Opened 43 hours ago

Closed 5 hours ago

#19453 closed defect (fixed)

MemoryError saving session

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

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open D:\Téléchargements\emd_3883.map~\80S.cxs format session

Opened emd_3883.map as #2, grid size 640,640,640, pixel 0.85, shown at level
0.0235, step 4, values float32  
Opened emd_3883.map 0 as #4.1, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 1 as #4.2, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 2 as #4.3, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 3 as #4.4, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 4 as #4.5, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 5 as #4.6, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Log from Fri Oct 24 17:20:34 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6QZP format mmcif fromDatabase pdb

6qzp title:  
High-resolution cryo-EM structure of the human 80S ribosome [more info...]  
  
Chain information for 6qzp #1  
---  
Chain | Description | UniProt  
L5 | 28S rRNA (3773-MER) |   
L7 | 5S rRNA (120-MER) |   
L8 | 5.8S rRNA (156-MER) |   
LA | 60S ribosomal protein L8 | RL8_HUMAN 2-249  
LB | 60S ribosomal protein L3 | RL3_HUMAN 2-403  
LC | 60S ribosomal protein L4 | RL4_HUMAN 1-368  
LD | 60S ribosomal protein L5 | RL5_HUMAN 2-294  
LE | 60S ribosomal protein L6 | RL6_HUMAN 42-288  
LF | 60S ribosomal protein L7 | RL7_HUMAN 24-248  
LG | 60S ribosomal protein L7a | RL7A_HUMAN 26-266  
LH | 60S ribosomal protein L9 | RL9_HUMAN 1-190  
LI | 60S ribosomal protein L10-like | RL10L_HUMAN 2-214  
LJ | 60S ribosomal protein L11 | RL11_HUMAN 3-178  
LL | 60S ribosomal protein L13 | RL13_HUMAN 2-211  
LM | 60S ribosomal protein L14 | RL14_HUMAN 2-140  
LN | 60S ribosomal protein L15 | RL15_HUMAN 2-204  
LO | 60S ribosomal protein L13a | RL13A_HUMAN 3-203  
LP | 60S ribosomal protein L17 | RL17_HUMAN 2-154  
LQ | 60S ribosomal protein L18 | RL18_HUMAN 2-188  
LR | 60S ribosomal protein L19 | RL19_HUMAN 2-188  
LS | 60S ribosomal protein L18a | RL18A_HUMAN 2-176  
LT | 60S ribosomal protein L21 | RL21_HUMAN 2-160  
LU | 60S ribosomal protein L22 | RL22_HUMAN 17-117  
LV | 60S ribosomal protein L23 | RL23_HUMAN 10-140  
LW | 60S ribosomal protein L24 | RL24_HUMAN 1-124  
LX | 60S ribosomal protein L23a | RL23A_HUMAN 37-156  
LY | 60S ribosomal protein L26 | RL26_HUMAN 1-134  
LZ | 60S ribosomal protein L27 | RL27_HUMAN 2-136  
La | 60S ribosomal protein L27a | RL27A_HUMAN 2-148  
Lb | 60S ribosomal protein L29 | RL29_HUMAN 2-122  
Lc | 60S ribosomal protein L30 | RL30_HUMAN 9-106  
