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Opened 2 years ago
Closed 2 years ago
#9441 closed defect (not a bug)
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-10-10.0.19045
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> 'J3603_3604_3605_consensus_80s.mrc 6' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> 'J3603_3604_3605_consensus_80s.mrc 6' ->
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Log:
> surface dust #3.1 size 10.7
> surface dust #3.4 size 10.7
> surface dust #3.5 size 10.7
> surface dust #3.6 size 10.7
> surface dust #3.7 size 10.7
> surface dust #3.7 size 30
> surface dust #3.7 size 10
> surface dust #3.1 size 30
> volume #3.1 level 0.05
> volume #3.4 level 0.05
> surface dust #3.1 size 50
> volume #3.1 level 0.04
> save
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/04_cryosparc/mRNA.mrc
> models #3.1
> hide #!3.4 models
> hide #!3.5 models
> hide #!3.6 models
> hide #!3.7 models
> surface dust #3.1 size 10
> surface dust #3.1 size 50
> open pdb:7osm
7osm title:
Intermediate translocation complex of 80 S.cerevisiae ribosome with eEF2 and
ligands [more info...]
Chain information for 7osm #4
---
Chain | Description | UniProt
18S | 18S rRNA |
25S | 25S rRNA |
58S | 5.8S rRNA |
AB | 5S rRNA |
ASIT | PHE tRNA |
PSIT | FMET tRNA |
RACK | BJ4_G0022010.mRNA.1.CDS.1 | A0A6L1BKH8_YEASX
eEF2 | Elongation factor 2 | A0A6A5Q7K2_YEASX
eL13 | 60S ribosomal protein L13 | A0A6L1AF71_YEASX
eL14 | 60S ribosomal protein L14-A | RL14A_YEAST
eL15 | 60S ribosomal protein L15-A | RL15A_YEAST
eL18 | BJ4_G0033900.mRNA.1.CDS.1 | A0A6L1A7F6_YEASX
eL19 | 60S ribosomal protein L19-A | RL19A_YEAST
eL20 | 60S ribosomal protein L20 | A0A6V8RR03_YEASX
eL21 | BJ4_G0003770.mRNA.1.CDS.1 | A0A6L0YTI6_YEASX
eL22 | 60S ribosomal protein L22-A | A0A6L0ZZW6_YEASX
eL24 | 60S ribosomal protein L24-A | A0A6A5PY83_YEASX
eL27 | 60S ribosomal protein L27 | A0A6L0ZQQ7_YEASX
eL29 | 60S ribosomal protein L29 | A0A6A5PWR1_YEASX
eL30 | BJ4_G0020000.mRNA.1.CDS.1 | A0A6L0ZM08_YEASX
eL31 | BJ4_G0008090.mRNA.1.CDS.1 | A0A6L0YFR2_YEASX
eL32 | HN1_G0013350.mRNA.1.CDS.1 | A0A7I9CD28_YEASX
eL33 | BJ4_G0025510.mRNA.1.CDS.1 | A0A6L1C3H0_YEASX
eL34 | 60S ribosomal protein L34-A | A0A6L0ZFW3_YEASX
eL36 | 60S ribosomal protein L36-A | RL36A_YEAST
eL37 | Ribosomal protein L37 | A0A6L1BIE7_YEASX
eL38 | BJ4_G0032190.mRNA.1.CDS.1 | A0A6A5PUL8_YEASX
eL39 | 60S ribosomal protein L39 | A0A6L1ASX0_YEASX
eL40 | Ubiquitin | A0A6V8S9K0_YEASX
eL41 | eL41 |
eL42 | BJ4_G0001880.mRNA.1.CDS.1 | A0A6L1B5X0_YEASX
eL43 | 60S ribosomal protein L43-A | RL43A_YEAST
eL6 | 60S ribosomal protein L6 | A0A6L1BLT3_YEASX
eL8 | 60S ribosomal protein L8-A | RL8A_YEAST
eS1 | 40S ribosomal protein S1 | A0A6A5PRY4_YEASX
eS10 | 40S ribosomal protein S10-A | A0A6L0ZM59_YEASX
eS17 | BJ4_G0020710.mRNA.1.CDS.1 | A0A6L1BLL7_YEASX
eS19 | 40S ribosomal protein S19-A | A0A6L1BWT3_YEASX
eS21 | 40S ribosomal protein S21 | A0A6L1BDN3_YEASX
eS24 | 40S ribosomal protein S24 | A0A6L1AUB6_YEASX
eS25 | 40S ribosomal protein S25 | A0A6A5PZ18_YEASX
eS26 | 40S ribosomal protein S26 | A0A6A5PUG0_YEASX
eS27 | 40S ribosomal protein S27-A | RS27A_YEAST
eS28 | eS28 | A0A6A5Q700_YEASX
eS30 | 40S ribosomal protein S30 | A0A6L1A1E1_YEASX
eS31 | Ubiquitin-40S ribosomal protein S31 | A0A6A5PU37_YEASX
eS4 | 40S ribosomal protein S4 | A0A6L0Z3Q0_YEASX
eS6 | 40S ribosomal protein S6 | A0A6L1AMY1_YEASX
eS7 | 40S ribosomal protein S7 | A0A6L1ACT7_YEASX
eS8 | 40S ribosomal protein S8 | A0A6A5Q1H1_YEASX
mRNA | MRNA |
uL10 | 60S acidic ribosomal protein P0 | A0A6A5PT43_YEASX
uL11 | 60S ribosomal protein L12-B | A0A6A5Q275_YEASX
uL13 | 60S ribosomal protein L16-A | A0A6L0ZD57_YEASX
uL14 | 60S ribosomal protein L23-B | A0A6L0Z7E4_YEASX
uL15 | 60S ribosomal protein L28 | A0A6L0ZDK5_YEASX
uL16 | 60S ribosomal protein L10 | A0A6A5PUZ5_YEASX
uL18 | 60S ribosomal protein L5 | A0A6A5Q0W8_YEASX
uL2 | 60S ribosomal protein L2-B | A0A6L0Y8L2_YEASX
uL22 | BJ4_G0005750.mRNA.1.CDS.1 | A0A6L1BCL1_YEASX
uL23 | 60S ribosomal protein L25 | A0A6L0YSM0_YEASX
uL24 | 60S ribosomal protein L26-A | RL26A_YEAST
uL29 | BJ4_G0044250.mRNA.1.CDS.1 | A0A7I9BRN0_YEASX
uL3 | 60S ribosomal protein L3 | A0A6A5Q627_YEASX
uL30 | 60S ribosomal protein L7-A | A0A6V8RJA7_YEASX
uL4 | BJ4_G0008850.mRNA.1.CDS.1 | A0A6A5Q3W0_YEASX
uL5 | BJ4_G0027750.mRNA.1.CDS.1 | A0A6A5Q7I9_YEASX
uL6 | 60S ribosomal protein L9-A | RL9A_YEAST
uS10 | 40S ribosomal protein S20 | A0A6A5PVE9_YEASX
uS11 | 40S ribosomal protein S14-A | A0A6L1AAG7_YEASX
uS12 | 40S ribosomal protein S23 | A0A6L1B1T2_YEASX
uS13 | 40S ribosomal protein S18-B | A0A6L1AIT6_YEASX
uS14 | HLJ1_G0030400.mRNA.1.CDS.1 | A0A6A5PV92_YEASX
uS15 | 40S ribosomal protein S13 | A0A6L0YFM5_YEASX
uS17 | 40S ribosomal protein S11-B | A0A6L0YMX6_YEASX
uS19 | 40S ribosomal protein S15 | A0A6A5Q6F2_YEASX
uS2 | 40S ribosomal protein S0 | A0A6L0ZRP4_YEASX
uS3 | BJ4_G0045400.mRNA.1.CDS.1 | A0A6L0ZVK6_YEASX
uS4 | BJ4_G0026100.mRNA.1.CDS.1 | A0A7I9GPQ3_YEASX
uS5 | 40S ribosomal protein S2 | A0A6A5PWF7_YEASX
uS7 | Rps5p | A0A1L4AA68_YEASX
uS8 | 40S ribosomal protein S22-A | A0A6A5PSE9_YEASX
uS9 | BJ4_G0008010.mRNA.1.CDS.1 | A0A6L0YQ58_YEASX
Non-standard residues in 7osm #4
---
GTP — guanosine-5'-triphosphate
MG — magnesium ion
ZN — zinc ion
> ui tool show Matchmaker
> matchmaker #!4 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AT-P-E.pdb, chain LB (#2) with 7osm, chain uL3 (#4), sequence
alignment score = 1404.9
