Opened SI-A1cleaved.mrc 3 as #14.4, grid size 448,448,448, pixel 1.33, shown
at level 0.00983, step 1, values float32
Opened SI-A1cleaved.mrc 4 as #14.5, grid size 448,448,448, pixel 1.33, shown
at level 0.00983, step 1, values float32
> hide #!14.2 models
> show #!14.2 models
> select #14.1
2 models selected
> transparency sel 50
> select clear
> hide #!14.1 models
> hide #!9 models
> save "F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central
> domain/SI_3central.png" width 861 height 657 supersample 3
> transparentBackground true
> hide #!14.5 models
> hide #!14.4 models
> hide #!14.3 models
> hide #!14.2 models
> show #!14.1 models
> save "F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central
> domain/SI_all.png" width 861 height 657 supersample 3 transparentBackground
> true
> hide #!14.1 models
> hide #!14 models
> hide #!11 models
> show #!8.1 models
> transparency #8.1.1 0
> transparency #8.1.1 50
> save "F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central
> domain/SH_allv1.png" width 861 height 657 supersample 3
> hide #!8.1 models
> show #!8.2 models
> show #!8.3 models
> save "F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central
> domain/SHv1_3central.png" width 861 height 657 supersample 3
> save "F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central
> domain/SHv1_3central.png" width 861 height 657 supersample 3
> transparentBackground true
> hide #!8.2 models
> hide #!8.3 models
> show #!8.1 models
> save "F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central
> domain/SH_allv1.png" width 861 height 657 supersample 3
> transparentBackground true
> hide #!8 models
> hide #!8.1 models
> show #!13.2 models
> show #!13.3 models
> show #!13.4 models
> save "F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central
> domain/SHv1_3central.png" width 861 height 657 supersample 3
> show #!13.1 models
> hide #!13.2 models
> hide #!13.3 models
> hide #!13.4 models
> transparency #13.1.1 0
> transparency #13.1.1 50
> save "F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central
> domain/SH_allv1.png" width 861 height 657 supersample 3
> transparentBackground true
> hide #!13.1 models
> show #!13.2 models
> show #!13.3 models
> show #!13.4 models
> save "F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central
> domain/SHv1_3central.png" width 861 height 657 supersample 3
> save "F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central
> domain/SH_3central.png" width 861 height 657 supersample 3
> transparentBackground true
> hide #!13.4 models
> hide #!13.3 models
> hide #!13.2 models
> show #!13.1 models
> save "F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central
> domain/SH_allv1.png" width 861 height 657 supersample 3
> transparentBackground true
> hide #!13.1 models
> show #!13.2 models
> show #!13.3 models
> show #!13.4 models
> save "F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central
> domain/SHv1_3central.png" width 861 height 657 supersample 3
> transparentBackground true
> show #!3 models
> hide #!13.2 models
> hide #!13.3 models
> hide #!13.4 models
> save F:/data/paper/Dhr1_K420A_paper/awd_figure/fig3_5centrapmap.cxs
Traceback (most recent call last):
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "D:\program\ChimeraX 1.3.dev202109140730\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:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\map\session.py", line 316, in state_from_grid_data
s['array'] = dt.matrix().tobytes()
MemoryError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'models' ->
<chimerax.core.models.Models object at 0x0000020BBCE1CDC0> ->
<chimerax.map.volume.VolumeSurface object at 0x0000020BDA148CD0> 'surface' ->
<chimerax.map.volume.Volume object at 0x0000020BDA159A90> 'SI-A1cleaved.mrc 0'
-> <chimerax.map.session.GridDataState object at 0x0000020C2DE997C0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 882, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 611, in save
mgr.discovery(self._state_containers)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x0000020BBCE1CDC0> -> <chimerax.map.volume.VolumeSurface object at
0x0000020BDA148CD0> 'surface' -> <chimerax.map.volume.Volume object at
0x0000020BDA159A90> 'SI-A1cleaved.mrc 0' ->
<chimerax.map.session.GridDataState object at 0x0000020C2DE997C0>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x0000020BBCE1CDC0> -> <chimerax.map.volume.VolumeSurface object at
0x0000020BDA148CD0> 'surface' -> <chimerax.map.volume.Volume object at
0x0000020BDA159A90> 'SI-A1cleaved.mrc 0' ->
<chimerax.map.session.GridDataState object at 0x0000020C2DE997C0>
ValueError: error processing: 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0'
-> : Error while saving session data for 'models' -> -> 'surface' ->
'SI-A1cleaved.mrc 0' ->
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 262, 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:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "D:\program\ChimeraX 1.3.dev202109140730\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:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\map\session.py", line 316, in state_from_grid_data
s['array'] = dt.matrix().tobytes()
MemoryError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'models' ->
<chimerax.core.models.Models object at 0x0000020BBCE1CDC0> ->
<chimerax.map.volume.VolumeSurface object at 0x0000020BDA148CD0> 'surface' ->
<chimerax.map.volume.Volume object at 0x0000020BDA159A90> 'SI-A1cleaved.mrc 0'
-> <chimerax.map.session.GridDataState object at 0x0000020C2DE997C0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "D:\program\ChimeraX 1.3.dev202109140730\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:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "D:\program\ChimeraX 1.3.dev202109140730\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:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 882, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 611, in save
mgr.discovery(self._state_containers)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x0000020BBCE1CDC0> -> <chimerax.map.volume.VolumeSurface object at
0x0000020BDA148CD0> 'surface' -> <chimerax.map.volume.Volume object at
0x0000020BDA159A90> 'SI-A1cleaved.mrc 0' ->
<chimerax.map.session.GridDataState object at 0x0000020C2DE997C0>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x0000020BBCE1CDC0> -> <chimerax.map.volume.VolumeSurface object at
0x0000020BDA148CD0> 'surface' -> <chimerax.map.volume.Volume object at
0x0000020BDA159A90> 'SI-A1cleaved.mrc 0' ->
<chimerax.map.session.GridDataState object at 0x0000020C2DE997C0>
