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Opened 112 minutes ago
#19732 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-26.2-arm64-arm-64bit
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/jinfanwang/Downloads/6ZSE (1).cif"
Summary of feedback from opening /Users/jinfanwang/Downloads/6ZSE (1).cif
---
warning | Expected gap or connection between 004 /A:7 and MHT /A:8
6ZSE (1).cif title:
Human mitochondrial ribosome in complex with mRNA, A/P-tRNA and P/E-tRNA [more
info...]
Chain information for 6ZSE (1).cif #1
---
Chain | Description | UniProt
0 | 39S ribosomal protein L32, mitochondrial | RM32_HUMAN 1-188
1 | 39S ribosomal protein L33, mitochondrial | RM33_HUMAN 1-65
2 | 39S ribosomal protein L34, mitochondrial | RM34_HUMAN 1-92
3 | 39S ribosomal protein L35, mitochondrial | RM35_HUMAN 1-188
4 | 39S ribosomal protein L36, mitochondrial | RM36_HUMAN 1-103
5 | 39S ribosomal protein L37, mitochondrial | RM37_HUMAN 1-423
6 | 39S ribosomal protein L38, mitochondrial | RM38_HUMAN 1-380
7 | 39S ribosomal protein L39, mitochondrial | RM39_HUMAN 1-338
8 | 39S ribosomal protein L40, mitochondrial | RM40_HUMAN 1-206
9 | 39S ribosomal protein L41, mitochondrial | RM41_HUMAN 1-137
A | Quinupristin |
A0 | 28S ribosomal protein S34, mitochondrial | RT34_HUMAN 1-218
A1 | 28S ribosomal protein S35, mitochondrial | RT35_HUMAN 1-323
A2 | Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 | CHCH1_HUMAN 1-118
A3 | Aurora kinase A-interacting protein | AKIP_HUMAN 1-199
A4 | Pentatricopeptide repeat domain-containing protein 3, mitochondrial | PTCD3_HUMAN 1-689
AA | 12S mitochondrial rRNA |
AB | 28S ribosomal protein S2, mitochondrial | RT02_HUMAN 1-296
AC | 28S ribosomal protein S24, mitochondrial | RT24_HUMAN 1-167
AD | 28S ribosomal protein S5, mitochondrial | RT05_HUMAN 1-430
AE | 28S ribosomal protein S6, mitochondrial | RT06_HUMAN 1-125
AF | 28S ribosomal protein S7, mitochondrial | RT07_HUMAN 1-242
AG | 28S ribosomal protein S9, mitochondrial | RT09_HUMAN 1-396
AH | 28S ribosomal protein S10, mitochondrial | RT10_HUMAN 1-201
AI | 28S ribosomal protein S11, mitochondrial | RT11_HUMAN 1-194
AJ | 28S ribosomal protein S12, mitochondrial | RT12_HUMAN 1-138
AK | 28S ribosomal protein S14, mitochondrial | RT14_HUMAN 1-128
AL | 28S ribosomal protein S15, mitochondrial | RT15_HUMAN 1-257
AM | 28S ribosomal protein S16, mitochondrial | RT16_HUMAN 1-137
AN | 28S ribosomal protein S17, mitochondrial | RT17_HUMAN 1-130
AO | 28S ribosomal protein S18b, mitochondrial | RT18B_HUMAN 1-258
AP | 28S ribosomal protein S18c, mitochondrial | RT18C_HUMAN 1-142
AQ | 28S ribosomal protein S21, mitochondrial | RT21_HUMAN 1-87
AR | 28S ribosomal protein S22, mitochondrial | RT22_HUMAN 1-360
AS | 28S ribosomal protein S23, mitochondrial | RT23_HUMAN 1-190
AT | 28S ribosomal protein S25, mitochondrial | RT25_HUMAN 1-173
AU | 28S ribosomal protein S26, mitochondrial | RT26_HUMAN 1-205
AV | 28S ribosomal protein S27, mitochondrial | RT27_HUMAN 1-414
AW | 28S ribosomal protein S28, mitochondrial | RT28_HUMAN 1-187
AX | 28S ribosomal protein S29, mitochondrial | RT29_HUMAN 1-398
AY | 28S ribosomal protein S31, mitochondrial | RT31_HUMAN 1-395
AZ | 28S ribosomal protein S33, mitochondrial | RT33_HUMAN 1-106
XA | 16S mitochondrial rRNA |
XB | mitochondrial tRNAVal |
XD | 39S ribosomal protein L2, mitochondrial | RM02_HUMAN 1-305
XE | 39S ribosomal protein L3, mitochondrial | RM03_HUMAN 1-348
XF | 39S ribosomal protein L4, mitochondrial | RM04_HUMAN 1-311
XH | 39S ribosomal protein L9, mitochondrial | RM09_HUMAN 1-267
XI | 39S ribosomal protein L10, mitochondrial | RM10_HUMAN 1-261
XJ | 39S ribosomal protein L11, mitochondrial | RM11_HUMAN 1-190
XK | 39S ribosomal protein L13, mitochondrial | RM13_HUMAN 1-178
XL | 39S ribosomal protein L14, mitochondrial | RM14_HUMAN 1-145
XM | 39S ribosomal protein L15, mitochondrial | RM15_HUMAN 1-296
XN | 39S ribosomal protein L16, mitochondrial | RM16_HUMAN 1-251
XO | 39S ribosomal protein L17, mitochondrial | RM17_HUMAN 1-175
XP | 39S ribosomal protein L18, mitochondrial | RM18_HUMAN 0-179
XQ | 39S ribosomal protein L19, mitochondrial | RM19_HUMAN 1-292
XR | 39S ribosomal protein L20, mitochondrial | RM20_HUMAN 1-149
XS | 39S ribosomal protein L21, mitochondrial | RM21_HUMAN 1-205
XT | 39S ribosomal protein L22, mitochondrial | RM22_HUMAN 7-212
XU | 39S ribosomal protein L23, mitochondrial | RM23_HUMAN 1-153
XV | 39S ribosomal protein L24, mitochondrial | RM24_HUMAN 1-216
XW | 39S ribosomal protein L27, mitochondrial | RM27_HUMAN 1-148
XX | 39S ribosomal protein L28, mitochondrial | RM28_HUMAN 1-256
XY | 39S ribosomal protein L47, mitochondrial | RM47_HUMAN 1-250
XZ | 39S ribosomal protein L30, mitochondrial | RM30_HUMAN 1-161
a | 39S ribosomal protein L42, mitochondrial | RM42_HUMAN 1-142
b | 39S ribosomal protein L43, mitochondrial | RM43_HUMAN 1-215
c | 39S ribosomal protein L44, mitochondrial | RM44_HUMAN 1-332
d | 39S ribosomal protein L45, mitochondrial | RM45_HUMAN 8-306
e | 39S ribosomal protein L46, mitochondrial | RM46_HUMAN 1-279
f | 39S ribosomal protein L48, mitochondrial | RM48_HUMAN 1-212
g | 39S ribosomal protein L49, mitochondrial | RM49_HUMAN 1-166
h | 39S ribosomal protein L50, mitochondrial | RM50_HUMAN 1-158
i | 39S ribosomal protein L51, mitochondrial | RM51_HUMAN 1-128
j | 39S ribosomal protein L52, mitochondrial | RM52_HUMAN 1-123
k | 39S ribosomal protein L53, mitochondrial | RM53_HUMAN 1-112
l | 39S ribosomal protein L54, mitochondrial | RM54_HUMAN 1-138
m | 39S ribosomal protein L55, mitochondrial | RM55_HUMAN 1-127
o | Ribosomal protein 63, mitochondrial | RT63_HUMAN 1-102
p | Peptidyl-tRNA hydrolase ICT1, mitochondrial | ICT1_HUMAN 1-206
q | Growth arrest and DNA damage-inducible proteins-interacting protein 1 | G45IP_HUMAN 1-222
r | 39S ribosomal protein S18a, mitochondrial | RT18A_HUMAN 1-196
r1 | mRNA |
r2 | A/P-tRNA |
r3 | P/E-tRNA |
s | 39S ribosomal protein S30, mitochondrial | RT30_HUMAN 1-439
t1 t2 t3 t4 t5 t6 | 39S ribosomal protein L12, mitochondrial | RM12_HUMAN -60-137
Non-standard residues in 6ZSE (1).cif #1
---
004 — (2S)-amino(phenyl)ethanoic acid (L-Phenylglycine)
DBB — D-α-aminobutyric acid
DOL — 5-(2-diethylamino-
ethanesulfonyl)-21-hydroxy-10-isopropyl-11,19-dimethyl-9,26-dioxa-3,15,28-triaza-
tricyclo[23.2.1.00,255]octacosa-1(27),12,17,19,25(28)-pentaene-2,8,14,23-tetraone
(dalfopristin)
GTP — guanosine-5'-triphosphate
MG — magnesium ion
MHT — (3S)-3-(methylsulfanyl)-1-azabicyclo[2.2.2]octane
MHV — 4-oxo-L-pipecolic acid
MHW — 3-hydroxypicolinic acid
Y5P — 1-(5-O-phosphono-beta-D-ribofuranosyl)-1,4-dihydropyrimidine (pyrimidine
riboside-5'-monophosphate)
ZN — zinc ion
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open /Users/jinfanwang/Downloads/6ZSD.cif
Summary of feedback from opening /Users/jinfanwang/Downloads/6ZSD.cif
---
warnings | Expected gap or connection between 004 /A:7 and MHT /A:8
Atom HO5' is not in the residue template for G /XA:1671
6ZSD.cif title:
Human mitochondrial ribosome in complex with mRNA, P-site tRNA and E-site tRNA
[more info...]