RMSD between 376 pruned atom pairs is 0.745 angstroms; (across all 386 pairs:
1.323)
> hide #!4 models
> show #!3.4 models
> show #!3.6 models
> hide #!3.6 models
> hide #!3.4 models
> select #4/mRNA
170 atoms, 188 bonds, 9 residues, 1 model selected
> show #!4 models
> hide #* target a
> show sel target ab
> surface dust #3.1 size 10.7
> ui tool show "Map Eraser"
> volume erase #3.1 center 292.79,429.01,254.91 radius 99.984
> volume #3.1 level 0.03
> volume erase #3.1 center 216.04,351.7,194.75 radius 49.992 outside true
> volume erase #3.1 center 206.02,359.44,193.29 radius 27.975
> volume erase #3.1 center 210.16,379.23,208.11 radius 27.975
> volume erase #3.1 center 176.56,356.17,180.76 radius 27.975
> volume erase #3.1 center 223.25,343.55,137.1 radius 27.975
> volume erase #3.1 center 270.03,340.33,151.13 radius 27.975
> volume erase #3.1 center 274.93,313.47,181.16 radius 27.975
> volume erase #3.1 center 264.58,301.11,181.43 radius 27.975
> volume erase #3.1 center 244.19,302.36,165.41 radius 27.975
> volume erase #3.1 center 266.43,305.77,202.42 radius 27.975
> volume erase #3.1 center 274.38,323.67,168.2 radius 27.975
> hide #!4 models
> show #!4 models
> hide #!3.1 models
> show #!3.1 models
> hide #!4 models
> show #!4 models
> save
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/04_cryosparc/mRNA_er.mrc
> models #3.1
> hide #5 models
> volume #3.1 level 0.02273
> volume #3.1 level 0.03162
> volume #3.1 level 0.03485
> volume #3.1 level 0.03969
> surface dust #3.1 size 10.7
> select add #4
207066 atoms, 221714 bonds, 5069 pseudobonds, 17603 residues, 4 models
selected
> hide #!4 models
> select subtract #4
Nothing selected
> surface dust #3.1 size 0
> show #5 models
> volume erase #3.1 center 249.07,308.26,232.15 radius 27.888
> volume erase #3.1 center 241.61,343.32,244 radius 27.888
> volume erase #3.1 center 228.09,342.91,246.99 radius 27.888
> volume erase #3.1 center 203.98,354.25,252.08 radius 27.888
> volume erase #3.1 center 191.45,360.3,249.78 radius 27.888
> volume erase #3.1 center 221.7,344.87,248.98 radius 27.888
> volume erase #3.1 center 236.95,349.46,230.07 radius 27.888
> volume erase #3.1 center 248.45,362.29,214.3 radius 27.888
> volume erase #3.1 center 271.59,360.59,195.96 radius 27.888
> volume erase #3.1 center 264.14,338.97,218.71 radius 27.888
> volume erase #3.1 center 247.91,394.69,186.14 radius 27.888
> volume erase #3.1 center 208.01,388.02,189.07 radius 27.888
> volume erase #3.1 center 187.94,379.11,189.35 radius 27.888
> volume erase #3.1 center 215.67,358.43,238.03 radius 27.888
> volume erase #3.1 center 199.85,304.09,183.35 radius 27.888
> volume erase #3.1 center 186.7,318.55,176.33 radius 27.888
> volume erase #3.1 center 202.87,330.45,157.6 radius 27.888
> volume erase #3.1 center 161.42,309.29,176.41 radius 49.76
> volume erase #3.1 center 222.95,276.97,169.31 radius 49.76
> volume erase #3.1 center 228.05,300.1,145.76 radius 49.76
> volume erase #3.1 center 224.32,323.13,126.62 radius 49.76
> volume erase #3.1 center 185.76,352.22,126.81 radius 49.76
> volume erase #3.1 center 171.71,368.96,163.92 radius 49.76
> volume erase #3.1 center 187.22,321.21,162.05 radius 49.76
> volume erase #3.1 center 166.19,403.31,220.98 radius 49.76
> volume erase #3.1 center 186.58,305.1,216.9 radius 19.959
> volume erase #3.1 center 200.96,301.58,227.68 radius 19.959
> volume erase #3.1 center 228.29,297.65,218.8 radius 19.959
> volume erase #3.1 center 230.5,315.76,234.97 radius 19.959
> volume erase #3.1 center 263.79,347.57,166.76 radius 19.959
> volume erase #3.1 center 257.93,360.81,155.93 radius 19.959
> volume erase #3.1 center 256.57,376.02,184.11 radius 19.959
> volume erase #3.1 center 253.29,383.45,170.98 radius 19.959
> volume erase #3.1 center 222.28,350.97,206.41 radius 19.959
> volume erase #3.1 center 231.81,365.45,201.22 radius 19.959
> volume erase #3.1 center 271.21,344.09,191.1 radius 19.959
> save
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/04_cryosparc/mRNA_er.mrc
> models #3.1
> show #!3.2 models
> hide #5 models
> show #!3.3 models
> close session
> open
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/04_cryosparc/J3603_3604_3605_consensus_80s.mrc
Opened J3603_3604_3605_consensus_80s.mrc as #1, grid size 512,512,512, pixel
1.07, shown at level 0.0226, step 2, values float32
> volume #1 sdLevel 5
> volume #1 step 1
> volume #1 level 0.1567
> volume #1 level 0.1299
> volume #1 level 0.1146
> set bgColor white
> set bgColor #ffffff00
> lighting soft
> surface dust #1 size 10.7
> open
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/model/Hiber-E.pdb
Chain information for Hiber-E.pdb #2
---
Chain | Description
CA | No description available
CB | No description available
CD | No description available
Et | No description available
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
Ls | No description available
Lt | No description available
Lz | No description available
S2 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | 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
SL | No description available
SM | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sf | No description available
Sg | No description available
> open
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/model/P.pdb
Chain information for P.pdb #3
---
Chain | Description
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
Ls | No description available
Lt | No description available
Lz | No description available