Ld | 60S ribosomal protein L31 | RL31_HUMAN 18-124  
Le | 60S ribosomal protein L32 | RL32_HUMAN 2-129  
Lf | 60S ribosomal protein L35a | RL35A_HUMAN 2-110  
Lg | 60S ribosomal protein L34 | RL34_HUMAN 2-115  
Lh | 60S ribosomal protein L35 | RL35_HUMAN 2-123  
Li | 60S ribosomal protein L36 | RL36_HUMAN 2-103  
Lj | 60S ribosomal protein L37 | RL37_HUMAN 2-87  
Lk | 60S ribosomal protein L38 | RL38_HUMAN 2-70  
Ll | 60S ribosomal protein L39 | RL39_HUMAN 2-51  
Lm | Ubiquitin-60S ribosomal protein L40 | RL40_HUMAN 77-128  
Ln | 60S ribosomal protein L41 | RL41_HUMAN 1-24  
Lo | 60S ribosomal protein L36a | RL36A_HUMAN 2-106  
Lp | 60S ribosomal protein L37a | RL37A_HUMAN 2-92  
Lr | 60S ribosomal protein L28 | RL28_HUMAN 2-126  
Lz | 60S ribosomal protein L10a | RL10A_HUMAN 1-217  
S2 | 18S rRNA (1740-MER) |   
S6 | E site tRNA (75-MER) |   
SA | 40S ribosomal protein SA | RSSA_HUMAN 3-223  
SB | 40S ribosomal protein S3a | RS3A_HUMAN 21-234  
SC | 40S ribosomal protein S2 | RS2_HUMAN 59-280  
SD | 40S ribosomal protein S3 | RS3_HUMAN 1-227  
SE | 40S ribosomal protein S4, X isoform | RS4X_HUMAN 2-263  
SF | 40S ribosomal protein S5 | RS5_HUMAN 16-204  
SG | 40S ribosomal protein S6 | RS6_HUMAN 1-237  
SH | 40S ribosomal protein S7 | RS7_HUMAN 5-193  
SI | 40S ribosomal protein S8 | RS8_HUMAN 2-207  
SJ | 40S ribosomal protein S9 | RS9_HUMAN 2-186  
SK | 40S ribosomal protein S10 | RS10_HUMAN 1-98  
SL | 40S ribosomal protein S11 | RS11_HUMAN 2-154  
SM | 40S ribosomal protein S12 | RS12_HUMAN 11-132  
SN | 40S ribosomal protein S13 | RS13_HUMAN 2-151  
SO | 40S ribosomal protein S14 | RS14_HUMAN 12-151  
SP | 40S ribosomal protein S15 | RS15_HUMAN 10-136  
SQ | 40S ribosomal protein S16 | RS16_HUMAN 6-146  
SR | 40S ribosomal protein S17 | RS17_HUMAN 1-135  
SS | 40S ribosomal protein S18 | RS18_HUMAN 1-145  
ST | 40S ribosomal protein S19 | RS19_HUMAN 2-144  
SU | 40S ribosomal protein S20 | RS20_HUMAN 17-119  
SV | 40S ribosomal protein S21 | RS21_HUMAN 1-83  
SW | 40S ribosomal protein S15a | RS15A_HUMAN 2-130  
SX | 40S ribosomal protein S23 | RS23_HUMAN 2-142  
SY | 40S ribosomal protein S24 | RS24_HUMAN 2-132  
SZ | 40S ribosomal protein S25 | RS25_HUMAN 41-115  
Sa | 40S ribosomal protein S26 | RS26_HUMAN 2-103  
Sb | 40S ribosomal protein S27 | RS27_HUMAN 2-84  
Sc | 40S ribosomal protein S28 | RS28_HUMAN 5-68  
Sd | 40S ribosomal protein S29 | RS29_HUMAN 2-56  
Se | 40S ribosomal protein S30 | RS30_HUMAN 2-59  
Sf | Ubiquitin-40S ribosomal protein S27a | RS27A_HUMAN 85-151  
Sg | Receptor of activated protein C kinase 1 | RACK1_HUMAN 2-314  
  