Chain information for 6ZSD.cif #2
---
Chain | Description | UniProt
0 | 39S ribosomal protein L32, mitochondrial | RM32_HUMAN 1-188
1 | 39S ribosomal protein L33, mitochondrial | RM33_HUMAN 1-65
2 | 39S ribosomal protein L34, mitochondrial | RM34_HUMAN 1-92
3 | 39S ribosomal protein L35, mitochondrial | RM35_HUMAN 1-188
4 | 39S ribosomal protein L36, mitochondrial | RM36_HUMAN 1-103
5 | 39S ribosomal protein L37, mitochondrial | RM37_HUMAN 1-423
6 | 39S ribosomal protein L38, mitochondrial | RM38_HUMAN 1-380
7 | 39S ribosomal protein L39, mitochondrial | RM39_HUMAN 1-338
8 | 39S ribosomal protein L40, mitochondrial | RM40_HUMAN 1-206
9 | 39S ribosomal protein L41, mitochondrial | RM41_HUMAN 1-137
A | Quinupristin |
A0 | 28S ribosomal protein S34, mitochondrial | RT34_HUMAN 1-218
A1 | 28S ribosomal protein S35, mitochondrial | RT35_HUMAN 1-323
A2 | Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 | CHCH1_HUMAN 1-118
A3 | Aurora kinase A-interacting protein | AKIP_HUMAN 1-199
A4 | Pentatricopeptide repeat domain-containing protein 3, mitochondrial | PTCD3_HUMAN 1-689
AA | 12S mitochondrial rRNA |
AB | 28S ribosomal protein S2, mitochondrial | RT02_HUMAN 1-296
AC | 28S ribosomal protein S24, mitochondrial | RT24_HUMAN 1-167
AD | 28S ribosomal protein S5, mitochondrial | RT05_HUMAN 1-430
AE | 28S ribosomal protein S6, mitochondrial | RT06_HUMAN 1-125
AF | 28S ribosomal protein S7, mitochondrial | RT07_HUMAN 1-242
AG | 28S ribosomal protein S9, mitochondrial | RT09_HUMAN 1-396
AH | 28S ribosomal protein S10, mitochondrial | RT10_HUMAN 1-201
AI | 28S ribosomal protein S11, mitochondrial | RT11_HUMAN 1-194
AJ | 28S ribosomal protein S12, mitochondrial | RT12_HUMAN 1-138
AK | 28S ribosomal protein S14, mitochondrial | RT14_HUMAN 1-128
AL | 28S ribosomal protein S15, mitochondrial | RT15_HUMAN 1-257
AM | 28S ribosomal protein S16, mitochondrial | RT16_HUMAN 1-137
AN | 28S ribosomal protein S17, mitochondrial | RT17_HUMAN 1-130
AO | 28S ribosomal protein S18b, mitochondrial | RT18B_HUMAN 1-258
AP | 28S ribosomal protein S18c, mitochondrial | RT18C_HUMAN 1-142
AQ | 28S ribosomal protein S21, mitochondrial | RT21_HUMAN 1-87
AR | 28S ribosomal protein S22, mitochondrial | RT22_HUMAN 1-360
AS | 28S ribosomal protein S23, mitochondrial | RT23_HUMAN 1-190
AT | 28S ribosomal protein S25, mitochondrial | RT25_HUMAN 1-173
AU | 28S ribosomal protein S26, mitochondrial | RT26_HUMAN 1-205
AV | 28S ribosomal protein S27, mitochondrial | RT27_HUMAN 1-414
AW | 28S ribosomal protein S28, mitochondrial | RT28_HUMAN 1-187
AX | 28S ribosomal protein S29, mitochondrial | RT29_HUMAN 1-398
AY | 28S ribosomal protein S31, mitochondrial | RT31_HUMAN 1-395
AZ | 28S ribosomal protein S33, mitochondrial | RT33_HUMAN 1-106
XA | 16S mitochondrial rRNA |
XB | mitochondrial tRNAVal |
XD | 39S ribosomal protein L2, mitochondrial | RM02_HUMAN 1-305
XE | 39S ribosomal protein L3, mitochondrial | RM03_HUMAN 1-348
XF | 39S ribosomal protein L4, mitochondrial | RM04_HUMAN 1-311
XH | 39S ribosomal protein L9, mitochondrial | RM09_HUMAN 1-267
XI | 39S ribosomal protein L10, mitochondrial | RM10_HUMAN 1-261
XJ | 39S ribosomal protein L11, mitochondrial | RM11_HUMAN 1-190
XK | 39S ribosomal protein L13, mitochondrial | RM13_HUMAN 1-178
XL | 39S ribosomal protein L14, mitochondrial | RM14_HUMAN 1-145
XM | 39S ribosomal protein L15, mitochondrial | RM15_HUMAN 1-296
XN | 39S ribosomal protein L16, mitochondrial | RM16_HUMAN 1-251
XO | 39S ribosomal protein L17, mitochondrial | RM17_HUMAN 1-175
XP | 39S ribosomal protein L18, mitochondrial | RM18_HUMAN 0-179
XQ | 39S ribosomal protein L19, mitochondrial | RM19_HUMAN 1-292
XR | 39S ribosomal protein L20, mitochondrial | RM20_HUMAN 1-149
XS | 39S ribosomal protein L21, mitochondrial | RM21_HUMAN 1-205
XT | 39S ribosomal protein L22, mitochondrial | RM22_HUMAN 7-212
XU | 39S ribosomal protein L23, mitochondrial | RM23_HUMAN 1-153
XV | 39S ribosomal protein L24, mitochondrial | RM24_HUMAN 1-216
XW | 39S ribosomal protein L27, mitochondrial | RM27_HUMAN 1-148
XX | 39S ribosomal protein L28, mitochondrial | RM28_HUMAN 1-256
XY | 39S ribosomal protein L47, mitochondrial | RM47_HUMAN 1-250
XZ | 39S ribosomal protein L30, mitochondrial | RM30_HUMAN 1-161
a | 39S ribosomal protein L42, mitochondrial | RM42_HUMAN 1-142
b | 39S ribosomal protein L43, mitochondrial | RM43_HUMAN 1-215
c | 39S ribosomal protein L44, mitochondrial | RM44_HUMAN 1-332
d | 39S ribosomal protein L45, mitochondrial | RM45_HUMAN 8-306
e | 39S ribosomal protein L46, mitochondrial | RM46_HUMAN 1-279
f | 39S ribosomal protein L48, mitochondrial | RM48_HUMAN 1-212
g | 39S ribosomal protein L49, mitochondrial | RM49_HUMAN 1-166
h | 39S ribosomal protein L50, mitochondrial | RM50_HUMAN 1-158
i | 39S ribosomal protein L51, mitochondrial | RM51_HUMAN 1-128
j | 39S ribosomal protein L52, mitochondrial | RM52_HUMAN 1-123
k | 39S ribosomal protein L53, mitochondrial | RM53_HUMAN 1-112
l | 39S ribosomal protein L54, mitochondrial | RM54_HUMAN 1-138
m | 39S ribosomal protein L55, mitochondrial | RM55_HUMAN 1-127
o | Ribosomal protein 63, mitochondrial | RT63_HUMAN 1-102
p | Peptidyl-tRNA hydrolase ICT1, mitochondrial | ICT1_HUMAN 1-206
q | Growth arrest and DNA damage-inducible proteins-interacting protein 1 | G45IP_HUMAN 1-222
r | 39S ribosomal protein S18a, mitochondrial | RT18A_HUMAN 1-196
r1 | mRNA |
r3 | P-site tRNA |
r4 | E-site tRNA |
s | 39S ribosomal protein S30, mitochondrial | RT30_HUMAN 1-439
t1 t2 t3 t4 t5 t6 | 39S ribosomal protein L12, mitochondrial | RM12_HUMAN -60-137
Non-standard residues in 6ZSD.cif #2
---
004 — (2S)-amino(phenyl)ethanoic acid (L-Phenylglycine)
DBB — D-α-aminobutyric acid
DOL — 5-(2-diethylamino-
ethanesulfonyl)-21-hydroxy-10-isopropyl-11,19-dimethyl-9,26-dioxa-3,15,28-triaza-
tricyclo[23.2.1.00,255]octacosa-1(27),12,17,19,25(28)-pentaene-2,8,14,23-tetraone
(dalfopristin)
GTP — guanosine-5'-triphosphate
MG — magnesium ion
MHT — (3S)-3-(methylsulfanyl)-1-azabicyclo[2.2.2]octane
MHV — 4-oxo-L-pipecolic acid
MHW — 3-hydroxypicolinic acid
Y5P — 1-(5-O-phosphono-beta-D-ribofuranosyl)-1,4-dihydropyrimidine (pyrimidine
riboside-5'-monophosphate)
ZN — zinc ion
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open "/Users/jinfanwang/Downloads/6ZSA (2).cif"
Summary of feedback from opening /Users/jinfanwang/Downloads/6ZSA (2).cif
---
warning | Atom OP2 has no neighbors to form bonds with according to residue template for A /XA:2355
6ZSA (2).cif title:
Human mitochondrial ribosome bound to mRNA, A-site tRNA and P-site tRNA [more
info...]