Pt | No description available
S2 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | 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
SL | No description available
SM | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sf | No description available
Sg | No description available
> close #2
> close #3
> open
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/model/AT-
> P-E.pdb
Chain information for AT-P-E.pdb #2
---
Chain | Description
AT | No description available
CF | No description available
Et | No description available
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
Ls | No description available
Lt | No description available
Lz | No description available
Pt | No description available
S2 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | 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
SL | No description available
SM | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sf | No description available
Sg | No description available
> hide #!2 models
> save
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/Fig/0720_consensus_01.png
> width 1285 height 1162 supersample 3 transparentBackground true
> show #!2 models
> ui tool show "Color Zone"
> color zone #1 near #2 distance 3
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> color single #1
> color zone #1 near #2 distance 2
> color single #1
> color zone #1 near #2 distance 2.5
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> color single #1
> select #2/L*
143516 atoms, 154455 bonds, 16 pseudobonds, 11373 residues, 2 models selected
> show #!2 models
> ui tool show "Color Actions"
> color (#!2 & sel) #d17d86ff
> color (#!2 & sel) #add8e6ff
> color zone #1 near sel & #2 distance 6.41
> color (#!2 & sel) #d66c03ff
> color (#!2 & sel) #c3757eff
> select #2/S*
76029 atoms, 81008 bonds, 5 pseudobonds, 6675 residues, 2 models selected
> color (#!2 & sel) #94bac5ff
> color zone #1 near #2 distance 2.5
> hide #!2 models
> select #2/S*
76029 atoms, 81008 bonds, 5 pseudobonds, 6675 residues, 2 models selected
> color #1 #e1cca4ff
> select #2/S*
76029 atoms, 81008 bonds, 5 pseudobonds, 6675 residues, 2 models selected
> show #!2 models
> color single #1
> color zone #1 near #2 distance 3
> hide #!2 models
> show #!2 models
> color single #1
> color zone #1 near #2 distance 3
> color (#!2 & sel) #ffaa7fff
> color (#!2 & sel) #e1cca4ff
> color single #1
> color zone #1 near #2 distance 3
> hide #!2 models
> open
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/04_cryosparc/cryosparc_P9_J3589_004_volume_mask_refine_60s.mrc
Opened cryosparc_P9_J3589_004_volume_mask_refine_60s.mrc as #3, grid size
512,512,512, pixel 1.07, shown at level 1, step 2, values float32
> volume #3 level 1
> close #3
> open
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/04_cryosparc/cryosparc_P9_J3591_004_volume_mask_refine_40sbody.mrc
Opened cryosparc_P9_J3591_004_volume_mask_refine_40sbody.mrc as #3, grid size
512,512,512, pixel 1.07, shown at level 1, step 2, values float32
> volume #3 level 1
> open
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/04_cryosparc/cryosparc_P9_J3593_007_volume_mask_refine_40shead.mrc
Opened cryosparc_P9_J3593_007_volume_mask_refine_40shead.mrc as #4, grid size
512,512,512, pixel 1.07, shown at level 1, step 2, values float32
> volume #4 level 1
> transparancy #3 50
Unknown command: transparancy #3 50
> transperancy #3 50
Unknown command: transperancy #3 50
> transparency #3 50
> transparency #4 50
> hide #!3 models
> hide #!4 models
> show #!3 models
> show #!4 models
> transparency #3,4 90
> select add #2
227713 atoms, 244260 bonds, 24 pseudobonds, 18714 residues, 2 models selected
> ui tool show "Color Actions"
> color sel bychain
> show #!2 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> color sel bychain
> color sel byelement
> color sel byhetero
> color sel bychain
> color sel bypolymer
> color sel bychain
> color sel bypolymer
> select subtract #2
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> color single #1
> color #1 grey
> lighting simple
> lighting full
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> color zone #1 near #2 distance 3
> color bychain
> color single #1
> color zone #1 near #2 distance 3
[Repeated 1 time(s)]
> ui mousemode right clip
> volume splitbyzone #1
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\colorzonegui.py", line 253, in _split_map
run(self.session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\colorzone.py", line 378, in
split_volumes_by_color_zone
vlist.extend(split_volume_by_color_zone(v))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\colorzone.py", line 321, in
split_volume_by_color_zone
grids = split_zones_by_color(volume, zc.points, zc.point_colors, zc.distance)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\colorzone.py", line 362, in split_zones_by_color
g = masked_grid_data(sg, mask, m)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_data\arrays.py", line 324, in masked_grid_data
masked = zeros(matrix.shape, matrix.dtype)
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 512. MiB for an
array with shape (512, 512, 512) and data type float32
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 512. MiB for an
array with shape (512, 512, 512) and data type float32
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_data\arrays.py", line 324, in masked_grid_data
masked = zeros(matrix.shape, matrix.dtype)
See log for complete Python traceback.
