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Opened 5 hours ago
#20313 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-15.7.5-arm64-arm-64bit
ChimeraX Version: 1.12rc202605050149 (2026-05-05 01:49:00 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 1100000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,12",
"coalitionID" : 172205,
"osVersion" : {
"train" : "macOS 15.7.5",
"build" : "24G624",
"releaseType" : "User"
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"captureTime" : "2026-05-12 15:39:34.6373 -0400",
"codeSigningMonitor" : 1,
"incident" : "E0263C64-2078-4F93-B1DF-4D03040AC2BD",
"pid" : 5774,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2026-05-07 17:28:23.0709 -0400",
"procStartAbsTime" : 16316259588306,
"procExitAbsTime" : 26527603564920,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.11.1","CFBundleVersion":"1.11.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "30DF2564-42BE-6E2B-F7D5-B32A853D86DE",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "5D9FA118-1FA2-4B2E-8C11-B92F78293102",
"sip" : "enabled",
"vmRegionInfo" : "0x8 is not in any region. Bytes before following region: 4339826680
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 102ac8000-102acc000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000008","rawCodes":[1,8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000008"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":5774},
"vmregioninfo" : "0x8 is not in any region. Bytes before following region: 4339826680
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
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===== Log before crash start =====
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/DEAHelicase_reference_models/RabbitCorrected_ma-u3zgf.cif
Summary of feedback from opening
/Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/DEAHelicase_reference_models/RabbitCorrected_ma-u3zgf.cif
---
warnings | Unknown polymer entity '1' on line 299
Unable to fetch template for '.': will connect using distance criteria
Unknown polymer entity '1' on line 299
Unknown polymer entity '2' on line 116841
Unknown polymer entity '3' on line 121877
Unknown polymer entity '4' on line 125711
Unknown polymer entity '5' on line 129672
77 messages similar to the above omitted
Missing or incorrect sequence information. Inferred polymer connectivity.
note | PDBx/mmCIF styling lost on line 300. Rereading mmCIF file from the beginning.
RabbitCorrected_ma-u3zgf.cif title:
rabbit-80S-corrected [more info...]
Chain information for RabbitCorrected_ma-u3zgf.cif #1
---
Chain | Description
A | 28S ribosomal RNA
A3 | 5.8S ribosomal RNA
A4 | 5S ribosomal RNA
AA | ribosomal protein uL2
AB | ribosomal protein uL3
AC | ribosomal protein uL4
AD | ribosomal protein uL18
AE | ribosomal protein eL6
AF | ribosomal protein uL30
AG | ribosomal protein eL8
AH | ribosomal protein uL6
AI | ribosomal protein uL16
AJ | ribosomal protein uL5
AK | ribosomal protein uL10
AL | ribosomal protein eL13
AM | ribosomal protein eL14
AN | ribosomal protein eL15
AO | ribosomal protein uL13
AP | ribosomal protein uL22
AQ | ribosomal protein eL18
AR | ribosomal protein eL19
AS | ribosomal protein eL20
AT | ribosomal protein eL21
AU | ribosomal protein eL22
AV | ribosomal protein uL14
AW | ribosomal protein eL24
AX | ribosomal protein uL23
AY | ribosomal protein uL24
AZ | ribosomal protein eL27
Aa | ribosomal protein uL15
Ab | ribosomal protein eL29
Ac | ribosomal protein eL30
Ad | ribosomal protein eL31
Ae | ribosomal protein eL32
Af | ribosomal protein eL33
Ag | ribosomal protein eL34
Ah | ribosomal protein uL29
Ai | ribosomal protein eL36
Aj | ribosomal protein eL37
Ak | ribosomal protein eL38
Al | ribosomal protein eL39