Chain information for 6ZSA (2).cif #3
---
Chain | Description | UniProt
0 | 39S ribosomal protein L32, mitochondrial | RM32_HUMAN 1-188
1 | 39S ribosomal protein L33, mitochondrial | RM33_HUMAN 1-65
2 | 39S ribosomal protein L34, mitochondrial | RM34_HUMAN 1-92
3 | 39S ribosomal protein L35, mitochondrial | RM35_HUMAN 1-188
4 | 39S ribosomal protein L36, mitochondrial | RM36_HUMAN 1-103
5 | 39S ribosomal protein L37, mitochondrial | RM37_HUMAN 1-423
6 | 39S ribosomal protein L38, mitochondrial | RM38_HUMAN 1-380
7 | 39S ribosomal protein L39, mitochondrial | RM39_HUMAN 1-338
8 | 39S ribosomal protein L40, mitochondrial | RM40_HUMAN 1-206
9 | 39S ribosomal protein L41, mitochondrial | RM41_HUMAN 1-137
A0 | 28S ribosomal protein S34, mitochondrial | RT34_HUMAN 1-218
A1 | 28S ribosomal protein S35, mitochondrial | RT35_HUMAN 1-323
A2 | Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 | CHCH1_HUMAN 1-118
A3 | Aurora kinase A-interacting protein | AKIP_HUMAN 1-199
A4 | Pentatricopeptide repeat domain-containing protein 3, mitochondrial | PTCD3_HUMAN 1-689
AA | 12S mitochondrial rRNA |
AB | 28S ribosomal protein S2, mitochondrial | RT02_HUMAN 1-296
AC | 28S ribosomal protein S24, mitochondrial | RT24_HUMAN 1-167
AD | 28S ribosomal protein S5, mitochondrial | RT05_HUMAN 1-430
AE | 28S ribosomal protein S6, mitochondrial | RT06_HUMAN 1-125
AF | 28S ribosomal protein S7, mitochondrial | RT07_HUMAN 1-242
AG | 28S ribosomal protein S9, mitochondrial | RT09_HUMAN 1-396
AH | 28S ribosomal protein S10, mitochondrial | RT10_HUMAN 1-201
AI | 28S ribosomal protein S11, mitochondrial | RT11_HUMAN 1-194
AJ | 28S ribosomal protein S12, mitochondrial | RT12_HUMAN 1-138
AK | 28S ribosomal protein S14, mitochondrial | RT14_HUMAN 1-128
AL | 28S ribosomal protein S15, mitochondrial | RT15_HUMAN 1-257
AM | 28S ribosomal protein S16, mitochondrial | RT16_HUMAN 1-137
AN | 28S ribosomal protein S17, mitochondrial | RT17_HUMAN 1-130
AO | 28S ribosomal protein S18b, mitochondrial | RT18B_HUMAN 1-258
AP | 28S ribosomal protein S18c, mitochondrial | RT18C_HUMAN 1-142
AQ | 28S ribosomal protein S21, mitochondrial | RT21_HUMAN 1-87
AR | 28S ribosomal protein S22, mitochondrial | RT22_HUMAN 1-360
AS | 28S ribosomal protein S23, mitochondrial | RT23_HUMAN 1-190
AT | 28S ribosomal protein S25, mitochondrial | RT25_HUMAN 1-173
AU | 28S ribosomal protein S26, mitochondrial | RT26_HUMAN 1-205
AV | 28S ribosomal protein S27, mitochondrial | RT27_HUMAN 1-414
AW | 28S ribosomal protein S28, mitochondrial | RT28_HUMAN 1-187
AX | 28S ribosomal protein S29, mitochondrial | RT29_HUMAN 1-398
AY | 28S ribosomal protein S31, mitochondrial | RT31_HUMAN 1-395
AZ | 28S ribosomal protein S33, mitochondrial | RT33_HUMAN 1-106
XA | 16S mitochondrial rRNA |
XB | mitochondrial tRNAVal |
XD | 39S ribosomal protein L2, mitochondrial | RM02_HUMAN 1-305
XE | 39S ribosomal protein L3, mitochondrial | RM03_HUMAN 1-348
XF | 39S ribosomal protein L4, mitochondrial | RM04_HUMAN 1-311
XH | 39S ribosomal protein L9, mitochondrial | RM09_HUMAN 1-267
XI | 39S ribosomal protein L10, mitochondrial | RM10_HUMAN 1-261
XJ | 39S ribosomal protein L11, mitochondrial | RM11_HUMAN 1-190
XK | 39S ribosomal protein L13, mitochondrial | RM13_HUMAN 1-178
XL | 39S ribosomal protein L14, mitochondrial | RM14_HUMAN 1-145
XM | 39S ribosomal protein L15, mitochondrial | RM15_HUMAN 1-296
XN | 39S ribosomal protein L16, mitochondrial | RM16_HUMAN 1-251
XO | 39S ribosomal protein L17, mitochondrial | RM17_HUMAN 1-175
XP | 39S ribosomal protein L18, mitochondrial | RM18_HUMAN 0-179
XQ | 39S ribosomal protein L19, mitochondrial | RM19_HUMAN 1-292
XR | 39S ribosomal protein L20, mitochondrial | RM20_HUMAN 1-149
XS | 39S ribosomal protein L21, mitochondrial | RM21_HUMAN 1-205
XT | 39S ribosomal protein L22, mitochondrial | RM22_HUMAN 7-212
XU | 39S ribosomal protein L23, mitochondrial | RM23_HUMAN 1-153
XV | 39S ribosomal protein L24, mitochondrial | RM24_HUMAN 1-216
XW | 39S ribosomal protein L27, mitochondrial | RM27_HUMAN 1-148
XX | 39S ribosomal protein L28, mitochondrial | RM28_HUMAN 1-256
XY | 39S ribosomal protein L47, mitochondrial | RM47_HUMAN 1-250
XZ | 39S ribosomal protein L30, mitochondrial | RM30_HUMAN 1-161
a | 39S ribosomal protein L42, mitochondrial | RM42_HUMAN 1-142
b | 39S ribosomal protein L43, mitochondrial | RM43_HUMAN 1-215
c | 39S ribosomal protein L44, mitochondrial | RM44_HUMAN 1-332
d | 39S ribosomal protein L45, mitochondrial | RM45_HUMAN 8-306
e | 39S ribosomal protein L46, mitochondrial | RM46_HUMAN 1-279
f | 39S ribosomal protein L48, mitochondrial | RM48_HUMAN 1-212
g | 39S ribosomal protein L49, mitochondrial | RM49_HUMAN 1-166
h | 39S ribosomal protein L50, mitochondrial | RM50_HUMAN 1-158
i | 39S ribosomal protein L51, mitochondrial | RM51_HUMAN 1-128
j | 39S ribosomal protein L52, mitochondrial | RM52_HUMAN 1-123
k | 39S ribosomal protein L53, mitochondrial | RM53_HUMAN 1-112
l | 39S ribosomal protein L54, mitochondrial | RM54_HUMAN 1-138
m | 39S ribosomal protein L55, mitochondrial | RM55_HUMAN 1-127
o | Ribosomal protein 63, mitochondrial | RT63_HUMAN 1-102
p | Peptidyl-tRNA hydrolase ICT1, mitochondrial | ICT1_HUMAN 1-206
q | Growth arrest and DNA damage-inducible proteins-interacting protein 1 | G45IP_HUMAN 1-222
r | 39S ribosomal protein S18a, mitochondrial | RT18A_HUMAN 1-196
r1 | mRNA |
r2 | A-site tRNA |
r3 | P-site tRNA |
s | 39S ribosomal protein S30, mitochondrial | RT30_HUMAN 1-439
t1 t2 t3 t4 t5 t6 | 39S ribosomal protein L12, mitochondrial | RM12_HUMAN -60-137
Non-standard residues in 6ZSA (2).cif #3
---
DOL — 5-(2-diethylamino-
ethanesulfonyl)-21-hydroxy-10-isopropyl-11,19-dimethyl-9,26-dioxa-3,15,28-triaza-
tricyclo[23.2.1.00,255]octacosa-1(27),12,17,19,25(28)-pentaene-2,8,14,23-tetraone
(dalfopristin)
GTP — guanosine-5'-triphosphate
H8Q —
~{N}-[(3~{S},6~{R},12~{R},15~{S},16~{S},19~{S},22~{S},25~{S})-25-[[(3~{S})-1-azabicyclo[2.2.2]octan-3-yl]sulfanylmethyl]-3-[[4-(dimethylamino)phenyl]methyl]-12-ethyl-4,16-dimethyl-2,5,11,14,18,21,24-heptakis(oxidanylidene)-19-phenyl-17-oxa-1,4,10,13,20-pentazatricyclo[20.4.0.0^{6,10}]hexacosan-15-yl]-3-oxidanyl-
pyridine-2-carboxamide (quinupristin)
MG — magnesium ion
Y5P — 1-(5-O-phosphono-beta-D-ribofuranosyl)-1,4-dihydropyrimidine (pyrimidine
riboside-5'-monophosphate)
ZN — zinc ion
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open /Users/jinfanwang/Downloads/6ZSG.cif
Summary of feedback from opening /Users/jinfanwang/Downloads/6ZSG.cif
---
warning | Expected gap or connection between 004 /A:7 and MHT /A:8
6ZSG.cif title:
Human mitochondrial ribosome in complex with mRNA, A-site tRNA, P-site tRNA
and E-site tRNA [more info...]