> close #4
> close #3
> close #2
> volume splitbyzone #1
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\colorzonegui.py", line 253, in _split_map
run(self.session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\colorzone.py", line 378, in
split_volumes_by_color_zone
vlist.extend(split_volume_by_color_zone(v))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\colorzone.py", line 321, in
split_volume_by_color_zone
grids = split_zones_by_color(volume, zc.points, zc.point_colors, zc.distance)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\colorzone.py", line 362, in split_zones_by_color
g = masked_grid_data(sg, mask, m)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_data\arrays.py", line 324, in masked_grid_data
masked = zeros(matrix.shape, matrix.dtype)
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 512. MiB for an
array with shape (512, 512, 512) and data type float32
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 512. MiB for an
array with shape (512, 512, 512) and data type float32
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_data\arrays.py", line 324, in masked_grid_data
masked = zeros(matrix.shape, matrix.dtype)
See log for complete Python traceback.
> open
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/model/A-P-E.pdb
Chain information for A-P-E.pdb #2
---
Chain | Description
At | No description available
Et | No description available
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
Ls | No description available
Lt | No description available
Lz | No description available
Pt | No description available
S2 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | 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
SL | No description available
SM | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sf | No description available
Sg | No description available
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> close #2
> color single #1
> open
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/model/AP-
> PE-eEF2.pdb
Chain information for AP-PE-eEF2.pdb #2
---
Chain | Description
AP | No description available
CB | No description available
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
Ls | No description available
Lt | No description available
Lz | No description available
PE | No description available
S2 | No description available
S3 | No description available
S4 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | 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
SL | No description available
SM | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sf | No description available
Sg | No description available
> close #2
> open
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/model/AP-
> PE-Rot-eEF2.pdb
Chain information for AP-PE-Rot-eEF2.pdb #2
---
Chain | Description
AP | No description available
CB | No description available
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
Ls | No description available
Lt | No description available
Lz | No description available
PE | No description available
S2 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | 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
SL | No description available
SM | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sf | No description available
Sg | No description available
> close #2
> open
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/model/AT-
> P-E.pdb
Chain information for AT-P-E.pdb #2
---
Chain | Description
AT | No description available
CF | No description available
Et | No description available
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
Ls | No description available
Lt | No description available
Lz | No description available
Pt | No description available
S2 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | 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
SL | No description available
SM | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sf | No description available
Sg | No description available
> fitmap #2 inMap #1
Fit molecule AT-P-E.pdb (#2) to map J3603_3604_3605_consensus_80s.mrc (#1)
using 227713 atoms
average map value = 0.3022, steps = 40
shifted from previous position = 0.0918
rotated from previous position = 0.0418 degrees
atoms outside contour = 67949, contour level = 0.1146
Position of AT-P-E.pdb (#2) relative to J3603_3604_3605_consensus_80s.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999975 0.00020350 0.00067499 -0.30596802
-0.00020337 0.99999996 -0.00019011 0.13801601
-0.00067503 0.00018997 0.99999975 0.14801589
Axis 0.26026819 0.92446453 -0.27861408
Axis point 221.87916683 0.00000000 455.96264661
Rotation angle (degrees) 0.04183542
Shift along axis 0.00671785
> fitmap #2/LR inMap #1
Fit molecule AT-P-E.pdb (#2) to map J3603_3604_3605_consensus_80s.mrc (#1)
using 1566 atoms
average map value = 0.317, steps = 48
shifted from previous position = 0.36
rotated from previous position = 0.244 degrees
atoms outside contour = 418, contour level = 0.1146
Position of AT-P-E.pdb (#2) relative to J3603_3604_3605_consensus_80s.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999466 -0.00242067 -0.00219459 1.22956627
0.00241642 0.99999521 -0.00193621 -0.12916999
0.00219927 0.00193090 0.99999572 -1.03490324
Axis 0.50928033 -0.57865075 0.63702187
Axis point 44.46378465 499.07781525 -0.00000000
Rotation angle (degrees) 0.21753196
Shift along axis 0.04168222
> fitmap #2 inMap #1
Fit molecule AT-P-E.pdb (#2) to map J3603_3604_3605_consensus_80s.mrc (#1)
using 227713 atoms
average map value = 0.3023, steps = 68
shifted from previous position = 0.0983
rotated from previous position = 0.245 degrees
atoms outside contour = 67981, contour level = 0.1146
Position of AT-P-E.pdb (#2) relative to J3603_3604_3605_consensus_80s.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999972 0.00015142 0.00073292 -0.30659115
-0.00015128 0.99999997 -0.00019084 0.11570757
-0.00073295 0.00019073 0.99999971 0.16524306
Axis 0.24702252 0.94898657 -0.19597031
Axis point 225.73673732 0.00000000 418.96937143
Rotation angle (degrees) 0.04425149
Shift along axis 0.00168728
> color bychain
> select #2/L*