Am | ribosomal protein eL40
An | ribosomal protein eL41
Ao | ribosomal protein eL42
Ap | ribosomal protein eL43
Aq | ribosomal protein uL11
At | ribosomal protein eL28
Au | ribosomal protein uL1
B | 18S ribosomal RNA
BA | ribosomal protein uS2
BB | ribosomal protein eS1
BC | ribosomal protein uS5
BD | ribosomal protein uS3
BE | ribosomal protein eS4
BF | ribosomal protein uS7
BG | ribosomal protein eS6
BH | ribosomal protein eS7
BI | ribosomal protein eS8
BJ | ribosomal protein uS4
BK | ribosomal protein eS10
BL | ribosomal protein uS17
BM | ribosomal protein eS12
BN | ribosomal protein uS15
BO | ribosomal protein uS11
BP | ribosomal protein uS19
BQ | ribosomal protein uS9
BR | ribosomal protein eS17
BS | ribosomal protein uS13
BT | ribosomal protein eS19
BU | ribosomal protein uS10
BV | ribosomal protein eS21
BW | ribosomal protein uS8
BX | ribosomal protein uS12
BY | ribosomal protein eS24
BZ | ribosomal protein eS25
Ba | ribosomal protein eS26
Bb | ribosomal protein eS27
Bc | ribosomal protein eS28
Bd | ribosomal protein uS14
Be | ribosomal protein eS30
Bf | ribosomal protein eS31
Bg | ribosomal protein RACK 1
Non-standard residues in RabbitCorrected_ma-u3zgf.cif #1
---
MG — (MG)
ZN — (ZN)
> show cartoons
> hide atoms
> delete #1/A,A3,A4,AA
> delete #1/A*
> save
> /Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/DEAHelicase_reference_models/RabbitCorrected40S_ma-u3zgf.cif
> relModel #1
Not saving entity_poly_seq for non-authoritative sequences
> close session
> open
> /Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/DEAHelicase_reference_models/RabbitCorrected40S_ma-u3zgf.cif
Summary of feedback from opening
/Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/DEAHelicase_reference_models/RabbitCorrected40S_ma-u3zgf.cif
---
warnings | Unknown polymer entity '1' on line 197
Unknown polymer entity '2' on line 55063
Unknown polymer entity '3' on line 58471
Unknown polymer entity '4' on line 61987
Unknown polymer entity '5' on line 65519
29 messages similar to the above omitted
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for RabbitCorrected40S_ma-u3zgf.cif #1
---
Chain | Description
B | 18S ribosomal RNA
BA | ribosomal protein uS2
BB | ribosomal protein eS1
BC | ribosomal protein uS5
BD | ribosomal protein uS3
BE | ribosomal protein eS4
BF | ribosomal protein uS7
BG | ribosomal protein eS6
BH | ribosomal protein eS7
BI | ribosomal protein eS8
BJ | ribosomal protein uS4
BK | ribosomal protein eS10
BL | ribosomal protein uS17
BM | ribosomal protein eS12
BN | ribosomal protein uS15
BO | ribosomal protein uS11
BP | ribosomal protein uS19
BQ | ribosomal protein uS9
BR | ribosomal protein eS17
BS | ribosomal protein uS13
BT | ribosomal protein eS19
BU | ribosomal protein uS10
BV | ribosomal protein eS21
BW | ribosomal protein uS8
BX | ribosomal protein uS12
BY | ribosomal protein eS24
BZ | ribosomal protein eS25
Ba | ribosomal protein eS26
Bb | ribosomal protein eS27
Bc | ribosomal protein eS28
Bd | ribosomal protein uS14
Be | ribosomal protein eS30
Bf | ribosomal protein eS31
Bg | ribosomal protein RACK 1
> show cartoons
> style stick
Changed 133919 atom styles
> open
> /Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/40S-eIF3-DHX29-ATPgammaS/maps_after_polish/DHX29_40S_eIF3_U70_2026may7fit2J1716_2.pdb
Chain information for DHX29_40S_eIF3_U70_2026may7fit2J1716_2.pdb #2
---
Chain | Description
0 | No description available
2 | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
n | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
x | No description available
y | No description available
z | No description available
> style stick
Changed 366889 atom styles
> show cartoons
> hide atoms
> ui tool show Matchmaker
> select #1/B
