id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9441 MemoryError saving map in session shuhui_wang@… Tom Goddard "{{{ 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' -> -> -> 'surface' -> 'J3603_3604_3605_consensus_80s.mrc 1 1' -> 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' -> -> -> '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' -> 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' -> -> -> 'surface' -> 'J3603_3604_3605_consensus_80s.mrc 1 1' -> 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 *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' -> -> -> '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' -> 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' -> -> -> 'surface' -> 'J3603_3604_3605_consensus_80s.mrc 6' -> 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' -> -> -> 'surface' -> 'J3603_3604_3605_consensus_80s.mrc 6' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> 'J3603_3604_3605_consensus_80s.mrc 6' -> 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' -> -> -> 'surface' -> 'J3603_3604_3605_consensus_80s.mrc 6' -> 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 *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' -> -> -> 'surface' -> 'J3603_3604_3605_consensus_80s.mrc 6' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> 'J3603_3604_3605_consensus_80s.mrc 6' -> 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 }}} " defect closed normal Sessions not a bug all ChimeraX