Chain information for 6ZSG.cif #4
---
Chain | Description | UniProt
0 | 39S ribosomal protein L32, mitochondrial | RM32_HUMAN 1-188
1 | 39S ribosomal protein L33, mitochondrial | RM33_HUMAN 1-65
2 | 39S ribosomal protein L34, mitochondrial | RM34_HUMAN 1-92
3 | 39S ribosomal protein L35, mitochondrial | RM35_HUMAN 1-188
4 | 39S ribosomal protein L36, mitochondrial | RM36_HUMAN 1-103
5 | 39S ribosomal protein L37, mitochondrial | RM37_HUMAN 1-423
6 | 39S ribosomal protein L38, mitochondrial | RM38_HUMAN 1-380
7 | 39S ribosomal protein L39, mitochondrial | RM39_HUMAN 1-338
8 | 39S ribosomal protein L40, mitochondrial | RM40_HUMAN 1-206
9 | 39S ribosomal protein L41, mitochondrial | RM41_HUMAN 1-137
A | Quinupristin |
A0 | 28S ribosomal protein S34, mitochondrial | RT34_HUMAN 1-218
A1 | 28S ribosomal protein S35, mitochondrial | RT35_HUMAN 1-323
A2 | Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 | CHCH1_HUMAN 1-118
A3 | Aurora kinase A-interacting protein | AKIP_HUMAN 1-199
A4 | Pentatricopeptide repeat domain-containing protein 3, mitochondrial | PTCD3_HUMAN 1-689
AA | 12S mitochondrial rRNA |
AB | 28S ribosomal protein S2, mitochondrial | RT02_HUMAN 1-296
AC | 28S ribosomal protein S24, mitochondrial | RT24_HUMAN 1-167
AD | 28S ribosomal protein S5, mitochondrial | RT05_HUMAN 1-430
AE | 28S ribosomal protein S6, mitochondrial | RT06_HUMAN 1-125
AF | 28S ribosomal protein S7, mitochondrial | RT07_HUMAN 1-242
AG | 28S ribosomal protein S9, mitochondrial | RT09_HUMAN 1-396
AH | 28S ribosomal protein S10, mitochondrial | RT10_HUMAN 1-201
AI | 28S ribosomal protein S11, mitochondrial | RT11_HUMAN 1-194
AJ | 28S ribosomal protein S12, mitochondrial | RT12_HUMAN 1-138
AK | 28S ribosomal protein S14, mitochondrial | RT14_HUMAN 1-128
AL | 28S ribosomal protein S15, mitochondrial | RT15_HUMAN 1-257
AM | 28S ribosomal protein S16, mitochondrial | RT16_HUMAN 1-137
AN | 28S ribosomal protein S17, mitochondrial | RT17_HUMAN 1-130
AO | 28S ribosomal protein S18b, mitochondrial | RT18B_HUMAN 1-258
AP | 28S ribosomal protein S18c, mitochondrial | RT18C_HUMAN 1-142
AQ | 28S ribosomal protein S21, mitochondrial | RT21_HUMAN 2-87
AR | 28S ribosomal protein S22, mitochondrial | RT22_HUMAN 1-360
AS | 28S ribosomal protein S23, mitochondrial | RT23_HUMAN 1-190
AT | 28S ribosomal protein S25, mitochondrial | RT25_HUMAN 1-173
AU | 28S ribosomal protein S26, mitochondrial | RT26_HUMAN 1-205
AV | 28S ribosomal protein S27, mitochondrial | RT27_HUMAN 1-414
AW | 28S ribosomal protein S28, mitochondrial | RT28_HUMAN 1-187
AX | 28S ribosomal protein S29, mitochondrial | RT29_HUMAN 1-398
AY | 28S ribosomal protein S31, mitochondrial | RT31_HUMAN 1-395
AZ | 28S ribosomal protein S33, mitochondrial | RT33_HUMAN 1-106
XA | 16S mitochondrial rRNA |
XB | mitochondrial tRNAVal |
XD | 39S ribosomal protein L2, mitochondrial | RM02_HUMAN 1-305
XE | 39S ribosomal protein L3, mitochondrial | RM03_HUMAN 1-348
XF | 39S ribosomal protein L4, mitochondrial | RM04_HUMAN 1-311
XH | 39S ribosomal protein L9, mitochondrial | RM09_HUMAN 1-267
XI | 39S ribosomal protein L10, mitochondrial | RM10_HUMAN 1-261
XJ | 39S ribosomal protein L11, mitochondrial | RM11_HUMAN 1-190
XK | 39S ribosomal protein L13, mitochondrial | RM13_HUMAN 1-178
XL | 39S ribosomal protein L14, mitochondrial | RM14_HUMAN 1-145
XM | 39S ribosomal protein L15, mitochondrial | RM15_HUMAN 1-296
XN | 39S ribosomal protein L16, mitochondrial | RM16_HUMAN 1-251
XO | 39S ribosomal protein L17, mitochondrial | RM17_HUMAN 1-175
XP | 39S ribosomal protein L18, mitochondrial | RM18_HUMAN 0-179
XQ | 39S ribosomal protein L19, mitochondrial | RM19_HUMAN 1-292
XR | 39S ribosomal protein L20, mitochondrial | RM20_HUMAN 1-149
XS | 39S ribosomal protein L21, mitochondrial | RM21_HUMAN 1-205
XT | 39S ribosomal protein L22, mitochondrial | RM22_HUMAN 7-212
XU | 39S ribosomal protein L23, mitochondrial | RM23_HUMAN 1-153
XV | 39S ribosomal protein L24, mitochondrial | RM24_HUMAN 1-216
XW | 39S ribosomal protein L27, mitochondrial | RM27_HUMAN 1-148
XX | 39S ribosomal protein L28, mitochondrial | RM28_HUMAN 1-256
XY | 39S ribosomal protein L47, mitochondrial | RM47_HUMAN 1-250
XZ | 39S ribosomal protein L30, mitochondrial | RM30_HUMAN 1-161
a | 39S ribosomal protein L42, mitochondrial | RM42_HUMAN 1-142
b | 39S ribosomal protein L43, mitochondrial | RM43_HUMAN 1-215
c | 39S ribosomal protein L44, mitochondrial | RM44_HUMAN 1-332
d | 39S ribosomal protein L45, mitochondrial | RM45_HUMAN 8-306
e | 39S ribosomal protein L46, mitochondrial | RM46_HUMAN 1-279
f | 39S ribosomal protein L48, mitochondrial | RM48_HUMAN 1-212
g | 39S ribosomal protein L49, mitochondrial | RM49_HUMAN 1-166
h | 39S ribosomal protein L50, mitochondrial | RM50_HUMAN 1-158
i | 39S ribosomal protein L51, mitochondrial | RM51_HUMAN 1-128
j | 39S ribosomal protein L52, mitochondrial | RM52_HUMAN 1-123
k | 39S ribosomal protein L53, mitochondrial | RM53_HUMAN 1-112
l | 39S ribosomal protein L54, mitochondrial | RM54_HUMAN 1-138
m | 39S ribosomal protein L55, mitochondrial | RM55_HUMAN 1-127
o | Ribosomal protein 63, mitochondrial | RT63_HUMAN 1-102
p | Peptidyl-tRNA hydrolase ICT1, mitochondrial | ICT1_HUMAN 1-206
q | Growth arrest and DNA damage-inducible proteins-interacting protein 1 | G45IP_HUMAN 1-222
r | 39S ribosomal protein S18a, mitochondrial | RT18A_HUMAN 1-196
r1 | mRNA |
r2 | A-site tRNA |
r3 | P-site tRNA |
r4 | E-site tRNA |
s | 39S ribosomal protein S30, mitochondrial | RT30_HUMAN 1-439
t1 t2 t3 t4 t5 t6 | 39S ribosomal protein L12, mitochondrial | RM12_HUMAN -60-137
Non-standard residues in 6ZSG.cif #4
---
004 — (2S)-amino(phenyl)ethanoic acid (L-Phenylglycine)
DBB — D-α-aminobutyric acid
DOL — 5-(2-diethylamino-
ethanesulfonyl)-21-hydroxy-10-isopropyl-11,19-dimethyl-9,26-dioxa-3,15,28-triaza-
tricyclo[23.2.1.00,255]octacosa-1(27),12,17,19,25(28)-pentaene-2,8,14,23-tetraone
(dalfopristin)
GTP — guanosine-5'-triphosphate
MG — magnesium ion
MHT — (3S)-3-(methylsulfanyl)-1-azabicyclo[2.2.2]octane
MHV — 4-oxo-L-pipecolic acid
MHW — 3-hydroxypicolinic acid
Y5P — 1-(5-O-phosphono-beta-D-ribofuranosyl)-1,4-dihydropyrimidine (pyrimidine
riboside-5'-monophosphate)
ZN — zinc ion
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide atoms
> show cartoons
> set bgColor white
> lighting simple
> graphics silhouettes true
> open /Users/jinfanwang/Downloads/emd_11397.map
Opened emd_11397.map as #5, grid size 520,520,520, pixel 1.05, shown at level
0.0211, step 4, values float32
> open "/Users/jinfanwang/Downloads/7A5G (6).cif"
7A5G (6).cif title:
Structure of the elongating human mitoribosome bound to mtEF-Tu.GMPPCP and A/T
mt-tRNA [more info...]