54866 atoms, 59177 bonds, 6 pseudobonds, 1708 residues, 2 models selected
> select #2/2
59813 atoms, 64497 bonds, 1863 residues, 1 model selected
> select add #1/B
114679 atoms, 123674 bonds, 6 pseudobonds, 3571 residues, 3 models selected
> matchmaker #!1 & sel to #2 & sel
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 DHX29_40S_eIF3_U70_2026may7fit2J1716_2.pdb, chain 2 (#2) with
RabbitCorrected40S_ma-u3zgf.cif, chain B (#1), sequence alignment score =
6523.8
RMSD between 1295 pruned atom pairs is 1.181 angstroms; (across all 1702
pairs: 3.518)
> select clear
> save
> /Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/DEAHelicase_reference_models/RabbitCorrected40S_ma-u3zgf_fit2J1716_0.cif
> relModel #2
Not saving entity_poly_seq for non-authoritative sequences
> close #1
> open
> /Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/DEAHelicase_reference_models/RabbitCorrected40S_ma-u3zgf_fit2J1716_0.cif
Summary of feedback from opening
/Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/DEAHelicase_reference_models/RabbitCorrected40S_ma-u3zgf_fit2J1716_0.cif
---
warnings | Unknown polymer entity '1' on line 197
Unknown polymer entity '2' on line 55063
Unknown polymer entity '3' on line 58471
Unknown polymer entity '4' on line 61987
Unknown polymer entity '5' on line 65519
29 messages similar to the above omitted
Missing or incorrect sequence information. Inferred polymer connectivity.
Unknown polymer entity '4' on line 223856
Unknown polymer entity '47' on line 375121
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom H2' is not in the residue template for C4J /2:1244
Atom HO5' is not in the residue template for U /2:1
note | Fetching CCD C4J from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/J/C4J/C4J.cif
Chain information for RabbitCorrected40S_ma-u3zgf_fit2J1716_0.cif
---
Chain | Description
1.2/0 | No description available
1.2/2 | No description available
1.1/B | 18S ribosomal RNA
1.1/BA | ribosomal protein uS2
1.1/BB | ribosomal protein eS1
1.1/BC | ribosomal protein uS5
1.1/BD | ribosomal protein uS3
1.1/BE | ribosomal protein eS4
1.1/BF | ribosomal protein uS7
1.1/BG | ribosomal protein eS6
1.1/BH | ribosomal protein eS7
1.1/BI | ribosomal protein eS8
1.1/BJ | ribosomal protein uS4
1.1/BK | ribosomal protein eS10
1.1/BL | ribosomal protein uS17
1.1/BM | ribosomal protein eS12
1.1/BN | ribosomal protein uS15
1.1/BO | ribosomal protein uS11
1.1/BP | ribosomal protein uS19
1.1/BQ | ribosomal protein uS9
1.1/BR | ribosomal protein eS17
1.1/BS | ribosomal protein uS13
1.1/BT | ribosomal protein eS19
1.1/BU | ribosomal protein uS10
1.1/BV | ribosomal protein eS21
1.1/BW | ribosomal protein uS8
1.1/BX | ribosomal protein uS12
1.1/BY | ribosomal protein eS24
1.1/BZ | ribosomal protein eS25
1.1/Ba | ribosomal protein eS26
1.1/Bb | ribosomal protein eS27
1.1/Bc | ribosomal protein eS28
1.1/Bd | ribosomal protein uS14
1.1/Be | ribosomal protein eS30
1.1/Bf | ribosomal protein eS31
1.1/Bg | ribosomal protein RACK 1
1.2/C | No description available
1.2/D | No description available
1.2/E | No description available
1.2/F | No description available
1.2/G | No description available
1.2/H | No description available
1.2/I | No description available
1.2/J | No description available
1.2/K | No description available
1.2/L | No description available
1.2/M | No description available
1.2/N | No description available
1.2/O | No description available
1.2/P | No description available
1.2/Q | No description available
1.2/R | No description available
1.2/S | No description available
1.2/T | No description available
1.2/U | No description available
1.2/V | No description available
1.2/W | No description available
1.2/X | No description available
1.2/Y | No description available
1.2/Z | No description available
