The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
tried to select residues and then show the respective sequence. was a ribosome, which apparantly crashed things
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> cd /Users/ljs/Desktop/Figures/Structures
Current working directory is: /Users/ljs/Desktop/Figures/Structures
> open Rib_Encu.cif
Rib_Encu.cif title:
Cryo-EM structure of the ribosome from Encephalitozoon cuniculi [more info...]
Chain information for Rib_Encu.cif #1
---
Chain | Description | UniProt
1 | 5.8S-23S ribosomal RNA |
2 | 5S ribosomal RNA |
3 | 18S ribosomal RNA |
C0 | 40S ribosomal protein S10 | Q8SS17_ENCCU
C1 | 40S ribosomal protein S11 | Q8SS53_ENCCU
C2 | 40S ribosomal protein S12 | Q8SSK9_ENCCU
C3 | 40S ribosomal protein S13 | RS13_ENCCU
C4 | 40S ribosomal protein S14 | RS14_ENCCU
C5 | ribosomal protein S15 | Q8SRE7_ENCCU
C6 | 40S ribosomal protein S16 | Q8SSC2_ENCCU
C7 | 40S ribosomal protein S17 | RS17_ENCCU
C8 | 40S ribosomal protein S18 | RS18_ENCCU
C9 | 40S ribosomal protein S19 | RS19_ENCCU
D0 | 40S ribosomal protein S20 | Q8SQX6_ENCCU
D1 | ECU11_0225 protein | I7L8M6_ENCCU
D2 | 40S RIBOSOMAL PROTEIN S15A (S22 in yeast) | Q8SQL9_ENCCU
D3 | 40S ribosomal protein S23 | RS23_ENCCU
D4 | 40S ribosomal protein S24 | Q8SR06_ENCCU
D5 | 40S ribosomal protein S25 | RS25_ENCCU
D6 | 40S ribosomal protein S26 | RS26_ENCCU
D7 | 40S ribosomal protein S27 | Q8SS34_ENCCU
D8 | 40S ribosomal protein S28 | Q8SQM2_ENCCU
D9 | 40S ribosomal protein S29 |
E1 | Similarity to monoubiquitin/carboxy-extension protein fusion |
Q8SWB3_ENCCU
L1 | 60S ribosomal protein L1 | RL1_ENCCU
L2 | 60S ribosomal protein L8 | RL8_ENCCU
L3 | 60S ribosomal protein L3 | RL3_ENCCU
L4 | 60S ribosomal protein L4 | Q8SRC2_ENCCU
L5 | 60S ribosomal protein L5 | Q8SRQ3_ENCCU
L6 | 60S ribosomal protein L6 | Q8SR91_ENCCU
L7 | 60S ribosomal protein L7 | RL7_ENCCU
L8 | 60S ribosomal protein L7a | RL7A_ENCCU
L9 | 60S ribosomal protein L9 | Q8SSF7_ENCCU
M0 | 60S ribosomal protein L10 | RL10_ENCCU
M1 | 60S ribosomal protein L11 | RL11_ENCCU
M3 | 60S ribosomal protein L13 | Q8SSC1_ENCCU
M4 | ECU06_1215 protein | I7L8J2_ENCCU
M5 | Ribosomal protein L15 | Q8SQU2_ENCCU
M6 | 60S ribosomal protein L13A (L16) | Q8SS16_ENCCU
M7 | 60S ribosomal protein L17 | Q8SRH7_ENCCU
M8 | 60S ribosomal protein L18 | Q8SS76_ENCCU
M9 | 60S ribosomal protein L19 | Q8SRP5_ENCCU
MD | Uncharacterized protein ECU01_0250 | Y125_ENCCU
MS | ECU06_1135 protein | I7IV41_ENCCU
N0 | 60S ribosomal protein L20 | Q8SRD7_ENCCU
N1 | 60S ribosomal protein L21 | RL21_ENCCU
N2 | 60S ribosomal protein L22 | RL22_ENCCU
N3 | 60S ribosomal protein L23 | RL23_ENCCU
N4 | Similarity to 60S RIBOSOMAL PROTEIN L24 | Q8SUZ9_ENCCU
N5 | 60S ribosomal protein L23A | Q8SR87_ENCCU
N6 | 60S ribosomal protein L26 | Q8SRE6_ENCCU
N7 | 60S ribosomal protein L27 | Q8SS64_ENCCU
N8 | 60S ribosomal protein L27a | RL27A_ENCCU
N9 | 60S ribosomal protein L29 | I7JTZ6_ENCCU
O0 | 60S ribosomal protein L30 | Q8SRU1_ENCCU
O1 | 60S ribosomal protein L31 | RL31_ENCCU
O2 | 60S ribosomal protein L32 | RL32_ENCCU
O3 | 60S ribosomal protein L35A (L33) | Q8SSF3_ENCCU
O4 | 60S ribosomal protein L34 | RL34_ENCCU
O5 | 60S ribosomal protein L35-1 | RL351_ENCCU
O6 | 60S ribosomal protein L36 | RL36_ENCCU
O7 | 60S ribosomal protein L37 | RL37_ENCCU
O9 | 60S ribosomal protein L39 | RL39_ENCCU
P0 | ubiquitin/ L40 ribosomal protein fusion | Q8SRH8_ENCCU
P2 | 60S ribosomal protein L44 | RL44_ENCCU
P3 | 60S ribosomal protein L37A (L43) | Q8SRJ2_ENCCU
RA | Guanine nucleotide binding protein β subunit | M1K775_ENCCN
S0 | 40S ribosomal protein S0 | RSSA_ENCCU
S1 | 40S ribosomal protein S1 | RS3A_ENCCU
S2 | 40S ribosomal protein S2 | Q8SRG6_ENCCU
S3 | 40S ribosomal protein S3 | RS3_ENCCU
S4 | 40S ribosomal protein S4 | RS4_ENCCU
S5 | 40S ribosomal protein S5 | RS5_ENCCU
S6 | 40S ribosomal protein S6 | RS6_ENCCU
S7 | 40S ribosomal protein S7 | RS7_ENCCU
S8 | 40S ribosomal protein S8 | Q8SWC9_ENCCU
S9 | 40S ribosomal protein S9 | RS9_ENCCU
Non-standard residues in Rib_Encu.cif #1
---
AMP — adenosine monophosphate
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
ZN — zinc ion
> open Rib_Vnec.cif
Rib_Vnec.cif title:
Evolutionary compaction and adaptation visualized by the structure of the
dormant microsporidian ribosome [more info...]