Non-standard residues in 6qzp #1  
---  
B8N —
(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic
acid  
HMT —
(3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine
(Homoharringtonine; Cephalotaxine; [3(R)]-4-methyl
2-hydroxy-2-(4-hydroxy-4-methylpentyl)butanedioate)  
HYG — hygromycin B (hygromix; antihelmycin; hydromycin B; destomysin;
antibiotic A-396-II)  
MG — magnesium ion  
ZN — zinc ion  
  
64 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> open D:/Téléchargements/emd_3883.map~/emd_3883.map

Opened emd_3883.map as #2, grid size 640,640,640, pixel 0.85, shown at level
0.0235, step 4, values float32  

> color /LA /LB /LC /LD /LE /LF /LG /LH /LI /LJ /LL /LM /LN /LO /LP /LQ /LR
> /LS /LT /LU /LV /LW /LX /LY /LZ /La /Lb /Lc /Ld /Le /Lf /Lg /Lh /Li /Lj /Lk
> /Ll /Lm /Ln /Lo /Lp /Lr /Lz white

> color

> /SA /SB /SC /SD /SE /SF /SG /SH /SI /SJ /SK /SL /SM /SN /SO /SP /SQ /SR /SS
> /ST /SU /SV /SW /SX /SY /SZ /Sa /Sb /Sc /Sd /Se blue

Unknown command: /SA /SB /SC /SD /SE /SF /SG /SH /SI /SJ /SK /SL /SM /SN /SO
/SP /SQ /SR /SS /ST /SU /SV /SW /SX /SY /SZ /Sa /Sb /Sc /Sd /Se blue  

> color /SA /SB /SC /SD /SE /SF /SG /SH /SI /SJ /SK /SL /SM /SN /SO /SP /SQ
> /SR /SS /ST /SU /SV /SW /SX /SY /SZ /Sa /Sb /Sc /Sd /Se blue

> color /LA /LB /LC orange

> color /S2 red

> color zone #2 near #1 distance 2.5

> volume splitbyzone #2

Opened emd_3883.map 0 as #3.1, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 1 as #3.2, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 2 as #3.3, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 3 as #3.4, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 4 as #3.5, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 5 as #3.6, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 6 as #3.7, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 7 as #3.8, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 8 as #3.9, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 9 as #3.10, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 10 as #3.11, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 11 as #3.12, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 12 as #3.13, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 13 as #3.14, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 14 as #3.15, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 15 as #3.16, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  

> hide #!3.2 models

> hide #!3.3 models

> hide #!3.4 models

> hide #!3.5 models

> hide #!3.6 models

> hide #!3.7 models

> hide #!3.8 models

> hide #!3.9 models

> hide #!3.10 models

> hide #!3.11 models

> hide #!3.12 models

> hide #!3.13 models

> hide #!3.14 models

> hide #!3.15 models

> hide #!3.16 models

> hide #!3 models

> show #!3 models

> hide #!1 models

> hide #!3.1 models

> show #!3.2 models

> show #!3.3 models

> hide #!3.3 models

> show #!3.4 models

> hide #!3.4 models

> show #!3.5 models

> hide #!3.5 models

> show #!3.6 models

> hide #!3.6 models

> show #!3.6 models

> show #!3.8 models

> hide #!3.8 models

> show #!3.8 models

> hide #!3.8 models

> show #!3.9 models

> close #♥3

Expected a models specifier or a keyword  

> close #3

> color /LA /LB /LC /LD /LE /LF /LG /LH /LI /LJ /LL /LM /LN /LO /LP /LQ /LR
> /LS /LT /LU /LV /LW /LX /LY /LZ /La /Lb /Lc /Ld /Le /Lf /Lg /Lh /Li /Lj /Lk
> /Ll /Lm /Ln /Lo /Lp /Lr /Lz white

> show #!1 models

> save D:/Téléchargements/emd_3883.map~/80S.cxs

> color /SA /SB /SC /SD /SE /SF /SG /SH /SI /SJ /SK /SL /SM /SN /SO /SP /SQ
> /SR /SS /ST /SU /SV /SW /SX /SY /SZ /Sa /Sb /Sc /Sd /Se /Sf /Sg blue

> color /L5 /L7 /L8 black

> hide atoms

> show cartoons

> save D:/Téléchargements/emd_3883.map~/80S.cxs

> color zone #2 near #1 distance 2.5

> volume splitbyzone #2

Opened emd_3883.map 0 as #3.1, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 1 as #3.2, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 2 as #3.3, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 3 as #3.4, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 4 as #3.5, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 5 as #3.6, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  