143516 atoms, 154455 bonds, 16 pseudobonds, 11373 residues, 2 models selected
> color sel lightgrey
> select #2/S*
76029 atoms, 81008 bonds, 5 pseudobonds, 6675 residues, 2 models selected
> color sel grey
> ~select
Nothing selected
> select #2/S*
76029 atoms, 81008 bonds, 5 pseudobonds, 6675 residues, 2 models selected
> color sel Dark grey
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color sel Darkgrey
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color sel darkgrey
> ~select
Nothing selected
> color single #1
> color zone #1 near #2 distance 3
> hide #!1 models
> show #!1 models
> hide #!2 models
> select #2/S*
76029 atoms, 81008 bonds, 5 pseudobonds, 6675 residues, 2 models selected
> color sel grey
> color single #1
> color zone #1 near #2 distance 3
[Repeated 1 time(s)]
> volume #1 sdLevel 5
> volume #1 sdLevel 3
> lighting flat
> lighting full
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting full
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> ui mousemode right clip
> volume splitbyzone #1
Opened J3603_3604_3605_consensus_80s.mrc 0 as #3.1, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
Opened J3603_3604_3605_consensus_80s.mrc 1 as #3.2, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
Opened J3603_3604_3605_consensus_80s.mrc 2 as #3.3, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
Opened J3603_3604_3605_consensus_80s.mrc 3 as #3.4, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
Opened J3603_3604_3605_consensus_80s.mrc 4 as #3.5, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
Opened J3603_3604_3605_consensus_80s.mrc 5 as #3.6, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
Opened J3603_3604_3605_consensus_80s.mrc 6 as #3.7, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
> surface dust #3.1 size 10.7
> surface dust #3.2 size 10.7
> surface dust #3.3 size 10.7
> surface dust #3.4 size 10.7
> surface dust #3.5 size 10.7
> surface dust #3.6 size 10.7
> surface dust #3.7 size 10.7
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting full
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> save
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/Fig/0720_consensus_02.png
> width 1285 height 1162 supersample 3 transparentBackground true
> color
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color #2/Pt pink
> hide #!3.2 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.3 models
> show #!3.3 models
> hide #!3.3 models
> hide #!3.2 models
> hide #!3.1 models
> hide #!3.4 models
> show #!3.4 models
> hide #!3.7 models
> show #!3.7 models
> color #3.7 pink
> hide #!3.4 models
> show #!3.4 models
> color #2/At cyan
> color #3.4cyan
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #3.4 cyan
> color #3.4 lightcyan
> color #3.4 powder blue
> color #2/At powder blue
> hide #!3.7 models
> show #!3.7 models
> hide #!3.6 models
> show #!3.6 models
> hide #!3.4 models
> show #!3.4 models
> hide #!3.6 models
> show #!3.6 models
> color #3.6 magenta
> graphics silhouettes false
> color #3.6 orchid
> show #!3.3 models
> show #!3.2 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> save
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/Fig/0720_consensus_03.png
> width 1285 height 1162 supersample 3 transparentBackground true
> graphics silhouettes true
> save
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/Fig/0720_consensus_04.png
> width 1285 height 1162 supersample 3 transparentBackground true
> clip back 0.2
> ~clip back 0.2
Expected fewer arguments
> ~clip back
Expected fewer arguments
> clip back off
> save
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/Fig/0720_consensus_05.png
> width 1285 height 1162 supersample 3 transparentBackground true
> volume #3.3 level 0.1
> volume #3.3 level 0.11
> volume #3 level 0.15
> volume #3 level 0.11
> undo
[Repeated 1 time(s)]
> volume #3 level 0.15
> volume #3 level 0.11
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!2 models
> select add #2
227713 atoms, 244260 bonds, 24 pseudobonds, 18714 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select #2/L5
80071 atoms, 89313 bonds, 11 pseudobonds, 3951 residues, 2 models selected
> show #!3 models
> hide #!2 models
> save
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/Fig/0720_consensus.cxs
> select #2/L5:26-31,51-57
279 atoms, 310 bonds, 13 residues, 1 model selected
> show #!2 models
> hide #!2 models
> color sel #CEB496
> hide #!3.1 models
> show #!3.1 models
> hide #!3.2 models
> show #!3.2 models
> color zone #3.2 near sel distance 2
> volume splitbyzone #3.2
Opened J3603_3604_3605_consensus_80s.mrc 1 0 as #4.1, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
Opened J3603_3604_3605_consensus_80s.mrc 1 1 as #4.2, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
> hide #!4.1 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> show #!4.1 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.1 models
> show #!2 models
> hide #* target a
> show sel target ab
> hide sel cartoons
> hide #2 target c
> hide #2 target a
> show sel target ab
> nucleotides sel atoms
> style nucleic & sel stick
Changed 279 atom styles
> transparency #4.2 70
> ~select
Nothing selected
> select add #4.2
2 models selected
> view sel
> select #2/L5:26-31,51-57
279 atoms, 310 bonds, 13 residues, 1 model selected
> color sel byhetero
> ~select
Nothing selected
> select #2/L5:26-31,51-57
279 atoms, 310 bonds, 13 residues, 1 model selected
> color sel lightgrey
> color sel byhetero
> graphics silhouettes false
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> lighting full
> lighting soft
> lighting full
> color sel azure
> color sel lightblue
> color sel byhetero
> color sel light sea green
> color sel lightblue
> color sel #94bac5ff
> color sel #87a9b3ff
> color sel #90b5bfff
> color sel #94bac5ff
> color sel #add8e6ff
> color sel #94bac5ff
> color sel byhetero
> ~select
Nothing selected
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting soft
> lighting full
> transparency #4.2 50
> lighting simple
> hide #!4.2 models
> show #!4.2 models
> select #2/L5:26-31,51-57
279 atoms, 310 bonds, 13 residues, 1 model selected