Chain information for Rib_Vnec.cif #2
---
Chain | Description
L50 | 23S rRNA
L70 | 5S rRNA
LA0 | uL2
LAA | uL15
LB0 | uL3
LBB | eL29
LC0 | uL4
LCC | eL30
LD0 | uL18
LDD | eL31
LE0 | eL6
LEE | eL32
LF0 | uL30
LFF | eL33
LG0 | eL8
LGG | eL34
LH0 | uL6
LHH | uL29
LI0 | uL16
LII | eL36
LJ0 | uL5
LJJ | eL37
LL0 | eL13
LLL | eL39
LM0 | eL14
LMM | eL40
LN0 | eL15
LNN | MDF2
LO0 | uL13
LOO | eL42
LP0 | uL22
LPP | eL43
LQ0 | eL18
LR0 | eL19
LS0 | eL20
LT0 | eL21
LU0 | eL22
LV0 | uL14
LW0 | eL24
LX0 | uL23
LXX | msL1
LY0 | uL24
LZ0 | eL27
S60 | 16S rRNA
SA0 | uS2
SAA | eS26
SB0 | eS1
SBB | eS27
SC0 | uS5
SCC | eS28
SD0 | uS3
SDD | uS14
SE0 | eS4
SEE | eS30
SF0 | uS7
SFF | eS31
SG0 | eS6
SGG | RACK1
SH0 | eS7
SI0 | eS8
SJ0 | uS4
SK0 | eS10
SL0 | uS17
SM0 | eS12
SN0 | uS15
SNN | MDF1
SO0 | uS11
SP0 | uS19
SQ0 | uS9
SR0 | eS17
SS0 | uS13
ST0 | eS19
SU0 | uS10
SV0 | eS21
SW0 | uS8
SX0 | uS12
SY0 | eS24
SZ0 | eS25
Non-standard residues in Rib_Vnec.cif #2
---
MG — magnesium ion
ZN — zinc ion
> open Rib_Palo.cif
Rib_Palo.cif title:
Structure of the Paranosema locustae ribosome in complex with Lso2 [more
info...]
Chain information for Rib_Palo.cif #3
---
Chain | Description
L50 | 25S rRNA
L70 | 5S rRNA
LA0 | uL2
LAA | uL15
LB0 | uL3
LBB | eL29
LC0 | uL4
LCC | eL30
LD0 | uL18
LDD | eL31
LE0 | eL6
LEE | eL32
LF0 | uL30
LFF | eL33
LG0 | eL8
LGG | eL34
LH0 | uL6
LHH | uL29
LI0 | uL16
LII | eL36
LJ0 | uL5
LJJ | eL37
LL0 | eL13
LLL | eL39
LM0 | eL14
LMM | eL40
LN0 | eL15
LNN | Lso2
LO0 | uL13
LOO | eL42
LP0 | uL22
LPP | eL43
LQ0 | eL18
LR0 | eL19
LS0 | eL20
LT0 | eL21
LU0 | eL22
LV0 | uL14
LW0 | eL24
LX0 | uL23
LY0 | uL24
LZ0 | eL27
S60 | 18S rRNA
SA0 | uS2
SAA | eS26
SB0 | eS1
SBB | eS27
SC0 | uS5
SCC | eS28
SD0 | uS3
SDD | uS14
SE0 | eS4
SEE | eS30
SF0 | uS7
SG0 | eS6
SGG | RACK1
SH0 | eS7
SI0 | eS8
SJ0 | uS4
SK0 | eS10
SL0 | uS17
SN0 | uS15
SO0 | uS11
SP0 | uS19
SQ0 | uS9
SR0 | eS17
SS0 | uS13
ST0 | eS19
SU0 | uS10
SV0 | eS21
SW0 | uS8
SX0 | uS12
SY0 | eS24
SZ0 | eS25
Non-standard residues in Rib_Palo.cif #3
---
AMP — adenosine monophosphate
MG — magnesium ion
ZN — zinc ion
> open Sc_v2.pdb
Summary of feedback from opening Sc_v2.pdb
---
warnings | Duplicate atom serial number found: 99999
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Ignored bad PDB record found on line 97590
TER 100628 ALA h 120
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TER 101468 LEU I 103
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TER 102352 ALA I 221
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TER 103123 HIS i 100
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TER 104477 LYS J 174
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TER 105159 ALA j 88
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TER 105236 UNK K 23
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TER 106522 LEU k 78
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TER 108071 ALA L 195
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TER 108508 ILE l 51
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TER 109568 ALA M 138
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TER 109986 LYS m 128
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TER 111942 LYS n 25
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TER 115062 TYR O 199
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TER 115910 PHE o 106
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TER 117834 ALA p 92
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TER 119277 VAL Q 186
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TER 120356 UNK q 221
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TER 121878 ALA R 189
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TER 123560 TYR S 172
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TER 125068 ILE T 160
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TER 125847 TYR U 108
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TER 126851 VAL V 137
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TER 127890 SER W 135
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TER 128850 ILE X 142