Chain information for 7A5G (6).cif #6
---
Chain | Description | UniProt
03 | 39S ribosomal protein L32, mitochondrial | RM32_HUMAN 1-188
13 | 39S ribosomal protein L33, mitochondrial | RM33_HUMAN 1-65
23 | 39S ribosomal protein L34, mitochondrial | RM34_HUMAN 1-92
24 C | P tRNA |
33 | 39S ribosomal protein L35, mitochondrial | RM35_HUMAN 1-188
43 | 39S ribosomal protein L36, mitochondrial | RM36_HUMAN 1-103
53 | 39S ribosomal protein L37, mitochondrial | RM37_HUMAN 1-423
63 | 39S ribosomal protein L38, mitochondrial | RM38_HUMAN 1-380
73 | 39S ribosomal protein L39, mitochondrial | RM39_HUMAN 1-338
93 | 39S ribosomal protein L41, mitochondrial | RM41_HUMAN 1-137
A | 39S ribosomal protein L40, mitochondrial | RM40_HUMAN 1-206
A3 | 16S rRNA |
A5 | Oxa1L tail |
A6 | 12S rRNA |
B3 | mt-tRNAVal |
B6 | 28S ribosomal protein S2, mitochondrial | RT02_HUMAN 1-296
C6 | 28S ribosomal protein S24, mitochondrial | RT24_HUMAN 1-167
D H3 | 39S ribosomal protein L9, mitochondrial | RM09_HUMAN 1-267
D3 | 39S ribosomal protein L2, mitochondrial | RM02_HUMAN 1-305
D6 | 28S ribosomal protein S5, mitochondrial | RT05_HUMAN 1-430
E3 | 39S ribosomal protein L3, mitochondrial | RM03_HUMAN 1-348
E6 | 28S ribosomal protein S6, mitochondrial | RT06_HUMAN 1-125
F3 | 39S ribosomal protein L4, mitochondrial | RM04_HUMAN 1-311
F6 | 28S ribosomal protein S7, mitochondrial | RT07_HUMAN 1-242
G6 | 28S ribosomal protein S9, mitochondrial | RT09_HUMAN 1-396
H6 | 28S ribosomal protein S10, mitochondrial | RT10_HUMAN 1-201
I3 | 39S ribosomal protein L10, mitochondrial | RM10_HUMAN 1-261
I6 | 28S ribosomal protein S11, mitochondrial | RT11_HUMAN 1-194
J3 | 39S ribosomal protein L11, mitochondrial | RM11_HUMAN 1-192
J6 | 28S ribosomal protein S12, mitochondrial | RT12_HUMAN 1-138
K3 | 39S ribosomal protein L13, mitochondrial | RM13_HUMAN 1-178
K6 | 28S ribosomal protein S14, mitochondrial | RT14_HUMAN 1-128
L3 | 39S ribosomal protein L14, mitochondrial | RM14_HUMAN 1-145
L6 | 28S ribosomal protein S15, mitochondrial | RT15_HUMAN 1-257
M3 | 39S ribosomal protein L15, mitochondrial | RM15_HUMAN 1-296
M6 | 28S ribosomal protein S16, mitochondrial | RT16_HUMAN 1-137
N3 | 39S ribosomal protein L16, mitochondrial | RM16_HUMAN 1-251
N6 | 28S ribosomal protein S17, mitochondrial | RT17_HUMAN 1-130
O3 | 39S ribosomal protein L17, mitochondrial | RM17_HUMAN 1-175
O6 | 28S ribosomal protein S18b, mitochondrial | RT18B_HUMAN 1-258
P3 | 39S ribosomal protein L18, mitochondrial | RM18_HUMAN 0-179
P6 | 28S ribosomal protein S18c, mitochondrial | RT18C_HUMAN 1-142
Q3 | 39S ribosomal protein L19, mitochondrial | RM19_HUMAN 1-292
Q6 | 28S ribosomal protein S21, mitochondrial | RT21_HUMAN 1-87
R3 | 39S ribosomal protein L20, mitochondrial | RM20_HUMAN 1-149
R6 | 28S ribosomal protein S22, mitochondrial | RT22_HUMAN 1-360
S3 | 39S ribosomal protein L21, mitochondrial | RM21_HUMAN 1-205
S6 | 28S ribosomal protein S23, mitochondrial | RT23_HUMAN 1-190
T3 | 39S ribosomal protein L22, mitochondrial | RM22_HUMAN 7-212
T6 | 28S ribosomal protein S25, mitochondrial | RT25_HUMAN 1-173
U3 | 39S ribosomal protein L23, mitochondrial | RM23_HUMAN 1-153
U6 | 28S ribosomal protein S26, mitochondrial | RT26_HUMAN 1-205
V3 | 39S ribosomal protein L24, mitochondrial | RM24_HUMAN 1-216
V6 | 28S ribosomal protein S27, mitochondrial | RT27_HUMAN 1-414
W3 | 39S ribosomal protein L27, mitochondrial | RM27_HUMAN 1-148
W6 | 28S ribosomal protein S28, mitochondrial | RT28_HUMAN 1-187
X3 | 39S ribosomal protein L28, mitochondrial | RM28_HUMAN 1-256
X6 | 28S ribosomal protein S29, mitochondrial | RT29_HUMAN 1-398
Y2 | nascent chain |
Y3 | 39S ribosomal protein L47, mitochondrial | RM47_HUMAN 1-250
Y6 | 28S ribosomal protein S31, mitochondrial | RT31_HUMAN 1-395
Z | Elongation factor Tu, mitochondrial | EFTU_HUMAN 1-452
Z3 | 39S ribosomal protein L30, mitochondrial | RM30_HUMAN 1-161
Z6 | 28S ribosomal protein S33, mitochondrial | RT33_HUMAN 1-106
a3 | 39S ribosomal protein L42, mitochondrial | RM42_HUMAN 1-142
a6 | 28S ribosomal protein S34, mitochondrial | RT34_HUMAN 1-218
b3 | 39S ribosomal protein L43, mitochondrial | RM43_HUMAN 1-215
b6 | 28S ribosomal protein S35, mitochondrial | RT35_HUMAN 1-323
c3 | 39S ribosomal protein L44, mitochondrial | RM44_HUMAN 1-332
c6 | Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 | CHCH1_HUMAN 1-118
d3 | 39S ribosomal protein L45, mitochondrial | RM45_HUMAN 1-306
d6 | Aurora kinase A-interacting protein | AKIP_HUMAN 1-199
e3 | 39S ribosomal protein L46, mitochondrial | RM46_HUMAN 1-279
e6 | Pentatricopeptide repeat domain-containing protein 3, mitochondrial | PTCD3_HUMAN 1-689
f3 | 39S ribosomal protein L48, mitochondrial | RM48_HUMAN 1-212
g3 | 39S ribosomal protein L49, mitochondrial | RM49_HUMAN 1-166
h3 | 39S ribosomal protein L50, mitochondrial | RM50_HUMAN 1-158
i3 | 39S ribosomal protein L51, mitochondrial | RM51_HUMAN 1-128
i4 | mRNA |
j | E tRNA |
j3 | 39S ribosomal protein L52, mitochondrial | RM52_HUMAN 1-123
k3 | 39S ribosomal protein L53, mitochondrial | RM53_HUMAN 1-112
l3 | 39S ribosomal protein L54, mitochondrial | RM54_HUMAN 1-138
m3 | 39S ribosomal protein L55, mitochondrial | RM55_HUMAN 1-128
n | 50S ribosomal protein L1 | RL1_THET2 0-228
o3 | Ribosomal protein 63, mitochondrial | RT63_HUMAN 1-102
p3 | Peptidyl-tRNA hydrolase ICT1, mitochondrial | ICT1_HUMAN 1-206
q3 | Growth arrest and DNA damage-inducible proteins-interacting protein 1 | G45IP_HUMAN 1-222
r3 | 39S ribosomal protein S18a, mitochondrial | RT18A_HUMAN 1-196
s3 t3 | 39S ribosomal protein S30, mitochondrial,39S ribosomal protein S30, mitochondrial,mL65 | RT30_HUMAN -438-0 1-439
u3 | RNA (5'-R(P*CP*A)-3') |
Non-standard residues in 7A5G (6).cif #6
---
CL — chloride ion
GCP — phosphomethylphosphonic acid guanylate ester
GDP — guanosine-5'-diphosphate
MG — magnesium ion
MLI — malonate ion
NA — sodium ion
SO4 — sulfate ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
ZN — zinc ion
25 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide atoms
> show cartoons
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> ui tool show "Fit in Map"
> fitmap #6 inMap #5
Fit molecule 7A5G (6).cif (#6) to map emd_11397.map (#5) using 170482 atoms
average map value = 0.04181, steps = 204
shifted from previous position = 23.5
rotated from previous position = 11.5 degrees
atoms outside contour = 73163, contour level = 0.021051
Position of 7A5G (6).cif (#6) relative to emd_11397.map (#5) coordinates:
Matrix rotation and translation
0.98183051 -0.04179003 0.18510115 -37.85965512