1.2/a | No description available
1.2/b | No description available
1.2/c | No description available
1.2/d | No description available
1.2/e | No description available
1.2/f | No description available
1.2/g | No description available
1.2/h | No description available
1.2/i | No description available
1.2/j | No description available
1.2/k | No description available
1.2/l | No description available
1.2/n | No description available
1.2/p | No description available
1.2/q | No description available
1.2/r | No description available
1.2/s | No description available
1.2/t | No description available
1.2/u | No description available
1.2/x | No description available
1.2/y | No description available
1.2/z | No description available
> show cartoons
> style stick
Changed 599859 atom styles
> hide atoms
> open
> /Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/40S-eIF3-DHX29-ATPgammaS/maps_after_polish/cryosparc_P43_J1716_map2.9Afilt_DHXribomask.mrc
Opened cryosparc_P43_J1716_map2.9Afilt_DHXribomask.mrc as #3, grid size
512,512,512, pixel 0.825, shown at level 0.0792, step 2, values float32
> open
> /Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/40S-eIF3-DHX29-ATPgammaS/maps_after_polish/cryosparc_P43_J1717_005_volume_map_sharp_DHX_local.mrc
Opened cryosparc_P43_J1717_005_volume_map_sharp_DHX_local.mrc as #4, grid size
512,512,512, pixel 0.825, shown at level 0.081, step 2, values float32
> volume #3 step 1
> volume #4 step 1
> volume #3 level 0.09498
> volume #4 level 0.1093
> volume #3 level 0.1
> volume #4 level 0.1
> hide #!2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> close #1.2
> save
> /Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/DEAHelicase_reference_models/RabbitCorrected40S_ma-u3zgf_fit2J1716_0.cif
> models #1 relModel #2
Not saving entity_poly_seq for non-authoritative sequences
> show #!2 models
> hide #!1 models
> show #!1 models
> close #1
> open
> /Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/DEAHelicase_reference_models/RabbitCorrected40S_ma-u3zgf_fit2J1716_0.cif
Summary of feedback from opening
/Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/DEAHelicase_reference_models/RabbitCorrected40S_ma-u3zgf_fit2J1716_0.cif
---
warnings | Unknown polymer entity '1' on line 197
Unknown polymer entity '2' on line 55063
Unknown polymer entity '3' on line 58471
Unknown polymer entity '4' on line 61987
Unknown polymer entity '5' on line 65519
29 messages similar to the above omitted
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for RabbitCorrected40S_ma-u3zgf_fit2J1716_0.cif #1
---
Chain | Description
B | 18S ribosomal RNA
BA | ribosomal protein uS2
BB | ribosomal protein eS1
BC | ribosomal protein uS5
BD | ribosomal protein uS3
BE | ribosomal protein eS4
BF | ribosomal protein uS7
BG | ribosomal protein eS6
BH | ribosomal protein eS7
BI | ribosomal protein eS8
BJ | ribosomal protein uS4
BK | ribosomal protein eS10
BL | ribosomal protein uS17
BM | ribosomal protein eS12
BN | ribosomal protein uS15
BO | ribosomal protein uS11
BP | ribosomal protein uS19
BQ | ribosomal protein uS9
BR | ribosomal protein eS17
BS | ribosomal protein uS13
BT | ribosomal protein eS19
BU | ribosomal protein uS10
BV | ribosomal protein eS21
BW | ribosomal protein uS8
BX | ribosomal protein uS12
BY | ribosomal protein eS24
BZ | ribosomal protein eS25
Ba | ribosomal protein eS26
Bb | ribosomal protein eS27
Bc | ribosomal protein eS28
Bd | ribosomal protein uS14
Be | ribosomal protein eS30
Bf | ribosomal protein eS31
Bg | ribosomal protein RACK 1
> style stick
Changed 366889 atom styles
> hide atoms
> show cartoons
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
Cell requested for row 1 is out of bounds for table with 5 rows! Resizing
table model.