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TER 129844 GLU Y 127
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TER 130937 PHE Z 136
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TER 133726 U 6 132
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TER 145023 N 6 670
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TER 170545 PRO A 207
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TER 171315 PRO a 98
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TER 173039 GLY B 235
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TER 173650 LYS b 82
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TER 175287 GLN C 250
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TER 177520 TYR D 225
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TER 182680 ALA f 152
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TER 184437 GLU G 218
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TER 186880 ASN g 319
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TER 188372 SER H 187
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TER 192061 GLU K 84
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TER 192121 THR K 98
Duplicate atom serial number found: 99999
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1163 messages similar to the above omitted
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TER 193290 GLY L 147
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885 messages similar to the above omitted
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TER 194181 GLN M 143
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1187 messages similar to the above omitted
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944 messages similar to the above omitted
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TER 196324 LEU O 137
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TER 197364 PHE P 138
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TER 198476 ARG Q 143
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TER 199384 ILE R 122
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TER 200577 ALA S 146
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TER 201690 GLU T 144
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TER 202573 ASN U 121
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TER 203258 ARG V 87
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1016 messages similar to the above omitted
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TER 204280 TYR W 130
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TER 205402 SER X 145
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TER 206476 ASP Y 135
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553 messages similar to the above omitted
Chain information for Sc_v2.pdb #4
---
Chain | Description
5 | No description available
6 | No description available
7 | No description available
8 | 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
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
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
> matchmaker #1 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Sc_v2.pdb, chain B (#4) with Rib_Encu.cif, chain L3 (#1), sequence
alignment score = 1068.1
RMSD between 301 pruned atom pairs is 1.132 angstroms; (across all 361 pairs:
2.358)
> matchmaker #2 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Sc_v2.pdb, chain B (#4) with Rib_Vnec.cif, chain LB0 (#2), sequence
alignment score = 1086.1
RMSD between 252 pruned atom pairs is 1.274 angstroms; (across all 365 pairs:
3.072)
> matchmaker #3 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Sc_v2.pdb, chain B (#4) with Rib_Palo.cif, chain LB0 (#3), sequence
alignment score = 1052.3
RMSD between 336 pruned atom pairs is 0.844 angstroms; (across all 362 pairs:
1.618)
> hide #1 #2 #3 #4 atoms
> cartoon style modeHelix tube width 4 thickness 2
> set bgColor white
> set silhouettes true
> set silhouetteWidth 3.5
> lighting soft
> lighting shadows false
> lighting depthCueStart 0.3
> lighting depthCueEnd 0.7
> lighting ambientIntensity 0.8
> lighting fillIntensity 0.8
> show #1 &~ #1/N5/O7/L8/L2/MS surfaces