0.03000774 0.99736800 0.06600455 -5.26633235
-0.18737230 -0.05925081 0.98050036 84.99426276
Axis -0.31354992 0.93240735 0.17973031
Axis point 410.72063429 0.00000000 207.18381961
Rotation angle (degrees) 11.52160978
Shift along axis 22.23657021
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!5 models
> color #6 white
> color #4 #ff8ad8ff
> color #3 #0096ffff
> color #2 #ffd479ff
> color #1 #ff2600ff
> select #3/r2#4/r2
2971 atoms, 3351 bonds, 152 residues, 2 models selected
> select add #1/r2
4456 atoms, 5026 bonds, 228 residues, 3 models selected
> select add #6/j
6072 atoms, 6832 bonds, 68 pseudobonds, 304 residues, 5 models selected
> select add #2/r4#4/r4
9021 atoms, 10158 bonds, 68 pseudobonds, 455 residues, 6 models selected
> select add #6/Z
12095 atoms, 13289 bonds, 68 pseudobonds, 850 residues, 6 models selected
> select add #6/24#6/C
15189 atoms, 16751 bonds, 160 pseudobonds, 996 residues, 6 models selected
> select add #2/r3#3/r3#4/r3
19566 atoms, 21685 bonds, 160 pseudobonds, 1221 residues, 6 models selected
> select add #1/r3
20986 atoms, 23286 bonds, 160 pseudobonds, 1294 residues, 6 models selected
> select add #1/r3
20986 atoms, 23286 bonds, 160 pseudobonds, 1294 residues, 6 models selected
> select add #1/r1#2/r1#3/r1#4/r1#6/i4
22174 atoms, 24604 bonds, 160 pseudobonds, 1358 residues, 6 models selected
> select ~sel
1404754 atoms, 1448025 bonds, 12041 pseudobonds, 83110 residues, 22 models
selected
> cartoon hide (#!1-4,6 & sel)
> select ~sel & ##selected
22174 atoms, 24608 bonds, 175 pseudobonds, 1358 residues, 7 models selected
> show sel atoms
> style sel stick
Changed 22174 atom styles
> color (#!1-4,6 & sel) byhetero
> select clear
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> select #6/24:17@O4
1 atom, 1 residue, 1 model selected
> select add #6/j:19@N2
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #6/24:17@O4 #6/j:19@N2
Distance between 7A5G (6).cif #6/24 U 17 O4 and /j G 19 N2: 75.829Å
> select #6/C:17@O4
1 atom, 1 residue, 1 model selected
> select add #6/24:17@O4
2 atoms, 2 residues, 1 model selected
> distance #6/C:17@O4 #6/24:17@O4
Distance between 7A5G (6).cif #6/C U 17 O4 and /24 U 17 O4: 44.965Å
> hide #!6 models
> show #!1 models
> show #!6 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!6 models
> select #3/r2:20@N3
1 atom, 1 residue, 1 model selected
> select #3/r3:20@C5
1 atom, 1 residue, 1 model selected
> select add #3/r2:20@N3
2 atoms, 2 residues, 1 model selected
> distance #3/r3:20@C5 #3/r2:20@N3
Distance between 6ZSA (2).cif #3/r3 Y5P 20 C5 and /r2 Y5P 20 N3: 42.912Å
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!3 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!3 models
> select #1/r2:20@N3
1 atom, 1 residue, 1 model selected
> select add #1/r3:20@C6
2 atoms, 2 residues, 1 model selected
> distance #1/r2:20@N3 #1/r3:20@C6
Distance between 6ZSE (1).cif #1/r2 Y5P 20 N3 and /r3 Y5P 20 C6: 61.099Å
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!6 models
> open /Users/jinfanwang/Downloads/9P8H.cif
Summary of feedback from opening /Users/jinfanwang/Downloads/9P8H.cif
---
notes | Fetching CCD 4AC from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/4AC/4AC.cif
Fetching CCD UY1 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/UY1/UY1.cif
9P8H.cif title:
In situ human A/P-P/E state 80S ribosome [more info...]
Chain information for 9P8H.cif #8
---
Chain | Description | UniProt
AP | A/P site tRNA |
CH | Endothelial differentiation-related factor 1 | EDF1_HUMAN 16-147
CI | Transcription factor BTF3 | BTF3_HUMAN 49-79
L5 | 28S rRNA |
L7 | 5S rRNA |
L8 | 5.8S rRNA |
LA | 60S ribosomal protein L8 | RL8_HUMAN 2-249
LB | Large ribosomal subunit protein uL3 | RL3_HUMAN 2-403
LC | 60S ribosomal protein L4 | RL4_HUMAN 1-368
LD | Large ribosomal subunit protein uL18 | RL5_HUMAN 2-294
LE | Large ribosomal subunit protein eL6 | RL6_HUMAN 39-288
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 | Ribosomal protein uL16-like | RL10L_HUMAN 2-214
LJ | 60S ribosomal protein L11 | RL11_HUMAN 3-178
LL | Large ribosomal subunit protein eL13 | 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 | Heparin-binding protein HBp15 | Q7Z4W8_HUMAN 17-117
LV | 60S ribosomal protein L23 | RL23_HUMAN 10-140
LW | Ribosomal protein L24 | A0A994J4A5_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 | Large ribosomal subunit protein eL29 | 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 | Large ribosomal subunit protein eL40 | 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
Ls | 60S acidic ribosomal protein P0 | RLA0_HUMAN 5-200
Lt | Large ribosomal subunit protein uL11 | RL12_HUMAN 7-163
PE | P/E site tRNA |
S2 | 18S rRNA |
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 |
SE | Small ribosomal subunit protein eS4, 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 | Small ribosomal subunit protein eS7 | 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 | Small ribosomal subunit protein eS12 | RS12_HUMAN 11-132
SN | 40S ribosomal protein S13 | RS13_HUMAN 2-151
SO | Small ribosomal subunit protein uS11 | RS14_HUMAN 12-151
SP | 40S ribosomal protein S15 | RS15_HUMAN 10-136
SQ | Small ribosomal subunit protein uS9 | RS16_HUMAN 3-146
SR | Small ribosomal subunit protein eS17 | 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 16-119
SV | Small ribosomal subunit protein eS21 | 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 | Small ribosomal subunit protein eS25 | RS25_HUMAN 41-115
Sa | 40S ribosomal protein S26 | RS26_HUMAN 2-103
Sb | Small ribosomal subunit protein eS27 | RS27_HUMAN 2-84
Sc | 40S ribosomal protein S28 | RS28_HUMAN 5-68
Sd | 40S ribosomal protein S29 | RS29_HUMAN 2-56
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 9P8H.cif #8
---
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
MG — magnesium ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
SPM — spermine
UY1 — 2'-O-methylpseudouridine-5'-monophosphate
ZN — zinc ion
23 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select add #1
313628 atoms, 322721 bonds, 2473 pseudobonds, 16882 residues, 5 models
selected
> select subtract #1
Nothing selected
> select add #8
220503 atoms, 236653 bonds, 5858 pseudobonds, 17978 residues, 4 models
selected
> hide (#!8 & sel) target a
> cartoon (#!8 & sel)
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!6 models
> hide #!7 models
> hide #7.1 models
> open /Users/jinfanwang/Downloads/9P7Y.cif
9P7Y.cif title:
In situ human A-P-E state 80S ribosome [more info...]