> color sel lightgrey
> select #2/L5:27-31,52-57
237 atoms, 263 bonds, 11 residues, 1 model selected
> hide #* target a
> show sel target ab
> color sel lightblue
> color zone #4.2 near sel distance 2
> volume splitbyzone #4.2
Opened J3603_3604_3605_consensus_80s.mrc 1 1 0 as #5.1, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
Opened J3603_3604_3605_consensus_80s.mrc 1 1 1 as #5.2, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
> hide #!4 models
> hide #!5.1 models
> color #5.2 #CEB496
> transparency #5.2 50
> color sel byhetero
> select clear
> volume #5.2 level 0.15
> volume #5.2 level 0.11
> volume #1 sdLevel 5
> volume #5.2 level 0.183
> save
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/Fig/0720_consensus_06.png
> width 1285 height 1162 supersample 3 transparentBackground true
> save
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/Fig/0720_consensus_07.png
> width 1285 height 1162 supersample 3 transparentBackground true
> hide #!5.2 models
> close #4
> select #2/LS:101-106
35 atoms, 34 bonds, 6 residues, 1 model selected
> hide #* target a
> show sel target ab
> view sel
> hide sel atoms
> show sel cartoons
> select #2/LS:101-116
116 atoms, 116 bonds, 16 residues, 1 model selected
> hide #* target a
> show sel target ab
> hide sel atoms
> show sel cartoons
> select #2/LS:102-116
109 atoms, 109 bonds, 15 residues, 1 model selected
> hide #* target a
> show sel target ab
> hide sel atoms
> select #2/LS:101-116
116 atoms, 116 bonds, 16 residues, 1 model selected
> hide sel cartoons
> select #2/LS:102-116
109 atoms, 109 bonds, 15 residues, 1 model selected
> show sel cartoons
> color sel lightblue
> color single #3.2
> color zone #3.2 near sel distance 2
> volume splitbyzone #3.2
Opened J3603_3604_3605_consensus_80s.mrc 1 0 as #4.1, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
Opened J3603_3604_3605_consensus_80s.mrc 1 1 as #4.2, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
> hide #!4.1 models
> color #4.2 #CEB496
> transparency #4.2 50
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> hide sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> show sel target ab
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> hide #!2 models
> show #!2 models
> style sel stick
Changed 109 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 109 atom styles
> color sel byhetero
> hide sel cartoons
> show sel cartoons
> select clear
> cartoon style helix width 1.0 thickness 0.5
> cartoon style helix width 1.2 thickness 0.5
> select clear
> lighting soft
> lighting full
> lighting simple
> save
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/Fig/0720_consensus_08.png
> width 1285 height 1162 supersample 3 transparentBackground true
> transparency #4.2 60
> transparency #4.2 70
> save
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/Fig/0720_consensus_09.png
> width 1285 height 1162 supersample 3 transparentBackground true
> transparency #4.2 60
> save
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/Fig/0720_consensus_10.png
> width 1285 height 1162 supersample 3 transparentBackground true
> show #!5.1 models
> show #!5.2 models
> hide #!5.2 models
> hide #!5.1 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.1 models
> hide #!5.1 models
> hide #!4.2 models
> show #!4.2 models
> show #!4.1 models
> hide #!4.1 models
> select #2/LO:6-10
38 atoms, 37 bonds, 5 residues, 1 model selected
> hide #* target a
> show sel target ab
> view sel
> hide sel atoms
> show sel cartoons
> style sel stick
Changed 38 atom styles
> show sel atoms
> color sel lightblue
> close #5.1
> close #4.1
> color single #3.2
> color zone #3.2 near sel distance 2
> volume splitbyzone #3.2
Opened J3603_3604_3605_consensus_80s.mrc 1 0 as #6.1, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
Opened J3603_3604_3605_consensus_80s.mrc 1 1 as #6.2, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
> hide #!6.1 models
> close #6
> select #2/LO:4-12
69 atoms, 68 bonds, 9 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 69 atom styles
> show sel cartoons
> hide sel atoms
> hide sel cartoons
> select #2/LO:5-11
51 atoms, 50 bonds, 7 residues, 1 model selected
> show sel cartoons
> show sel atoms
> color sel lightblue
> color single #3.2
> color zone #3.2 near sel distance 2
> volume splitbyzone #3.2
Opened J3603_3604_3605_consensus_80s.mrc 1 0 as #6.1, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
Opened J3603_3604_3605_consensus_80s.mrc 1 1 as #6.2, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
> close #6.1
> color #6.2 #CEB496
> transparency #4.2 50
> transparency #6.2 50
> color sel byhetero
> hide sel cartoons
> surface dust #4.2 size 10.7
> surface dust #6.2 size 10.7
> select clear
> volume #4.2 style mesh
> hide #!5 models
> hide #!4 models
> hide #!3.7 models
> hide #!3.6 models
> hide #!3.5 models
> hide #!3.4 models
> hide #!3.3 models
> hide #!3.1 models
> volume #6.2 level 0.183
> volume #6.2 style image
> volume #6.2 style mesh
> volume #6.2 style image
> undo
> hide #!3.1 models
> volume #6.2 level 0,0 level 0.09904,0.8 level 0.9904,1
> volume #6.2 level 0,0 level 0.1311,0.3231 level 0.9904,1
> volume #6.2 level 0,0 level 0.565,0.2923 level 0.9904,1
> volume #6.2 level 0,0 level 0.07169,0.6308 level 0.9904,1
> volume #6.2 style surface
> volume #6.2 style image
> volume #6.2 color #ffaaff color white color white
> volume #6.2 level 0.11,0 level 0.07169,0.6308 level 0.9904,1
> volume #6.2 level 0.1213,0.6462 level 0.07169,0.6308 level 0.9904,1
> volume #6.2 level 0.1213,0.6462 level 0.07735,0.5692 level 0.9904,1
> volume #6.2 level 0.1062,0.6462 level 0.07735,0.5692 level 0.9904,1
> volume #6.2 level 0.9904,0.6615 level 0.07735,0.5692 level 0.9904,1
> volume #6.2 level 0.9904,0.6615 level 0.07735,0.5692 level 0.6509,0.5385
> volume #6.2 level 0.9904,0.6615 level 0.07735,0.5692 level 0.5735,0.5077
> volume #6.2 maximumIntensityProjection true
> volume #6.2 style surface maximumIntensityProjection false
> volume #6.2 subdivideSurface true subdivisionLevels 2
> volume #6.2 style mesh
> volume #6.2 subdivideSurface true subdivisionLevels 4