> hide #!3.3 models

> show #!3.3 models

> hide #!3.2 models

> hide #!3.1 models

> hide #!3.4 models

> hide #!3.5 models

> hide #!3.6 models

> hide #!3.3 models

> show #!3.3 models

> hide #!3.3 models

> show #!3.3 models

> hide #!1 models

> show #!3.1 models

> hide #!3.1 models

> show #!3.2 models

> hide #!3.2 models

> show #!3.4 models

> show #!3.5 models

> show #!3.6 models

> show #!3.1 models

> hide #!3.1 models

> show #!3.2 models

> show #!1 models

> hide #!1 models

> set bgColor white

> set bgColor #ffffff00

> hide #!3 models

> show #!1 models

> set bgColor black

> set bgColor transparent

> show #!3 models

> show #!3.1 models

> color #3.1 #aa0000ff models

> hide #!3.1 models

> show #!3.1 models

> hide #!3.2 models

> hide #!3.3 models

> hide #!3.4 models

> hide #!3.5 models

> hide #!3.6 models

> hide #!1 models

> close 3

Expected a models specifier or a keyword  

> close #3

> color zone #2 near #1 distance 3.2

> volume splitbyzone #2

Opened emd_3883.map 0 as #3.1, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 1 as #3.2, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 2 as #3.3, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 3 as #3.4, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 4 as #3.5, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 5 as #3.6, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  

> hide #!3.2 models

> hide #!3.3 models

> hide #!3.4 models

> hide #!3.5 models

> hide #!3.6 models

> color zone #2 near #1 distance 5

> volume splitbyzone #2

Opened emd_3883.map 0 as #4.1, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 1 as #4.2, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 2 as #4.3, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 3 as #4.4, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 4 as #4.5, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  
Opened emd_3883.map 5 as #4.6, grid size 640,640,640, pixel 0.85, shown at
level 0.0235, step 1, values float32  

> hide #!4.1 models

> hide #!4.2 models

> hide #!4.3 models

> hide #!4.4 models

> hide #!4.5 models

> hide #!4.6 models

> hide #!3.1 models

> show #!3.1 models

> hide #!4 models

> show #!4 models

> hide #!3.1 models

> show #!3.1 models

> show #!4.1 models

> hide #!3.1 models

> show #!3.1 models

> show #!3.6 models

> show #!1 models

> hide #!3.6 models

> hide #!4 models

> close #3

> show #!4.2 models

> show #!4.3 models

> show #!4.4 models

> show #!4.5 models

> show #!4.6 models

> set bgColor white

> set bgColor #ffffff00

> hide atoms

> select all

219463 atoms, 235341 bonds, 5578 pseudobonds, 18069 residues, 18 models
selected  

> hide sel atoms

> show sel cartoons

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4.1 models

> show #!4.1 models

> color #4.1 #b2b2b250 models

> color #4.1 #b2b2b20a models

> color #4.1 #b2b2b232 models

> color #4.1 #8fa8b232 models

> color #4.1 #9eb2a332 models

> color #4.1 #a1b2a532 models

> color #4.2 #225687ff models

> color #4.2 #232387ff models

> color #4.2 #354487ff models

> color #4.2 #008087ff models

> color #4.2 #107187ff models

> color #4.3 #29d1ffff models

> color #4.2 #29d1ffff models

> color #4.4 #00aa00ff models

> color #4.5 #00aa00ff models

> color #4.6 #00aa00ff models

> hide #!4 models

> color /LA /LB /LC /LD /LE /LF /LG /LH /LI /LJ /LL /LM /LN /LO /LP /LQ /LR
> /LS /LT /LU /LV /LW /LX /LY /LZ /La /Lb /Lc /Ld /Le /Lf /Lg /Lh /Li /Lj /Lk
> /Ll /Lm /Ln /Lo /Lp /Lr /Lz turquoise

> color /L5 /L7 /L8 turquoise

> color /L5 /L7 /L8 #29d1ff

> select clear

> show #!4 models

> hide #!4.1 models

> show #!4.1 models

> color #4.4 #28aa05ff models

> color #4.4 #5caa02ff models

> color #4.4 #6faa01ff models

> color #4.5 #6faa01ff models

> color #4.6 #6faa01ff models

> hide #!4 models

> color /SA /SB /SC /SD /SE /SF /SG /SH /SI /SJ /SK /SL /SM /SN /SO /SP /SQ
> /SR /SS /ST /SU /SV /SW /SX /SY /SZ /Sa /Sb /Sc /Sd /Se /Sf /Sg #6faa01