ValueError: error processing: 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0'
-> : Error while saving session data for 'models' -> -> 'surface' ->
'SI-A1cleaved.mrc 0' ->
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/figmap.cxs
Traceback (most recent call last):
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "D:\program\ChimeraX 1.3.dev202109140730\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:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\map\session.py", line 316, in state_from_grid_data
s['array'] = dt.matrix().tobytes()
MemoryError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'models' ->
<chimerax.core.models.Models object at 0x0000020BBCE1CDC0> ->
<chimerax.map.volume.VolumeSurface object at 0x0000020BDA148CD0> 'surface' ->
<chimerax.map.volume.Volume object at 0x0000020BDA159A90> 'SI-A1cleaved.mrc 0'
-> <chimerax.map.session.GridDataState object at 0x0000020C2F4013A0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 882, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 611, in save
mgr.discovery(self._state_containers)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x0000020BBCE1CDC0> -> <chimerax.map.volume.VolumeSurface object at
0x0000020BDA148CD0> 'surface' -> <chimerax.map.volume.Volume object at
0x0000020BDA159A90> 'SI-A1cleaved.mrc 0' ->
<chimerax.map.session.GridDataState object at 0x0000020C2F4013A0>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x0000020BBCE1CDC0> -> <chimerax.map.volume.VolumeSurface object at
0x0000020BDA148CD0> 'surface' -> <chimerax.map.volume.Volume object at
0x0000020BDA159A90> 'SI-A1cleaved.mrc 0' ->
<chimerax.map.session.GridDataState object at 0x0000020C2F4013A0>
ValueError: error processing: 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0'
-> : Error while saving session data for 'models' -> -> 'surface' ->
'SI-A1cleaved.mrc 0' ->
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 262, 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:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "D:\program\ChimeraX 1.3.dev202109140730\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:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\map\session.py", line 316, in state_from_grid_data
s['array'] = dt.matrix().tobytes()
MemoryError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'models' ->
<chimerax.core.models.Models object at 0x0000020BBCE1CDC0> ->
<chimerax.map.volume.VolumeSurface object at 0x0000020BDA148CD0> 'surface' ->
<chimerax.map.volume.Volume object at 0x0000020BDA159A90> 'SI-A1cleaved.mrc 0'
-> <chimerax.map.session.GridDataState object at 0x0000020C2F4013A0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "D:\program\ChimeraX 1.3.dev202109140730\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:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "D:\program\ChimeraX 1.3.dev202109140730\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:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 882, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 611, in save
mgr.discovery(self._state_containers)
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x0000020BBCE1CDC0> -> <chimerax.map.volume.VolumeSurface object at
0x0000020BDA148CD0> 'surface' -> <chimerax.map.volume.Volume object at
0x0000020BDA159A90> 'SI-A1cleaved.mrc 0' ->
<chimerax.map.session.GridDataState object at 0x0000020C2F4013A0>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x0000020BBCE1CDC0> -> <chimerax.map.volume.VolumeSurface object at
0x0000020BDA148CD0> 'surface' -> <chimerax.map.volume.Volume object at
0x0000020BDA159A90> 'SI-A1cleaved.mrc 0' ->
<chimerax.map.session.GridDataState object at 0x0000020C2F4013A0>
ValueError: error processing: 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0'
-> : Error while saving session data for 'models' -> -> 'surface' ->
'SI-A1cleaved.mrc 0' ->
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 262, 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 461.43
OpenGL renderer: GeForce MX450/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 82NC
OS: Microsoft Windows 10 家庭中文版 (Build 19042)
Memory: 16,952,647,680
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i5-11300H @ 3.10GHz
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.0
chardet: 4.0.0
ChimeraX-AddCharge: 1.1.4
ChimeraX-AddH: 2.1.10
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.29.1
ChimeraX-AtomicLibrary: 4.1.4
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.3
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: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.4.1
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3.dev202109140730
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.1
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.1
ChimeraX-MDcrds: 2.5
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2
ChimeraX-ModelPanel: 1.1.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.12.1
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.10.0
Cython: 0.29.24
decorator: 5.1.0
distlib: 0.3.2
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.4.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.20
imagecodecs: 2021.4.28
imagesize: 1.2.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.7.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.7.3
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.2
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.20
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pywin32: 228
pyzmq: 22.2.1
qtconsole: 5.1.1
QtPy: 1.11.1
RandomWords: 0.3.0
requests: 2.25.1
scipy: 1.7.1
setuptools: 58.0.4
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.1.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.0
urllib3: 1.26.6
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MemoryError saving map in session |
comment:2 by , 4 years ago
| Resolution: | → limitation |
|---|---|
| Status: | assigned → closed |
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Out of memory error saving a session trying to convert to a byte stream some 500 Mbyte maps that were computed by ChimeraX using several calls to "volume splitbyzone" and not saved in separate files. User Windows computer had 16 Gbytes so somewhat surprising that it ran of memory.
Traceback (most recent call last):
File "D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "D:\program\ChimeraX 1.3.dev202109140730\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:\program\ChimeraX 1.3.dev202109140730\bin\lib\site-
packages\chimerax\map\session.py", line 316, in state_from_grid_data
sarray = dt.matrix().tobytes()
MemoryError