> show #1/N5/O7/L8/L2/MS cartoons
> color #1 &~ #1/N5/O7/L8/L2/MS/1:85-104, 1153-1166, 1365-1370, 1187-1194,
> 1360-1366, 1540-1544 white smoke
> color #1/N5 #7C02A7
> color #1/O7 #EFF821
> color #1/L2 #E56B5C
> color #1/L8 #A82296
> color #1/MS #00FF00
> color #1/1:85-104 #CA4678 surfaces
> color #1/1:1153-1166 #0C0786 surfaces
> color #1/1:1365-1370 #F79341 surfaces
> color #1/1:1187-1194, 1360-1366 #FDC328 surfaces
> color #1/1:1540-1544 #4A02A0 surfaces
> show #1/1:85-104, 1163-1167, 1153-1164, 1365-1370, 1187-1194, 1540-1544
> surfaces
> surface #1 &~ #1/N5/O7/L8/L2/MS resolution 8
72 Gaussian surfaces, threshold level 0.073 - 0.105
> show #2 &~ #2/LXX/LX0/LJJ/LG0/LA0 surfaces
> show #2/LXX/LX0/LJJ/LG0/LA0 cartoons
> color #2&~#2/LXX/LX0/LJJ/LG0/LA0/L50:80-105, 1191-1206, 1228-1236,1359-1367,
> 1188-1191,1368-1371, 1542-1545 white surfaces
> color #2/LX0 #7C02A7
> color #2/LJJ #E56B5C
> color #2/LA0 #7C02A7
> color #2/LG0 #A82296
> color #2/LXX #00FA9A
> color #2/L50:80-105 #CA4678
> color #2/L50:1191-1206 #0C0786
> color #2/L50:1228-1236,1359-1367 #FDC328
> color #2/L50:1188-1191,1368-1371 #F79341
> color #2/L50:1542-1545 #4A02A0
> surface #2 &~ #2/LXX/LX0/LJJ/LG0/LA0 resolution 8
73 Gaussian surfaces, threshold level 0.074 - 0.112
> show #3 &~ #3/LX0/LJJ/LA0/LG0 surfaces
> show #3/LX0/LJJ/LA0/LG0 cartoons
> color #3 &~ #3/L50:95-113, 1233-1264, 1288-1294, 1463-1470, 1642-1647
> #3/LX0/LJJ/LA0/LG0 white surfaces
> color #3/LX0 #7C02A7
> color #3/LJJ #E56B5C
> color #3/LA0 #7C02A7
> color #3/LG0 #A82296
> color #3/L50:95-113 #CA4678
> color #3/L50:1233-1264 #0C0786
> color #3/L50:1288-1294, 1463-1470 #FDC328
> color #3/L50:1468-1473 #F79341
> color #3/L50:1642-1647 #4A02A0
> surface #3 &~ #3/LX0/LJJ/LA0/LG0 resolution 8
70 Gaussian surfaces, threshold level 0.074 - 0.112
> show #4 &~ #4/X/j/A/G surfaces
> show #4/X/j/A/G cartoons
> color #4/X #7C02A7
> color #4/j #EFF821
> color #4/A #E56B5C
> color #4/G #A82296
> color #4/8:108-139 #CA4678
> color #4/5:3-10/8:146-158 #D7566C
> color #4/5:1537-1584 #0C0786
> color #4/5:2514-2595 #F79341
> color #4/5:1615-1626, 1819-1829 #FDC328
> color #4/5:2158-2160 #4A02A0
> color #4 &~ #4/8:108-139,146-158 #4/5:3-10,1537-1584,2514-2595,1615-1626,
> 1819-1829, 2158-2160 #4/X/j/A/G white surfaces
> surface #4 &~ #4/X/j/A/G resolution 8
45 Gaussian surfaces, threshold level 0.070 - 0.105
> lighting shadows true intensity 0.5
> lighting shadows false
> cd /Users/ljs/Desktop/Figures/Figure1/1a
Current working directory is: /Users/ljs/Desktop/Figures/Figure1/1a
> view matrix camera
> -0.21148,0.78962,0.57599,497.47,-0.64221,-0.55651,0.52711,462.22,0.73676,-0.25844,0.6248,509.75
> hide #1 #2 #3 #4 target m
> show #4 target m
> save F1_Sace_2.png width 1000 height 1000
> hide #4 target m
> show #3 target m
> save F1_Palo_2.png width 1000 height 1000
> hide #3 target m
> show #2 target m
> save F1_Vane_2.png width 1000 height 1000
> hide #2 target m
> show #1 target m
> save F1_Encu_2.png width 1000 height 1000
> hide #1 target m
> close session
> cd /Users/ljs/Desktop/Figures/Structures
Current working directory is: /Users/ljs/Desktop/Figures/Structures
> open Rib_Encu.cif
Rib_Encu.cif title:
Cryo-EM structure of the ribosome from Encephalitozoon cuniculi [more info...]
Chain information for Rib_Encu.cif #1
---
Chain | Description | UniProt
1 | 5.8S-23S ribosomal RNA |
2 | 5S ribosomal RNA |
3 | 18S ribosomal RNA |
C0 | 40S ribosomal protein S10 | Q8SS17_ENCCU
C1 | 40S ribosomal protein S11 | Q8SS53_ENCCU
C2 | 40S ribosomal protein S12 | Q8SSK9_ENCCU
C3 | 40S ribosomal protein S13 | RS13_ENCCU
C4 | 40S ribosomal protein S14 | RS14_ENCCU
C5 | ribosomal protein S15 | Q8SRE7_ENCCU
C6 | 40S ribosomal protein S16 | Q8SSC2_ENCCU
C7 | 40S ribosomal protein S17 | RS17_ENCCU
C8 | 40S ribosomal protein S18 | RS18_ENCCU
C9 | 40S ribosomal protein S19 | RS19_ENCCU
D0 | 40S ribosomal protein S20 | Q8SQX6_ENCCU
D1 | ECU11_0225 protein | I7L8M6_ENCCU
D2 | 40S RIBOSOMAL PROTEIN S15A (S22 in yeast) | Q8SQL9_ENCCU
D3 | 40S ribosomal protein S23 | RS23_ENCCU
D4 | 40S ribosomal protein S24 | Q8SR06_ENCCU