> color /S2 #6faa01

> show #!4 models

> color #4.2 #29d1ff78 models

> color #4.2 #29d1ff32 models

> color #4.3 #29d1ff32 models

> color #4.4 #6faa0132 models

> color #4.5 #6faa0132 models

> color #4.6 #6faa0132 models

> color #4.1 #a1b2a54b models

> color #4.1 #a1b2a57d models

> volume splitbyzone #1

> split bycolor #1

Expected a structures specifier or a keyword  

> split bycolor #1

Expected a structures specifier or a keyword  

> split bycolor #1

Expected a structures specifier or a keyword  

> split bycolor

Expected a structures specifier or a keyword  

> split bycolor

Expected a structures specifier or a keyword  

> split #1 bycolor

Expected a keyword  

> volume splitbycolor #1

Expected a density maps specifier or a keyword  

> split

Split 6qzp (#1) into 81 models  
Chain information for 6qzp L5 #1.1  
---  
Chain | Description  
L5 | No description available  
  
Chain information for 6qzp L7 #1.2  
---  
Chain | Description  
L7 | No description available  
  
Chain information for 6qzp L8 #1.3  
---  
Chain | Description  
L8 | No description available  
  
Chain information for 6qzp LA #1.4  
---  
Chain | Description  
LA | No description available  
  
Chain information for 6qzp LB #1.5  
---  
Chain | Description  
LB | No description available  
  
Chain information for 6qzp LC #1.6  
---  
Chain | Description  
LC | No description available  
  
Chain information for 6qzp LD #1.7  
---  
Chain | Description  
LD | No description available  
  
Chain information for 6qzp LE #1.8  
---  
Chain | Description  
LE | No description available  
  
Chain information for 6qzp LF #1.9  
---  
Chain | Description  
LF | No description available  
  
Chain information for 6qzp LG #1.10  
---  
Chain | Description  
LG | No description available  
  
Chain information for 6qzp LH #1.11  
---  
Chain | Description  
LH | No description available  
  
Chain information for 6qzp LI #1.12  
---  
Chain | Description  
LI | No description available  
  
Chain information for 6qzp LJ #1.13  
---  
Chain | Description  
LJ | No description available  
  
Chain information for 6qzp LL #1.14  
---  
Chain | Description  
LL | No description available  
  
Chain information for 6qzp LM #1.15  
---  
Chain | Description  
LM | No description available  
  
Chain information for 6qzp LN #1.16  
---  
Chain | Description  
LN | No description available  
  
Chain information for 6qzp LO #1.17  
---  
Chain | Description  
LO | No description available  
  
Chain information for 6qzp LP #1.18  
---  
Chain | Description  
LP | No description available  
  
Chain information for 6qzp LQ #1.19  
---  
Chain | Description  
LQ | No description available  
  
Chain information for 6qzp LR #1.20  
---  
Chain | Description  
LR | No description available  
  
Chain information for 6qzp LS #1.21  
---  
Chain | Description  
LS | No description available  
  
Chain information for 6qzp LT #1.22  
---  
Chain | Description  
LT | No description available  
  
Chain information for 6qzp LU #1.23  
---  
Chain | Description  
LU | No description available  
  
Chain information for 6qzp LV #1.24  
---  
Chain | Description  
LV | No description available  
  
Chain information for 6qzp LW #1.25  
---  
Chain | Description  
LW | No description available  
  
Chain information for 6qzp LX #1.26  
---  
Chain | Description  
LX | No description available  
  
Chain information for 6qzp LY #1.27  
---  
Chain | Description  
LY | No description available  
  
Chain information for 6qzp LZ #1.28  
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Chain | Description  
LZ | No description available  
  
Chain information for 6qzp La #1.29  
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Chain | Description  
La | No description available  
  
Chain information for 6qzp Lb #1.30  
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Chain | Description  
Lb | No description available  
  
Chain information for 6qzp Lc #1.31  
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Chain | Description  
Lc | No description available  
  