> select add #2/0
2058 atoms, 2071 bonds, 136 residues, 1 model selected
> hide #!1 models
> select
> #2/0,2,Z,O,f,R,C,E,G,I,J,K,L,N,P,X,Y,N,c,i,F,H,M,O,,S,T,V,W,,d,e,g,n,U,R
Expected an objects specifier or a keyword
> select
> #2/0,2,Z,O,f,R,C,E,G,I,J,K,L,N,P,X,Y,N,c,i,F,H,M,O,,S,T,V,W,,d,e,g,n,U,R
Expected an objects specifier or a keyword
> select
> #2/0,2,Z,O,f,R,C,E,G,I,J,K,L,N,P,X,Y,N,c,i,F,H,M,O,,S,T,V,W,,d,e,g,n,U,R
Expected an objects specifier or a keyword
> select add
> #2/0,2,Z,O,f,R,C,E,G,I,J,K,L,N,P,X,Y,N,c,i,F,H,M,O,,S,T,V,W,,d,e,g,n,U,R
Expected an objects specifier or a keyword
> select #2/0 #2/2 #2/Z #2/O #2/f #2/R #2/C #2/E #2/G #2/I #2/J #2/K #2/L #2/N
> #2/P #2/X #2/Y #2/c #2/i #2/F #2/H #2/M #2/S #2/T #2/V #2/W #2/d #2/e #2/g
> #2/n #2/U
132579 atoms, 137866 bonds, 6322 residues, 1 model selected
> delete #2/0 #2/2 #2/Z #2/O #2/f #2/R #2/C #2/E #2/G #2/I #2/J #2/K #2/L #2/N
> #2/P #2/X #2/Y #2/c #2/i #2/F #2/H #2/M #2/S #2/T #2/V #2/W #2/d #2/e #2/g
> #2/n #2/U
> select #2/I
Nothing selected
> select #2/I
Nothing selected
> select #2/l:12
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
487 atoms, 488 bonds, 23 residues, 1 model selected
> select up
529 atoms, 530 bonds, 25 residues, 1 model selected
> select #2/l
529 atoms, 530 bonds, 25 residues, 1 model selected
> delete #2/l
> delete #2/b
> delete #2/x
> delete #2/a
> select #2/h
16796 atoms, 16949 bonds, 3 pseudobonds, 1040 residues, 2 models selected
> select ~sel & ##selected
75699 atoms, 76476 bonds, 2 pseudobonds, 4723 residues, 2 models selected
> save
> /Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/DEAHelicase_reference_models/eIF3_fit2J1716.cif
> models #2 selectedOnly true relModel #3
Not saving entity_poly_seq for non-authoritative sequences
> show #!1 models
> save
> /Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/DEAHelicase_reference_models/DHX29_40Scorr_eIF3_U70_2026may12fit2J1716_0.cif
> relModel #3
Not saving entity_poly_seq for non-authoritative sequences
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.12rc202605050149 (2026-05-05)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/DEAHelicase_reference_models/DHX29_40Scorr_eIF3_U70_2026may12fit2J1716_0.cif
Summary of feedback from opening
/Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/DEAHelicase_reference_models/DHX29_40Scorr_eIF3_U70_2026may12fit2J1716_0.cif
---
warnings | Unknown polymer entity '1' on line 10160
Unknown polymer entity '12' on line 86375
Missing or incorrect sequence information. Inferred polymer connectivity.