D5 | 40S ribosomal protein S25 | RS25_ENCCU
D6 | 40S ribosomal protein S26 | RS26_ENCCU
D7 | 40S ribosomal protein S27 | Q8SS34_ENCCU
D8 | 40S ribosomal protein S28 | Q8SQM2_ENCCU
D9 | 40S ribosomal protein S29 |
E1 | Similarity to monoubiquitin/carboxy-extension protein fusion |
Q8SWB3_ENCCU
L1 | 60S ribosomal protein L1 | RL1_ENCCU
L2 | 60S ribosomal protein L8 | RL8_ENCCU
L3 | 60S ribosomal protein L3 | RL3_ENCCU
L4 | 60S ribosomal protein L4 | Q8SRC2_ENCCU
L5 | 60S ribosomal protein L5 | Q8SRQ3_ENCCU
L6 | 60S ribosomal protein L6 | Q8SR91_ENCCU
L7 | 60S ribosomal protein L7 | RL7_ENCCU
L8 | 60S ribosomal protein L7a | RL7A_ENCCU
L9 | 60S ribosomal protein L9 | Q8SSF7_ENCCU
M0 | 60S ribosomal protein L10 | RL10_ENCCU
M1 | 60S ribosomal protein L11 | RL11_ENCCU
M3 | 60S ribosomal protein L13 | Q8SSC1_ENCCU
M4 | ECU06_1215 protein | I7L8J2_ENCCU
M5 | Ribosomal protein L15 | Q8SQU2_ENCCU
M6 | 60S ribosomal protein L13A (L16) | Q8SS16_ENCCU
M7 | 60S ribosomal protein L17 | Q8SRH7_ENCCU
M8 | 60S ribosomal protein L18 | Q8SS76_ENCCU
M9 | 60S ribosomal protein L19 | Q8SRP5_ENCCU
MD | Uncharacterized protein ECU01_0250 | Y125_ENCCU
MS | ECU06_1135 protein | I7IV41_ENCCU
N0 | 60S ribosomal protein L20 | Q8SRD7_ENCCU
N1 | 60S ribosomal protein L21 | RL21_ENCCU
N2 | 60S ribosomal protein L22 | RL22_ENCCU
N3 | 60S ribosomal protein L23 | RL23_ENCCU
N4 | Similarity to 60S RIBOSOMAL PROTEIN L24 | Q8SUZ9_ENCCU
N5 | 60S ribosomal protein L23A | Q8SR87_ENCCU
N6 | 60S ribosomal protein L26 | Q8SRE6_ENCCU
N7 | 60S ribosomal protein L27 | Q8SS64_ENCCU
N8 | 60S ribosomal protein L27a | RL27A_ENCCU
N9 | 60S ribosomal protein L29 | I7JTZ6_ENCCU
O0 | 60S ribosomal protein L30 | Q8SRU1_ENCCU
O1 | 60S ribosomal protein L31 | RL31_ENCCU
O2 | 60S ribosomal protein L32 | RL32_ENCCU
O3 | 60S ribosomal protein L35A (L33) | Q8SSF3_ENCCU
O4 | 60S ribosomal protein L34 | RL34_ENCCU
O5 | 60S ribosomal protein L35-1 | RL351_ENCCU
O6 | 60S ribosomal protein L36 | RL36_ENCCU
O7 | 60S ribosomal protein L37 | RL37_ENCCU
O9 | 60S ribosomal protein L39 | RL39_ENCCU
P0 | ubiquitin/ L40 ribosomal protein fusion | Q8SRH8_ENCCU
P2 | 60S ribosomal protein L44 | RL44_ENCCU
P3 | 60S ribosomal protein L37A (L43) | Q8SRJ2_ENCCU
RA | Guanine nucleotide binding protein β subunit | M1K775_ENCCN
S0 | 40S ribosomal protein S0 | RSSA_ENCCU
S1 | 40S ribosomal protein S1 | RS3A_ENCCU
S2 | 40S ribosomal protein S2 | Q8SRG6_ENCCU
S3 | 40S ribosomal protein S3 | RS3_ENCCU
S4 | 40S ribosomal protein S4 | RS4_ENCCU
S5 | 40S ribosomal protein S5 | RS5_ENCCU
S6 | 40S ribosomal protein S6 | RS6_ENCCU
S7 | 40S ribosomal protein S7 | RS7_ENCCU
S8 | 40S ribosomal protein S8 | Q8SWC9_ENCCU
S9 | 40S ribosomal protein S9 | RS9_ENCCU
Non-standard residues in Rib_Encu.cif #1
---
AMP — adenosine monophosphate
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
ZN — zinc ion
> open Rib_Vnec.cif
Rib_Vnec.cif title:
Evolutionary compaction and adaptation visualized by the structure of the
dormant microsporidian ribosome [more info...]
Chain information for Rib_Vnec.cif #2
---
Chain | Description
L50 | 23S rRNA
L70 | 5S rRNA
LA0 | uL2
LAA | uL15
LB0 | uL3
LBB | eL29
LC0 | uL4
LCC | eL30
LD0 | uL18
LDD | eL31
LE0 | eL6
LEE | eL32
LF0 | uL30
LFF | eL33
LG0 | eL8
LGG | eL34
LH0 | uL6
LHH | uL29
LI0 | uL16
LII | eL36
LJ0 | uL5
LJJ | eL37
LL0 | eL13
LLL | eL39
LM0 | eL14
LMM | eL40
LN0 | eL15
LNN | MDF2
LO0 | uL13
LOO | eL42
LP0 | uL22
LPP | eL43
LQ0 | eL18
LR0 | eL19
LS0 | eL20
LT0 | eL21
LU0 | eL22
LV0 | uL14
LW0 | eL24
LX0 | uL23
LXX | msL1
LY0 | uL24
LZ0 | eL27
S60 | 16S rRNA
SA0 | uS2
SAA | eS26
SB0 | eS1
SBB | eS27
SC0 | uS5
SCC | eS28
SD0 | uS3
SDD | uS14
SE0 | eS4
SEE | eS30
SF0 | uS7
SFF | eS31
SG0 | eS6
SGG | RACK1
SH0 | eS7
SI0 | eS8
SJ0 | uS4
SK0 | eS10
SL0 | uS17
SM0 | eS12
SN0 | uS15
SNN | MDF1
SO0 | uS11
SP0 | uS19
SQ0 | uS9
SR0 | eS17
SS0 | uS13
ST0 | eS19
SU0 | uS10
SV0 | eS21
SW0 | uS8
SX0 | uS12
SY0 | eS24
SZ0 | eS25
Non-standard residues in Rib_Vnec.cif #2
---
MG — magnesium ion
ZN — zinc ion
> open Rib_Palo.cif
Rib_Palo.cif title:
Structure of the Paranosema locustae ribosome in complex with Lso2 [more
info...]