Chain information for 6qzp Ld #1.32  
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Ld | No description available  
  
Chain information for 6qzp Le #1.33  
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Le | No description available  
  
Chain information for 6qzp Lf #1.34  
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Lf | No description available  
  
Chain information for 6qzp Lg #1.35  
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Lg | No description available  
  
Chain information for 6qzp Lh #1.36  
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Lh | No description available  
  
Chain information for 6qzp Li #1.37  
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Li | No description available  
  
Chain information for 6qzp Lj #1.38  
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Lj | No description available  
  
Chain information for 6qzp Lk #1.39  
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Lk | No description available  
  
Chain information for 6qzp Ll #1.40  
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Ll | No description available  
  
Chain information for 6qzp Lm #1.41  
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Lm | No description available  
  
Chain information for 6qzp Ln #1.42  
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Ln | No description available  
  
Chain information for 6qzp Lo #1.43  
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Lo | No description available  
  
Chain information for 6qzp Lp #1.44  
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Lp | No description available  
  
Chain information for 6qzp Lr #1.45  
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Lr | No description available  
  
Chain information for 6qzp Lz #1.46  
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Lz | No description available  
  
Chain information for 6qzp S2 #1.47  
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Chain information for 6qzp S6 #1.48  
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Chain information for 6qzp SA #1.49  
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Chain information for 6qzp SB #1.50  
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SB | No description available  
  
Chain information for 6qzp SC #1.51  
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> split bycolor

Expected a structures specifier or a keyword  

> split bycolor #1

Expected a structures specifier or a keyword  

> color #1.1 #2f7fffff

> color /L7 #2f7fff

> color /L8 #2f7fff

> color #1.48 #6faa01ff

> color #1.47 #5aaa1dff

> color #1.47 #65aa37ff

> color #1.47 #37aa31ff

> color #1.48 #37aa31ff

> color #1.81 #4162aaff

> undo

> ui tool show "Color Zone"

> ui tool show "Volume Viewer"

> ui tool show "Show Volume Menu"

> volume

> combine #1.1 #1.2 #1.3 LrRNA

Expected a keyword  

> combine #1.1,#1.2,#1.3 LrRNA

Expected a keyword  

> combine models #1.1,#1.2,#1.3 LrRNA

Expected a keyword  

> combine models #1.1,#1.2,#1.3

Expected a keyword  

> combine models #1.1,#1.2,#1.3

Expected a keyword  

> combine models #1.1 #1.2 #1.3

Expected a keyword  

> combine #1.1 #1.2 #1.3

> select add #1.1

80530 atoms, 89711 bonds, 3556 pseudobonds, 4064 residues, 3 models selected  

> select subtract #1.1

Nothing selected  

> combine #1.1 #1.2 #1.3 name 80S

> combine #1.1 #1.2 #1.3 name 80S id #1.82

Expected a keyword  

> hide #!1 models

> hide #!4 models

> show #!4 models

> combine #1.1 #1.2 #1.3 name L_rRNA

> close #5

> combine models
> #1.4,#1.5,#1.6,#1.7,#1.8,#1.9,#1.10,#1.11,#1.12,#1.13,#1.14,#1.15,#1.16,#1.17,#1.18,#1.19,#1.20,#1.21,#1.22,#1.23,#1.24,#1.25,#1.26,#1.27,#1.28,#1.29,#1.30,#1.31,#1.32,#1.33,#1.34,#1.35,#1.36
> name L_prot

Expected a keyword  

> combine models #1.4 #1.5 #1.6 #1.7 #1.8 #1.9 #1.10 #1.11 #1.12 #1.13 #1.14
> #1.15 #1.16 #1.17 #1.18 #1.19 #1.20 #1.21 #1.22 #1.23 #1.24 #1.25 #1.26
> #1.27 #1.28 #1.29 #1.30 #1.31 #1.32 #1.33 #1.34 #1.35 #1.36 name L_prot