> volume #6.2 subdivideSurface true subdivisionLevels 3
> volume #6.2 subdivideSurface true subdivisionLevels 2
> volume #6.2 style image
> volume #6.2 style surface
> volume #4.2 style surface
> save
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/Fig/0720_consensus_11.png
> width 1285 height 1162 supersample 3 transparentBackground true
> hide #!6.2 models
> show #!6.2 models
> hide #!6 models
> select #2/LF:208-219
95 atoms, 99 bonds, 12 residues, 1 model selected
> hide #* target a
> show sel target ab
> view sel
> style sel stick
Changed 95 atom styles
> show #!3.2 models
> hide #!3 models
> transparency #3.2 50
> select add #3.2
95 atoms, 99 bonds, 12 residues, 3 models selected
> select subtract #3.2
95 atoms, 99 bonds, 12 residues, 1 model selected
> hide #!3.2 models
> show #!3.2 models
> color sel lightblue
> color single #3.2
> color zone #3.2 near sel distance 3
> volume splitbyzone #3.2
Opened J3603_3604_3605_consensus_80s.mrc 1 0 as #7.1, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
Opened J3603_3604_3605_consensus_80s.mrc 1 1 as #7.2, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
> hide #!7.1 models
> surface dust #7.2 size 10.7
> transparency #7.2 50
> color sel byhetero
> color #7.2 #CEB496
> close #7
> color zone #3.2 near sel distance 2
> color single #3.2
> color zone #3.2 near sel distance 2
> volume splitbyzone #3.2
Opened J3603_3604_3605_consensus_80s.mrc 1 0 as #7.1, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
Opened J3603_3604_3605_consensus_80s.mrc 1 1 as #7.2, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
Opened J3603_3604_3605_consensus_80s.mrc 1 2 as #7.3, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
Opened J3603_3604_3605_consensus_80s.mrc 1 3 as #7.4, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
> close #7
> color single #3.2
> color sel lightblue
> color single #3.2
> color zone #3.2 near sel distance 2
> volume splitbyzone #3.2
Opened J3603_3604_3605_consensus_80s.mrc 1 0 as #7.1, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
Opened J3603_3604_3605_consensus_80s.mrc 1 1 as #7.2, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
> hide #!7.1 models
> transparency #7.2 50
> color sel byhetero
> color #7.2 #CEB496
> select clear
> save
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/Fig/0720_consensus_12.png
> width 1285 height 1162 supersample 3 transparentBackground true
> select #2/LF:86-93
64 atoms, 65 bonds, 8 residues, 1 model selected
> hide #* target a
> show sel target ab
> hide #!7.2 models
> hide #!6.2 models
> view sel
> style sel stick
Changed 64 atom styles
> color sel lightblue
> color single #7.1
> color zone #7.1 near sel distance 2
> volume splitbyzone #7.1
Opened J3603_3604_3605_consensus_80s.mrc 1 0 0 as #8.1, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
Opened J3603_3604_3605_consensus_80s.mrc 1 0 1 as #8.2, grid size 512,512,512,
pixel 1.07, shown at level 0.11, step 1, values float32
> hide #!8.1 models
> surface dust #8.2 size 10.7
> color #8.2 #CEB496
> transparency #8.2 50
> color sel byhetero
> ~select
Nothing selected
> save
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/Fig/0720_consensus_13.png
> width 1285 height 1162 supersample 3 transparentBackground true
> color #8.2 lightgrey
> transparency #8.2 60
> save
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/Fig/0721_consensus_01.png
> width 1285 height 1162 supersample 3 transparentBackground true
> graphics silhouettes true
> save
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/Fig/0721_consensus_02.png
> width 1285 height 1162 supersample 3 transparentBackground true
> save
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/Fig/0721_consensus.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\session.py", line 310, in state_from_grid_data
bytes = dt.matrix().tobytes()
MemoryError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x000002100C91AA30> ->
<chimerax.surface.dust.Redust object at 0x00000210555A1340> ->
<chimerax.map.volume.VolumeSurface object at 0x000002101519A280> 'surface' ->
<chimerax.map.volume.Volume object at 0x0000021058BA5520>
'J3603_3604_3605_consensus_80s.mrc 1 1' -> <chimerax.map.session.GridDataState
object at 0x00000210BC3B6250>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x000002100C91AA30> ->
<chimerax.surface.dust.Redust object at 0x00000210555A1340> ->
<chimerax.map.volume.VolumeSurface object at 0x000002101519A280> 'surface' ->
<chimerax.map.volume.Volume object at 0x0000021058BA5520>
'J3603_3604_3605_consensus_80s.mrc 1 1' -> <chimerax.map.session.GridDataState
object at 0x00000210BC3B6250>: Error while saving session data for
'_surface_updaters' -> <chimerax.surface.updaters.SurfaceUpdaters object at
0x000002100C91AA30> -> <chimerax.surface.dust.Redust object at
0x00000210555A1340> -> <chimerax.map.volume.VolumeSurface object at
0x000002101519A280> 'surface' -> <chimerax.map.volume.Volume object at
0x0000021058BA5520> 'J3603_3604_3605_consensus_80s.mrc 1 1' ->
<chimerax.map.session.GridDataState object at 0x00000210BC3B6250>
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'J3603_3604_3605_consensus_80s.mrc 1 1' -> : Error while saving session data
for '_surface_updaters' -> -> -> 'surface' ->
'J3603_3604_3605_consensus_80s.mrc 1 1' ->
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\session.py", line 310, in state_from_grid_data
bytes = dt.matrix().tobytes()
MemoryError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x000002100C91AA30> ->
<chimerax.surface.dust.Redust object at 0x00000210555A1340> ->
<chimerax.map.volume.VolumeSurface object at 0x000002101519A280> 'surface' ->
<chimerax.map.volume.Volume object at 0x0000021058BA5520>
'J3603_3604_3605_consensus_80s.mrc 1 1' -> <chimerax.map.session.GridDataState
object at 0x00000210BC3B6250>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX\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\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\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\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x000002100C91AA30> ->