Chain information for Rib_Palo.cif #3
---
Chain | Description
L50 | 25S rRNA
L70 | 5S rRNA
LA0 | uL2
LAA | uL15
LB0 | uL3
LBB | eL29
LC0 | uL4
LCC | eL30
LD0 | uL18
LDD | eL31
LE0 | eL6
LEE | eL32
LF0 | uL30
LFF | eL33
LG0 | eL8
LGG | eL34
LH0 | uL6
LHH | uL29
LI0 | uL16
LII | eL36
LJ0 | uL5
LJJ | eL37
LL0 | eL13
LLL | eL39
LM0 | eL14
LMM | eL40
LN0 | eL15
LNN | Lso2
LO0 | uL13
LOO | eL42
LP0 | uL22
LPP | eL43
LQ0 | eL18
LR0 | eL19
LS0 | eL20
LT0 | eL21
LU0 | eL22
LV0 | uL14
LW0 | eL24
LX0 | uL23
LY0 | uL24
LZ0 | eL27
S60 | 18S rRNA
SA0 | uS2
SAA | eS26
SB0 | eS1
SBB | eS27
SC0 | uS5
SCC | eS28
SD0 | uS3
SDD | uS14
SE0 | eS4
SEE | eS30
SF0 | uS7
SG0 | eS6
SGG | RACK1
SH0 | eS7
SI0 | eS8
SJ0 | uS4
SK0 | eS10
SL0 | uS17
SN0 | uS15
SO0 | uS11
SP0 | uS19
SQ0 | uS9
SR0 | eS17
SS0 | uS13
ST0 | eS19
SU0 | uS10
SV0 | eS21
SW0 | uS8
SX0 | uS12
SY0 | eS24
SZ0 | eS25
Non-standard residues in Rib_Palo.cif #3
---
AMP — adenosine monophosphate
MG — magnesium ion
ZN — zinc ion
> open Sc_v2.pdb
Summary of feedback from opening Sc_v2.pdb
---
warnings | Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
623 messages similar to the above omitted
Ignored bad PDB record found on line 97590
TER 100628 ALA h 120
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
834 messages similar to the above omitted
Ignored bad PDB record found on line 98430
TER 101468 LEU I 103
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
878 messages similar to the above omitted
Ignored bad PDB record found on line 99314
TER 102352 ALA I 221
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
765 messages similar to the above omitted
Ignored bad PDB record found on line 100085
TER 103123 HIS i 100
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
1348 messages similar to the above omitted
Ignored bad PDB record found on line 101439
TER 104477 LYS J 174
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
676 messages similar to the above omitted
Ignored bad PDB record found on line 102121
TER 105159 ALA j 88
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
71 messages similar to the above omitted
Ignored bad PDB record found on line 102198
TER 105236 UNK K 23
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
120 messages similar to the above omitted
Ignored bad PDB record found on line 102324
TER 105362 UNK K 52
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
545 messages similar to the above omitted
Ignored bad PDB record found on line 102875
TER 105913 UNK K 163
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
603 messages similar to the above omitted
Ignored bad PDB record found on line 103484
TER 106522 LEU k 78
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
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Chain information for Sc_v2.pdb #4
---
Chain | Description
5 | No description available
6 | No description available
7 | No description available
8 | 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
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
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
> matchmaker #1 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Sc_v2.pdb, chain B (#4) with Rib_Encu.cif, chain L3 (#1), sequence
alignment score = 1068.1
RMSD between 301 pruned atom pairs is 1.132 angstroms; (across all 361 pairs:
2.358)
> matchmaker #2 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Sc_v2.pdb, chain B (#4) with Rib_Vnec.cif, chain LB0 (#2), sequence
alignment score = 1086.1
RMSD between 252 pruned atom pairs is 1.274 angstroms; (across all 365 pairs:
3.072)
> matchmaker #3 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Sc_v2.pdb, chain B (#4) with Rib_Palo.cif, chain LB0 (#3), sequence
alignment score = 1052.3
RMSD between 336 pruned atom pairs is 0.844 angstroms; (across all 362 pairs:
1.618)
> hide #1 #2 #3 #4 atoms
> cartoon style modeHelix tube width 4 thickness 2