Chain information for 9P7Y.cif #9
---
Chain | Description | UniProt
At | A site tRNA |
CI | Transcription factor BTF3 | BTF3_HUMAN 49-79
Et | E site tRNA |
L5 | 28S rRNA |
L7 | 5S rRNA [Homo sapiens] |
L8 | 5.8S rRNA [Homo sapiens] |
LA | 60S ribosomal protein L8 | RL8_HUMAN 2-249
LB | Large ribosomal subunit protein uL3 | RL3_HUMAN 2-403
LC | 60S ribosomal protein L4 | RL4_HUMAN 1-368
LD | Large ribosomal subunit protein uL18 | RL5_HUMAN 2-294
LE | Large ribosomal subunit protein eL6 | RL6_HUMAN 39-288
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 | Ribosomal protein uL16-like | RL10L_HUMAN 2-214
LJ | 60S ribosomal protein L11 | RL11_HUMAN 3-178
LL | Large ribosomal subunit protein eL13 | 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 | Heparin-binding protein HBp15 | Q7Z4W8_HUMAN 17-117
LV | 60S ribosomal protein L23 | RL23_HUMAN 10-140
LW | Ribosomal protein L24 | A0A994J4A5_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 | Large ribosomal subunit protein eL29 | 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 | Large ribosomal subunit protein eL40 | 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
Ls | 60S acidic ribosomal protein P0 | RLA0_HUMAN 5-200
Lt | Large ribosomal subunit protein uL11 | RL12_HUMAN 7-163
Pt | P site tRNA [Homo sapiens] |
S2 | 18S rRNA |
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 | Small ribosomal subunit protein uS3 | RS3_HUMAN 1-227
SE | Small ribosomal subunit protein eS4, 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 | Small ribosomal subunit protein eS7 | 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 | Small ribosomal subunit protein eS12 | RS12_HUMAN 11-132
SN | 40S ribosomal protein S13 | RS13_HUMAN 2-151
SO | Small ribosomal subunit protein uS11 | RS14_HUMAN 12-151
SP | Small ribosomal subunit protein uS19 | RS15_HUMAN 16-136
SQ | Small ribosomal subunit protein uS9 | RS16_HUMAN 3-146
SR | Small ribosomal subunit protein eS17 | 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 16-119
SV | Small ribosomal subunit protein eS21 | 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 | Small ribosomal subunit protein eS25 | RS25_HUMAN 41-115
Sa | 40S ribosomal protein S26 | RS26_HUMAN 2-103
Sb | Small ribosomal subunit protein eS27 | RS27_HUMAN 2-84
Sc | 40S ribosomal protein S28 | RS28_HUMAN 5-68
Sd | 40S ribosomal protein S29 | RS29_HUMAN 2-56
Se | Small ribosomal subunit protein eS30 | 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 9P7Y.cif #9
---
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
MG — magnesium ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
SPM — spermine
UY1 — 2'-O-methylpseudouridine-5'-monophosphate
ZN — zinc ion
23 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide sel atoms
> select subtract #8
Nothing selected
> select add #9
221461 atoms, 237791 bonds, 5936 pseudobonds, 17973 residues, 4 models
selected
> hide (#!9 & sel) target a
> cartoon (#!9 & sel)
> select clear
> color #8 #ffd479ff
> color #9 #0433ffff
> select clear
> select #8/PE
1593 atoms, 1779 bonds, 74 pseudobonds, 75 residues, 2 models selected
> select #8/AP,PE
3107 atoms, 3472 bonds, 148 pseudobonds, 146 residues, 2 models selected
> select ~sel & ##selected
217396 atoms, 233181 bonds, 5710 pseudobonds, 17832 residues, 4 models
selected
> cartoon hide (#!8 & sel)
> select #9/Et,Pt,At
4683 atoms, 5234 bonds, 213 pseudobonds, 220 residues, 2 models selected
> select ~sel & ##selected
216778 atoms, 232557 bonds, 5723 pseudobonds, 17753 residues, 4 models
selected
> cartoon hide (#!9 & sel)
> hide #!8 models
> hide #!9 models
> show #!1 models
> show #!6 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!7 models
> show #7.1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> select clear
[Repeated 1 time(s)]
> show #!3 models
> select clear
[Repeated 1 time(s)]
> open /Users/jinfanwang/Downloads/8ZHB.cif
8ZHB.cif title:
80S ribosome with A/A P/E tRNA and mRNA of WNV [more info...]
Chain information for 8ZHB.cif #10
---
Chain | Description | UniProt
LA | 25S rRNA (3393-MER) |
LB | 5S rRNA (121-MER) |
LC | 5.8S rRNA (158-MER) |
LD | Large ribosomal subunit protein uL2A | RL2A_YEAST 2-252
LE | Large ribosomal subunit protein uL3 | RL3_YEAST 2-387
LF | Large ribosomal subunit protein uL4A | RL4A_YEAST 2-362
LG | Large ribosomal subunit protein uL18 | RL5_YEAST 4-297
LH | Large ribosomal subunit protein eL6B | RL6B_YEAST 2-176
LI | Large ribosomal subunit protein uL30A | RL7A_YEAST 23-244
LJ | Large ribosomal subunit protein eL8A | RL8A_YEAST 24-256
LK | Large ribosomal subunit protein uL6A | RL9A_YEAST 1-191
LL | Large ribosomal subunit protein uL16 | RL10_YEAST 2-219
LM | Large ribosomal subunit protein uL5B | RL11B_YEAST 6-174
LN | Large ribosomal subunit protein eL13A | RL13A_YEAST 2-194
LO | Large ribosomal subunit protein eL14A | RL14A_YEAST 3-138
LP | Large ribosomal subunit protein eL15A | RL15A_YEAST 2-204
LQ | Large ribosomal subunit protein uL13A | RL16A_YEAST 3-199
LR | Large ribosomal subunit protein uL22A | RL17A_YEAST 2-184
LS | Large ribosomal subunit protein eL18A | RL18A_YEAST 2-186
LT | Large ribosomal subunit protein eL19A | RL19A_YEAST 2-189
LU | Large ribosomal subunit protein eL20A | RL20A_YEAST 2-172
LV | Large ribosomal subunit protein eL21A | RL21A_YEAST 2-160
LW | Large ribosomal subunit protein eL22A | RL22A_YEAST 9-108
LX | Large ribosomal subunit protein uL14A | RL23A_YEAST 2-137
LY | Large ribosomal subunit protein eL24A | RL24A_YEAST 1-65
LZ | Large ribosomal subunit protein uL23 | RL25_YEAST 22-142
La | Large ribosomal subunit protein uL24A | RL26A_YEAST 2-126
Lb | Large ribosomal subunit protein eL27A | RL27A_YEAST 2-136
Lc | Large ribosomal subunit protein uL15 | RL28_YEAST 2-149
Ld | Large ribosomal subunit protein eL29 | RL29_YEAST 2-59
Le | Large ribosomal subunit protein eL30 | RL30_YEAST 9-104
Lf | Large ribosomal subunit protein eL31A | RL31A_YEAST 4-112
Lg | Large ribosomal subunit protein eL32 | RL32_YEAST 2-128
Lh | Large ribosomal subunit protein eL33A | RL33A_YEAST 2-107
Li | Large ribosomal subunit protein eL34A | RL34A_YEAST 2-113
Lj | Large ribosomal subunit protein uL29A | RL35A_YEAST 2-120
Lk | Large ribosomal subunit protein eL36A | RL36A_YEAST 2-100
Ll | Large ribosomal subunit protein eL37A | RL37A_YEAST 2-82
Lm | Large ribosomal subunit protein eL38 | RL38_YEAST 2-78
Ln | Large ribosomal subunit protein eL39 | RL39_YEAST 2-51
Lo | Large ribosomal subunit protein eL40A | RL40A_YEAST 77-128
Lp | Large ribosomal subunit protein eL41A | RL41A_YEAST 1-25
Lq | Large ribosomal subunit protein eL42A | RL44A_YEAST 2-104
Lr | Large ribosomal subunit protein eL43A | RL43A_YEAST 2-92
S2 | chain 2 18S rRNA (1799-MER) |
SA | Small ribosomal subunit protein uS3 | RS3_YEAST 3-225
SB | Small ribosomal subunit protein uS7 | RS5_YEAST 20-225
SC | Small ribosomal subunit protein eS10A | RS10A_YEAST 1-92
SD | Small ribosomal subunit protein eS12 | RS12_YEAST 20-143
SE | Small ribosomal subunit protein uS19 | RS15_YEAST 13-129
SF | Small ribosomal subunit protein uS9A | RS16A_YEAST 3-143
SG | Small ribosomal subunit protein eS17A | RS17A_YEAST 2-126
SH | Small ribosomal subunit protein uS13A | RS18A_YEAST 2-146
SI | Small ribosomal subunit protein eS19A | RS19A_YEAST 2-144
SJ | Small ribosomal subunit protein uS10 | RS20_YEAST 19-119
SK | Small ribosomal subunit protein eS25A | RS25A_YEAST 24-105
SL | Small ribosomal subunit protein eS28A | RS28A_YEAST 5-67
SM | Small ribosomal subunit protein uS14A | RS29A_YEAST 4-56
SN | Small ribosomal subunit protein eS31 | RS31_YEAST 80-152
SO | Small ribosomal subunit protein RACK1 | GBLP_YEAST 5-316
SP | Small ribosomal subunit protein uS2A | RSSA1_YEAST 2-207
SQ | Small ribosomal subunit protein eS1A | RS3A1_YEAST 2-233
SR | Small ribosomal subunit protein uS5 | RS2_YEAST 34-250
SS | Small ribosomal subunit protein eS4A | RS4A_YEAST 2-261
ST | Small ribosomal subunit protein eS6A | RS6A_YEAST 1-228
SU | Small ribosomal subunit protein eS7A | RS7A_YEAST 3-187
SV | Small ribosomal subunit protein eS8A | RS8A_YEAST 2-200
SW | Small ribosomal subunit protein uS4A | RS9A_YEAST 2-186
SX | Small ribosomal subunit protein uS17A | RS11A_YEAST 2-147
SY | Small ribosomal subunit protein uS15 | RS13_YEAST 2-151
SZ | Small ribosomal subunit protein uS11B | RS14B_YEAST 10-137
Sa | Small ribosomal subunit protein eS21A | RS21A_YEAST 1-87
Sb | Small ribosomal subunit protein uS8A | RS22A_YEAST 2-130
Sc | Small ribosomal subunit protein uS12A | RS23A_YEAST 2-145
Sd | Small ribosomal subunit protein eS24A | RS24A_YEAST 2-135
Se | Small ribosomal subunit protein eS26B | RS26B_YEAST 2-98
Sf | Small ribosomal subunit protein eS27A | RS27A_YEAST 2-82
Sg | Small ribosomal subunit protein eS30A | RS30A_YEAST 5-61
Ta | tRNA (77-MER) |
Tb | tRNA (77-MER) |
mR | RNA (5'-R(P*GP*AP*UP*UP*GP*AP*CP*CP*CP*UP*U)-3') |
1555 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!1 models
> hide #!3 models
> hide #!6 models
> hide #!7 models
> hide #7.1 models
> select clear
> select add #10
202562 atoms, 217786 bonds, 4710 pseudobonds, 16469 residues, 3 models
selected
> hide (#!10 & sel) target a
> cartoon (#!10 & sel)
> select clear
> close #10
> show #!9 models
> show #!8 models
> hide #!8 models
> hide #!9 models
> show #!1 models
> sequence chain #1/AA
Alignment identifier is 1/AA
> select #1/AA:1555
33 atoms, 35 bonds, 1 residue, 1 model selected
> select #1/AA:1555
33 atoms, 35 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> select #1/AA:1551
34 atoms, 36 bonds, 1 residue, 1 model selected
> select #1/AA:1551-1561
360 atoms, 389 bonds, 11 residues, 1 model selected
> show sel cartoons
> select #1/AA:1494
31 atoms, 32 bonds, 1 residue, 1 model selected
> select #1/AA:1494
31 atoms, 32 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/AA:1186
33 atoms, 35 bonds, 1 residue, 1 model selected
> select #1/AA:1184-1186
94 atoms, 100 bonds, 3 residues, 1 model selected
> select #1/AA:1228
33 atoms, 35 bonds, 1 residue, 1 model selected
> select #1/AA:1220-1228
290 atoms, 312 bonds, 9 residues, 1 model selected
> show sel cartoons
> undo
Desktop color scheme is dark
Traceback (most recent call last):
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 3008, in
_update_histogram_colors
bins = self.histogram_bins()
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2806, in histogram_bins
return int(self.scene.sceneRect().width())
^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: wrapped C/C++ object of type QGraphicsScene has been deleted
Error processing trigger "color scheme changed":
RuntimeError: wrapped C/C++ object of type QGraphicsScene has been deleted
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2806, in histogram_bins
return int(self.scene.sceneRect().width())
^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Desktop color scheme is light
Traceback (most recent call last):
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 3008, in
_update_histogram_colors
bins = self.histogram_bins()
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2806, in histogram_bins