<chimerax.surface.dust.Redust object at 0x00000210555A1340> ->
<chimerax.map.volume.VolumeSurface object at 0x000002101519A280> 'surface' ->
<chimerax.map.volume.Volume object at 0x0000021058BA5520>
'J3603_3604_3605_consensus_80s.mrc 1 1' -> <chimerax.map.session.GridDataState
object at 0x00000210BC3B6250>: Error while saving session data for
'_surface_updaters' -> <chimerax.surface.updaters.SurfaceUpdaters object at
0x000002100C91AA30> -> <chimerax.surface.dust.Redust object at
0x00000210555A1340> -> <chimerax.map.volume.VolumeSurface object at
0x000002101519A280> 'surface' -> <chimerax.map.volume.Volume object at
0x0000021058BA5520> 'J3603_3604_3605_consensus_80s.mrc 1 1' ->
<chimerax.map.session.GridDataState object at 0x00000210BC3B6250>
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'J3603_3604_3605_consensus_80s.mrc 1 1' -> : Error while saving session data
for '_surface_updaters' -> -> -> 'surface' ->
'J3603_3604_3605_consensus_80s.mrc 1 1' ->
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save
> C:/DiskE/20230510_Work_in_Yale/20230609_EM/20230614_Ribo_Wei/01_maps_models/20230623/Fig/0721_consensus.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\session.py", line 310, in state_from_grid_data
bytes = dt.matrix().tobytes()
MemoryError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x000002100C91AA30> ->
<chimerax.surface.dust.Redust object at 0x000002100C939160> ->
<chimerax.map.volume.VolumeSurface object at 0x000002104A5F7280> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000211BA3DFD60>
'J3603_3604_3605_consensus_80s.mrc 6' -> <chimerax.map.session.GridDataState
object at 0x000002100C257520>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x000002100C91AA30> ->
<chimerax.surface.dust.Redust object at 0x000002100C939160> ->
<chimerax.map.volume.VolumeSurface object at 0x000002104A5F7280> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000211BA3DFD60>
'J3603_3604_3605_consensus_80s.mrc 6' -> <chimerax.map.session.GridDataState
object at 0x000002100C257520>: Error while saving session data for
'_surface_updaters' -> <chimerax.surface.updaters.SurfaceUpdaters object at
0x000002100C91AA30> -> <chimerax.surface.dust.Redust object at
0x000002100C939160> -> <chimerax.map.volume.VolumeSurface object at
0x000002104A5F7280> 'surface' -> <chimerax.map.volume.Volume object at
0x00000211BA3DFD60> 'J3603_3604_3605_consensus_80s.mrc 6' ->
<chimerax.map.session.GridDataState object at 0x000002100C257520>
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'J3603_3604_3605_consensus_80s.mrc 6' -> : Error while saving session data for
'_surface_updaters' -> -> -> 'surface' -> 'J3603_3604_3605_consensus_80s.mrc
6' ->
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\session.py", line 310, in state_from_grid_data
bytes = dt.matrix().tobytes()
MemoryError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x000002100C91AA30> ->
<chimerax.surface.dust.Redust object at 0x000002100C939160> ->
<chimerax.map.volume.VolumeSurface object at 0x000002104A5F7280> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000211BA3DFD60>
'J3603_3604_3605_consensus_80s.mrc 6' -> <chimerax.map.session.GridDataState
object at 0x000002100C257520>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX\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\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\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\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x000002100C91AA30> ->
<chimerax.surface.dust.Redust object at 0x000002100C939160> ->
<chimerax.map.volume.VolumeSurface object at 0x000002104A5F7280> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000211BA3DFD60>
'J3603_3604_3605_consensus_80s.mrc 6' -> <chimerax.map.session.GridDataState
object at 0x000002100C257520>: Error while saving session data for
'_surface_updaters' -> <chimerax.surface.updaters.SurfaceUpdaters object at
0x000002100C91AA30> -> <chimerax.surface.dust.Redust object at
0x000002100C939160> -> <chimerax.map.volume.VolumeSurface object at
0x000002104A5F7280> 'surface' -> <chimerax.map.volume.Volume object at
0x00000211BA3DFD60> 'J3603_3604_3605_consensus_80s.mrc 6' ->
<chimerax.map.session.GridDataState object at 0x000002100C257520>
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'J3603_3604_3605_consensus_80s.mrc 6' -> : Error while saving session data for
'_surface_updaters' -> -> -> 'surface' -> 'J3603_3604_3605_consensus_80s.mrc
6' ->
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 27.20.100.9621
OpenGL renderer: Intel(R) Iris(R) Plus Graphics
OpenGL vendor: Intel
Python: 3.9.11
Locale: en_US.cp936
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: Microsoft Corporation
Model: Surface Laptop 3
OS: Microsoft Windows 10 Home (Build 19045)
Memory: 8,155,959,296
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-1035G7 CPU @ 1.20GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
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: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pywin32: 303
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
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
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
WMI: 1.5.1
zipp: 3.11.0
Change History (2)
comment:1 by , 2 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 , 2 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | assigned → closed |
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The error message when ChimeraX is saving a session ("MemoryError") means your computer is out of memory. If you use the current ChimeraX version 1.6 it will give a clearer error message.
The reason it is out of memory is that your machine has only 8 GB of memory and you have many 512 by 512 by 512 float32 maps (each 0.5 GB) open. The reason you have some many of these maps is because you used the "volume splitbyzone" command which made lots of copies of the maps for each different color.
If you close some of the map copies made by splitbyzone it will probably have enough memory to save the session. The other solution is to use a computer with more memory.