> set bgColor white
> set silhouettes true
> set silhouetteWidth 3.5
> lighting soft
> lighting shadows false
> lighting depthCueStart 0.3
> lighting depthCueEnd 0.7
> lighting ambientIntensity 0.8
> lighting fillIntensity 0.8
> show #1 &~ #1/N5/O7/L8/L2/MS surfaces
> show #1/N5/O7/L8/L2/MS cartoons
> color #1 &~ #1/N5/O7/L8/L2/MS/1:85-104, 1153-1166, 1365-1370, 1187-1194,
> 1360-1366, 1540-1544 white smoke
> color #1/N5 #7C02A7
> color #1/O7 #EFF821
> color #1/L2 #E56B5C
> color #1/L8 #A82296
> color #1/MS #00FF00
> color #1/1:85-104 #008080 surfaces
> color #1/1:1153-1166 #00FFFF surfaces
> color #1/1:1365-1370 #00BFFF surfaces
> color #1/1:1187-1194, 1360-1366 #4169E1 surfaces
> color #1/1:1540-1544 #7B68EE surfaces
> show #1/1:85-104, 1163-1167, 1153-1164, 1365-1370, 1187-1194, 1540-1544
> surfaces
> surface #1 &~ #1/N5/O7/L8/L2/MS resolution 8
72 Gaussian surfaces, threshold level 0.073 - 0.105
> show #2 &~ #2/LXX/LX0/LJJ/LG0/LA0 surfaces
> show #2/LXX/LX0/LJJ/LG0/LA0 cartoons
> color #2&~#2/LXX/LX0/LJJ/LG0/LA0/L50:80-105, 1191-1206, 1228-1236,1359-1367,
> 1188-1191,1368-1371, 1542-1545 white surfaces
> color #2/LX0 #7C02A7
> color #2/LJJ #E56B5C
> color #2/LA0 #7C02A7
> color #2/LG0 #A82296
> color #2/LXX #00FA9A
> color #2/L50:80-105 #008080
> color #2/L50:1191-1206 #00FFFF
> color #2/L50:1228-1236,1359-1367 #4169E1
> color #2/L50:1188-1191,1368-1371 #00BFFF
> color #2/L50:1542-1545 #7B68EE
> surface #2 &~ #2/LXX/LX0/LJJ/LG0/LA0 resolution 8
73 Gaussian surfaces, threshold level 0.074 - 0.112
> show #3 &~ #3/LX0/LJJ/LA0/LG0 surfaces
> show #3/LX0/LJJ/LA0/LG0 cartoons
[had to delete a bunch of stuff to fit within ticket limits]
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Rib_Vnec.cif, chain LB0 (#2) with Rib_Encu.cif, chain L3 (#1),
sequence alignment score = 1313.3
RMSD between 339 pruned atom pairs is 0.751 angstroms; (across all 356 pairs:
1.118)
> view position #3 sameAsModels #1
> view position #4 sameAsModels #2
> hide #1 #2 atoms
> cartoon style modeHelix tube width 3 thickness 1.5
> set bgColor white
> set silhouettes true
> set silhouetteWidth 3.5
> lighting flat
> lighting shadows false
> lighting depthCueStart 0.4
> lighting depthCueEnd 1
> show #1/MS cartoons
> show #1/MS:24 atoms
> color #1/MS #00FF00
> color #1/MS:24 crimson
> volume zone #3 nearAtoms #1/MS range 1.5
> volume#3 step 1
Unknown command: volume#3 step 1
> color #3 grey
> transparency #3 80 surfaces
> show #2/LXX cartoons
> show #2/LXX:45 atoms
> color #2/LXX #00FA9A
> color #2/LXX:45 crimson
> volume zone #4 nearAtoms #2/LXX range 2
> volume #4 step 1
> color #4 grey
> transparency #4 80 surfaces
> style #2/LX:45 #1/MS:24 stick
Changed 9 atom styles
> view matrix camera
> -0.64937,0.32949,0.68539,471.78,-0.62325,-0.74702,-0.23137,178.75,0.43577,-0.57741,0.69044,442.1
> hide #!1 models
> hide #!3 models
> style #2/LXX:45 #1/MS:24 stick
Changed 18 atom styles
> volume gaussian #4 sDev 5
Opened Vane_density.map gaussian as #5, grid size 340,340,340, pixel 1.2,
shown at step 1, values float32
> undo
> redo
> volume #5 step 4
> volume #5 step 16
> hide #!5 models
> show #!4 models
> close #5
> volume gaussian #4 sDev 2
Opened Vane_density.map gaussian as #5, grid size 340,340,340, pixel 1.2,
shown at step 1, values float32
> close #5
> volume gaussian #4 sDev 1.5
Opened Vane_density.map gaussian as #5, grid size 340,340,340, pixel 1.2,
shown at step 1, values float32
> close #5
> volume gaussian #4 sDev 3
Opened Vane_density.map gaussian as #5, grid size 340,340,340, pixel 1.2,
shown at step 1, values float32
> hide #!2 models
> show #!2 models
> close #5
> close session
> cd /Users/ljs/Desktop/Figures/Structures
Current working directory is: /Users/ljs/Desktop/Figures/Structures
> open Rib_Encu.cif
Rib_Encu.cif title:
Cryo-EM structure of the ribosome from Encephalitozoon cuniculi [more info...]