Unknown polymer entity '1' on line 103244
Unknown polymer entity '2' on line 158110
Unknown polymer entity '3' on line 161518
Unknown polymer entity '4' on line 165034
Unknown polymer entity '5' on line 168566
29 messages similar to the above omitted
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for DHX29_40Scorr_eIF3_U70_2026may12fit2J1716_0.cif
---
Chain | Description
1.2/B | 18S ribosomal RNA
1.2/BA | ribosomal protein uS2
1.2/BB | ribosomal protein eS1
1.2/BC | ribosomal protein uS5
1.2/BD | ribosomal protein uS3
1.2/BE | ribosomal protein eS4
1.2/BF | ribosomal protein uS7
1.2/BG | ribosomal protein eS6
1.2/BH | ribosomal protein eS7
1.2/BI | ribosomal protein eS8
1.2/BJ | ribosomal protein uS4
1.2/BK | ribosomal protein eS10
1.2/BL | ribosomal protein uS17
1.2/BM | ribosomal protein eS12
1.2/BN | ribosomal protein uS15
1.2/BO | ribosomal protein uS11
1.2/BP | ribosomal protein uS19
1.2/BQ | ribosomal protein uS9
1.2/BR | ribosomal protein eS17
1.2/BS | ribosomal protein uS13
1.2/BT | ribosomal protein eS19
1.2/BU | ribosomal protein uS10
1.2/BV | ribosomal protein eS21
1.2/BW | ribosomal protein uS8
1.2/BX | ribosomal protein uS12
1.2/BY | ribosomal protein eS24
1.2/BZ | ribosomal protein eS25
1.2/Ba | ribosomal protein eS26
1.2/Bb | ribosomal protein eS27
1.2/Bc | ribosomal protein eS28
1.2/Bd | ribosomal protein uS14
1.2/Be | ribosomal protein eS30
1.2/Bf | ribosomal protein eS31
1.2/Bg | ribosomal protein RACK 1
1.1/D | No description available
1.1/Q | No description available
1.1/h | No description available
1.1/j | No description available
1.1/k | No description available
1.1/p | No description available
1.1/q | No description available
1.1/r | No description available
1.1/s | No description available
1.1/t | No description available
1.1/u | No description available
1.1/y | No description available
1.1/z | No description available
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac mini
Model Identifier: Mac14,12
Model Number: Z170000G0LL/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 32 GB
System Firmware Version: mBoot-18000.101.7
OS Loader Version: 11881.140.96.701.1
Software:
System Software Overview:
System Version: macOS 15.7.5 (24G624)
Kernel Version: Darwin 24.6.0
Time since boot: 12 days, 20 hours, 14 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Studio Display:
Display Type: Retina LCD
Resolution: 5120 x 2880 Retina
Display Serial Number: H70HGX7Y9X
Display Firmware Version: Version 17.0 (Build 21A329)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.1.2
bs4: 0.0.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.67.1
ChimeraX-AtomicLibrary: 14.4
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12rc202605050149
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.2
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchAlign: 1.1
ChimeraX-MatchMaker: 2.4
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.8
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.6
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
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
click: 8.3.3
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.5
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.20
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.62.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.13
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.20.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.9.6
plotly: 6.7.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.13.3
pydantic-settings: 2.14.0
pydantic_core: 2.46.3
pydata-sphinx-theme: 0.17.1
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.1
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.10.2
PyQt6-Qt6: 6.10.1
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.1
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.27
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.4.1
stack-data: 0.6.3
starlette: 1.0.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 3.2.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.5
tqdm: 4.67.3
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
Unidecode: 1.4.0
urllib3: 2.6.3
uvicorn: 0.46.0
wcwidth: 0.7.0
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
yarl: 1.23.0
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