Expected a keyword  

> combine #1.4 #1.5 #1.6 #1.7 #1.8 #1.9 #1.10 #1.11 #1.12 #1.13 #1.14 #1.15
> #1.16 #1.17 #1.18 #1.19 #1.20 #1.21 #1.22 #1.23 #1.24 #1.25 #1.26 #1.27
> #1.28 #1.29 #1.30 #1.31 #1.32 #1.33 #1.34 #1.35 #1.36 name L_prot

> close #5

> combine #1.4 #1.5 #1.6 #1.7 #1.8 #1.9 #1.10 #1.11 #1.12 #1.13 #1.14 #1.15
> #1.16 #1.17 #1.18 #1.19 #1.20 #1.21 #1.22 #1.23 #1.24 #1.25 #1.26 #1.27
> #1.28 #1.29 #1.30 #1.31 #1.32 #1.33 #1.34 #1.35 #1.36 #1.37 #1.38 #1.39
> #1.40 #1.41 #1.42 #1.43 #1.44 #1.45 #1.46 L_prot

Expected a keyword  

> combine #1.4 #1.5 #1.6 #1.7 #1.8 #1.9 #1.10 #1.11 #1.12 #1.13 #1.14 #1.15
> #1.16 #1.17 #1.18 #1.19 #1.20 #1.21 #1.22 #1.23 #1.24 #1.25 #1.26 #1.27
> #1.28 #1.29 #1.30 #1.31 #1.32 #1.33 #1.34 #1.35 #1.36 #1.37 #1.38 #1.39
> #1.40 #1.41 #1.42 #1.43 #1.44 #1.45 #1.46 name L_prot

> hide #!1.48 models

> show #!1.48 models

> hide #!1.47 models

> show #!1.47 models

> hide #!1.48 models

> show #!1.48 models

> hide #!1.48 models

> show #!1.48 models

> combine #1.47 #1.48 name S_rRNA

> combine #1.49 #1.50 #1.51 #1.52 #1.53 #1.54 #1.55 #1.56 #1.57 #1.58 #1.59
> #1.60 #1.61 #1.62 #1.63 #1.64 #1.65 #1.66 #1.67 #1.68 #1.69 #1.70 #1.71
> #1.72 #1.73 #1.74 #1.75 #1.76 #1.77 #1.78 #1.79 #1.80 #1.81

> name S_prot

"S_prot" is not defined  

> hide #!1 models

> color #7 #8faa8fff

> color #7 #7daa7aff

> color #7 #03aa46ff

> save D:/Téléchargements/emd_3883.map~/80S.cxs

——— End of log from Fri Oct 24 17:20:34 2025 ———

> view name session-start

opened ChimeraX session  

> combine #1.49 #1.50 #1.51 #1.52 #1.53 #1.54 #1.55 #1.56 #1.57 #1.58 #1.59
> #1.60 #1.61 #1.62 #1.63 #1.64 #1.65 #1.66 #1.67 #1.68 #1.69 #1.70 #1.71
> #1.72 #1.73 #1.74 #1.75 #1.76 #1.77 #1.78 #1.79 #1.80 #1.81 name S_prot

> hide #!4 models

> show #!2 models

> hide #!2 models

> vop zone #2 near #5 cutoff 3 model #50 name L_prot_map

> volume zone #2 nearAtoms #5 cutoff 3 model #50 name L_prot_map

Expected a keyword  

> volume zone #2 nearAtoms #5 range 3 modelId #50 name L_prot_map

Expected '.' or a keyword  

> volume zone #2 nearAtoms #5

> volume zone #2 nearAtoms #5 range 3 newMap true

Opened emd_3883.map zone as #10, grid size 640,640,640, pixel 0.85, shown at
step 1, values float32  

> volume zone #2 nearAtoms #6 range 3 newMap true

Opened emd_3883.map zone as #11, grid size 640,640,640, pixel 0.85, shown at
step 1, values float32  

> volume zone #2 nearAtoms #7 range 3 newMap true

Opened emd_3883.map zone as #12, grid size 640,640,640, pixel 0.85, shown at
step 1, values float32  

> volume zone #2 nearAtoms #9 range 3 newMap true

Opened emd_3883.map zone as #13, grid size 640,640,640, pixel 0.85, shown at
step 1, values float32  