return int(self.scene.sceneRect().width())
^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: wrapped C/C++ object of type QGraphicsScene has been deleted
Error processing trigger "color scheme changed":
RuntimeError: wrapped C/C++ object of type QGraphicsScene has been deleted
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2806, in histogram_bins
return int(self.scene.sceneRect().width())
^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Desktop color scheme is dark
Traceback (most recent call last):
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 3008, in
_update_histogram_colors
bins = self.histogram_bins()
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2806, in histogram_bins
return int(self.scene.sceneRect().width())
^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: wrapped C/C++ object of type QGraphicsScene has been deleted
Error processing trigger "color scheme changed":
RuntimeError: wrapped C/C++ object of type QGraphicsScene has been deleted
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2806, in histogram_bins
return int(self.scene.sceneRect().width())
^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Desktop color scheme is light
Traceback (most recent call last):
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 3008, in
_update_histogram_colors
bins = self.histogram_bins()
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2806, in histogram_bins
return int(self.scene.sceneRect().width())
^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: wrapped C/C++ object of type QGraphicsScene has been deleted
Error processing trigger "color scheme changed":
RuntimeError: wrapped C/C++ object of type QGraphicsScene has been deleted
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2806, in histogram_bins
return int(self.scene.sceneRect().width())
^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Desktop color scheme is dark
Traceback (most recent call last):
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 3008, in
_update_histogram_colors
bins = self.histogram_bins()
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2806, in histogram_bins
return int(self.scene.sceneRect().width())
^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: wrapped C/C++ object of type QGraphicsScene has been deleted
Error processing trigger "color scheme changed":
RuntimeError: wrapped C/C++ object of type QGraphicsScene has been deleted
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2806, in histogram_bins
return int(self.scene.sceneRect().width())
^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Desktop color scheme is light
Traceback (most recent call last):
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 3008, in
_update_histogram_colors
bins = self.histogram_bins()
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2806, in histogram_bins
return int(self.scene.sceneRect().width())
^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: wrapped C/C++ object of type QGraphicsScene has been deleted
Error processing trigger "color scheme changed":
RuntimeError: wrapped C/C++ object of type QGraphicsScene has been deleted
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2806, in histogram_bins
return int(self.scene.sceneRect().width())
^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> hide #!1 models
> show #!6 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> hide #!6 models
> show #!8 models
> show #!9 models
> hide #!3 models
> hide #!9 models
> select #8/AP:47
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #8/AP:8
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
Desktop color scheme is dark
Traceback (most recent call last):
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 3008, in
_update_histogram_colors
bins = self.histogram_bins()
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2806, in histogram_bins
return int(self.scene.sceneRect().width())
^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: wrapped C/C++ object of type QGraphicsScene has been deleted
Error processing trigger "color scheme changed":
RuntimeError: wrapped C/C++ object of type QGraphicsScene has been deleted
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2806, in histogram_bins
return int(self.scene.sceneRect().width())
^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Desktop color scheme is light
Traceback (most recent call last):
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 3008, in
_update_histogram_colors
bins = self.histogram_bins()
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2806, in histogram_bins
return int(self.scene.sceneRect().width())
^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: wrapped C/C++ object of type QGraphicsScene has been deleted
Error processing trigger "color scheme changed":
RuntimeError: wrapped C/C++ object of type QGraphicsScene has been deleted
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2806, in histogram_bins
return int(self.scene.sceneRect().width())
^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> open
> /Users/jinfanwang/Downloads/fold_2026_01_14_08_36_letm1_rbd_244_421_trnaval/fold_2026_01_14_08_36_letm1_rbd_244_421_trnaval_model_0.cif
Chain information for
fold_2026_01_14_08_36_letm1_rbd_244_421_trnaval_model_0.cif #10
---
Chain | Description
A | .
B | .
Computing secondary structure
> close #10
Desktop color scheme is dark
Traceback (most recent call last):
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 3008, in
_update_histogram_colors
bins = self.histogram_bins()
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2806, in histogram_bins
return int(self.scene.sceneRect().width())
^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: wrapped C/C++ object of type QGraphicsScene has been deleted
Error processing trigger "color scheme changed":
RuntimeError: wrapped C/C++ object of type QGraphicsScene has been deleted
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2806, in histogram_bins
return int(self.scene.sceneRect().width())
^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Desktop color scheme is light
Traceback (most recent call last):
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 3008, in
_update_histogram_colors
bins = self.histogram_bins()
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2806, in histogram_bins
return int(self.scene.sceneRect().width())
^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: wrapped C/C++ object of type QGraphicsScene has been deleted
Error processing trigger "color scheme changed":
RuntimeError: wrapped C/C++ object of type QGraphicsScene has been deleted
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2806, in histogram_bins
return int(self.scene.sceneRect().width())
^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,15
Model Number: Z18T000T4LL/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 13822.61.10
OS Loader Version: 13822.61.10
Software:
System Software Overview:
System Version: macOS 26.2 (25C56)
Kernel Version: Darwin 25.2.0
Time since boot: 10 days, 30 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
BL450:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
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aiohttp: 3.13.1
aiosignal: 1.4.0
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blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
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ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
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: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
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ChimeraX-AxesPlanes: 2.4
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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
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11
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: 1.1.4
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
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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: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
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ChimeraX-Maestro: 1.9.2
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ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
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ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
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ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
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ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
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ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
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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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
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ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
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ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
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
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ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
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ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
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: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
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ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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
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click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
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cxservices: 1.2.3
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h11: 0.16.0
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html2text: 2025.4.15
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httpx-sse: 0.4.3
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openvr: 1.26.701
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parso: 0.8.5
pep517: 0.13.1
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pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
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
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pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.5
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pytz: 2025.2
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.0.0
roman-numerals-py: 4.0.0
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
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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: 3.0.4
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
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typing_extensions: 4.15.0
tzdata: 2025.3
urllib3: 2.6.2
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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