> save C:/Users/benja/Desktop/80S.cxs

Traceback (most recent call last):  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\session.py", line 1058, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save  
fserialize(stream, data)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize  
stream.write(packer.pack(obj))  
^^^^^^^^^^^^^^^^  
File "msgpack\\\\_packer.pyx", line 283, in msgpack._cmsgpack.Packer.pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\\\_packer.pyx", line 283, in msgpack._cmsgpack.Packer.pack  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\session.py", line 1058, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save  
fserialize(stream, data)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize  
stream.write(packer.pack(obj))  
^^^^^^^^^^^^^^^^  
File "msgpack\\\\_packer.pyx", line 283, in msgpack._cmsgpack.Packer.pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\\\_packer.pyx", line 283, in msgpack._cmsgpack.Packer.pack  
  
See log for complete Python traceback.  
  

> save C:/Users/benja/Desktop/80S.cxs

Traceback (most recent call last):  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\session.py", line 1058, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save  
fserialize(stream, data)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize  
stream.write(packer.pack(obj))  
^^^^^^^^^^^^^^^^  
File "msgpack\\\\_packer.pyx", line 283, in msgpack._cmsgpack.Packer.pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\\\_packer.pyx", line 283, in msgpack._cmsgpack.Packer.pack  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\session.py", line 1058, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save  
fserialize(stream, data)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize  
stream.write(packer.pack(obj))  
^^^^^^^^^^^^^^^^  
File "msgpack\\\\_packer.pyx", line 283, in msgpack._cmsgpack.Packer.pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\\\_packer.pyx", line 283, in msgpack._cmsgpack.Packer.pack  
  
See log for complete Python traceback.  
  

> save C:/Users/benja/Desktop/80S-1.cxs

Traceback (most recent call last):  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\session.py", line 1058, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save  
fserialize(stream, data)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize  
stream.write(packer.pack(obj))  
^^^^^^^^^^^^^^^^  
File "msgpack\\\\_packer.pyx", line 283, in msgpack._cmsgpack.Packer.pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\\\_packer.pyx", line 283, in msgpack._cmsgpack.Packer.pack  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\session.py", line 1058, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save  
fserialize(stream, data)  
File "D:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize  
stream.write(packer.pack(obj))  
^^^^^^^^^^^^^^^^  
File "msgpack\\\\_packer.pyx", line 283, in msgpack._cmsgpack.Packer.pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\\\_packer.pyx", line 283, in msgpack._cmsgpack.Packer.pack  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 527.56
OpenGL renderer: NVIDIA GeForce GTX 960M/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: fr_FR.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: N501VW
OS: Microsoft Windows 10 Professionnel (Build 19045)
Memory: 17,070,321,664
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-6700HQ CPU @ 2.60GHz
OSLanguage: fr-FR

Installed Packages:
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    appdirs: 1.4.4
    asttokens: 3.0.0
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    ChimeraX-StructMeasure: 1.2.1
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    ChimeraX-TapeMeasure: 1.0
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    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.10
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    cxservices: 1.2.3
    cycler: 0.12.1
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    decorator: 5.2.1
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    executing: 2.2.0
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    imagecodecs: 2024.6.1
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Change History (3)

comment:1 by Eric Pettersen, 10 hours ago

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

Session includes programmatically generated maps.

comment:2 by Tom Goddard, 8 hours ago

The user has about 30 maps open about 1 GB each (640 x 640 x 640 float32) created with volume splitbyzone. The computer only has 16 GB of memory.

Probably would be good on session save memory error to give an error message instead of a traceback that says it ran out of memory trying to save a session and that this often is caused by creating many large density maps that have not been saved to memory (e.g. with command "volume splitbyzone". This can be fixed by closing maps or saving them to a file so they are not saved in the session (instead a path to the map file is saved).

comment:3 by Tom Goddard, 5 hours ago

Resolution: → fixed
Status: assigned → closed

I added an error message when saving a session file gets out of memory instead of showing a traceback. The error message includes info about how many volume models are being saved in the session and suggestions to close some of those.

Added in 1.11 release candidate and daily build.

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