Chain information for Rib_Encu.cif #1
---
Chain | Description | UniProt
1 | 5.8S-23S ribosomal RNA |
2 | 5S ribosomal RNA |
3 | 18S ribosomal RNA |
C0 | 40S ribosomal protein S10 | Q8SS17_ENCCU
C1 | 40S ribosomal protein S11 | Q8SS53_ENCCU
C2 | 40S ribosomal protein S12 | Q8SSK9_ENCCU
C3 | 40S ribosomal protein S13 | RS13_ENCCU
C4 | 40S ribosomal protein S14 | RS14_ENCCU
C5 | ribosomal protein S15 | Q8SRE7_ENCCU
C6 | 40S ribosomal protein S16 | Q8SSC2_ENCCU
C7 | 40S ribosomal protein S17 | RS17_ENCCU
C8 | 40S ribosomal protein S18 | RS18_ENCCU
C9 | 40S ribosomal protein S19 | RS19_ENCCU
D0 | 40S ribosomal protein S20 | Q8SQX6_ENCCU
D1 | ECU11_0225 protein | I7L8M6_ENCCU
D2 | 40S RIBOSOMAL PROTEIN S15A (S22 in yeast) | Q8SQL9_ENCCU
D3 | 40S ribosomal protein S23 | RS23_ENCCU
D4 | 40S ribosomal protein S24 | Q8SR06_ENCCU
D5 | 40S ribosomal protein S25 | RS25_ENCCU
D6 | 40S ribosomal protein S26 | RS26_ENCCU
D7 | 40S ribosomal protein S27 | Q8SS34_ENCCU
D8 | 40S ribosomal protein S28 | Q8SQM2_ENCCU
D9 | 40S ribosomal protein S29 |
E1 | Similarity to monoubiquitin/carboxy-extension protein fusion |
Q8SWB3_ENCCU
L1 | 60S ribosomal protein L1 | RL1_ENCCU
L2 | 60S ribosomal protein L8 | RL8_ENCCU
L3 | 60S ribosomal protein L3 | RL3_ENCCU
L4 | 60S ribosomal protein L4 | Q8SRC2_ENCCU
L5 | 60S ribosomal protein L5 | Q8SRQ3_ENCCU
L6 | 60S ribosomal protein L6 | Q8SR91_ENCCU
L7 | 60S ribosomal protein L7 | RL7_ENCCU
L8 | 60S ribosomal protein L7a | RL7A_ENCCU
L9 | 60S ribosomal protein L9 | Q8SSF7_ENCCU
M0 | 60S ribosomal protein L10 | RL10_ENCCU
M1 | 60S ribosomal protein L11 | RL11_ENCCU
M3 | 60S ribosomal protein L13 | Q8SSC1_ENCCU
M4 | ECU06_1215 protein | I7L8J2_ENCCU
M5 | Ribosomal protein L15 | Q8SQU2_ENCCU
M6 | 60S ribosomal protein L13A (L16) | Q8SS16_ENCCU
M7 | 60S ribosomal protein L17 | Q8SRH7_ENCCU
M8 | 60S ribosomal protein L18 | Q8SS76_ENCCU
M9 | 60S ribosomal protein L19 | Q8SRP5_ENCCU
MD | Uncharacterized protein ECU01_0250 | Y125_ENCCU
MS | ECU06_1135 protein | I7IV41_ENCCU
N0 | 60S ribosomal protein L20 | Q8SRD7_ENCCU
N1 | 60S ribosomal protein L21 | RL21_ENCCU
N2 | 60S ribosomal protein L22 | RL22_ENCCU
N3 | 60S ribosomal protein L23 | RL23_ENCCU
N4 | Similarity to 60S RIBOSOMAL PROTEIN L24 | Q8SUZ9_ENCCU
N5 | 60S ribosomal protein L23A | Q8SR87_ENCCU
N6 | 60S ribosomal protein L26 | Q8SRE6_ENCCU
N7 | 60S ribosomal protein L27 | Q8SS64_ENCCU
N8 | 60S ribosomal protein L27a | RL27A_ENCCU
N9 | 60S ribosomal protein L29 | I7JTZ6_ENCCU
O0 | 60S ribosomal protein L30 | Q8SRU1_ENCCU
O1 | 60S ribosomal protein L31 | RL31_ENCCU
O2 | 60S ribosomal protein L32 | RL32_ENCCU
O3 | 60S ribosomal protein L35A (L33) | Q8SSF3_ENCCU
O4 | 60S ribosomal protein L34 | RL34_ENCCU
O5 | 60S ribosomal protein L35-1 | RL351_ENCCU
O6 | 60S ribosomal protein L36 | RL36_ENCCU
O7 | 60S ribosomal protein L37 | RL37_ENCCU
O9 | 60S ribosomal protein L39 | RL39_ENCCU
P0 | ubiquitin/ L40 ribosomal protein fusion | Q8SRH8_ENCCU
P2 | 60S ribosomal protein L44 | RL44_ENCCU
P3 | 60S ribosomal protein L37A (L43) | Q8SRJ2_ENCCU
RA | Guanine nucleotide binding protein β subunit | M1K775_ENCCN
S0 | 40S ribosomal protein S0 | RSSA_ENCCU
S1 | 40S ribosomal protein S1 | RS3A_ENCCU
S2 | 40S ribosomal protein S2 | Q8SRG6_ENCCU
S3 | 40S ribosomal protein S3 | RS3_ENCCU
S4 | 40S ribosomal protein S4 | RS4_ENCCU
S5 | 40S ribosomal protein S5 | RS5_ENCCU
S6 | 40S ribosomal protein S6 | RS6_ENCCU
S7 | 40S ribosomal protein S7 | RS7_ENCCU
S8 | 40S ribosomal protein S8 | Q8SWC9_ENCCU
S9 | 40S ribosomal protein S9 | RS9_ENCCU
Non-standard residues in Rib_Encu.cif #1
---
AMP — adenosine monophosphate
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
ZN — zinc ion
> open Rib_Vnec.cif
Rib_Vnec.cif title:
Evolutionary compaction and adaptation visualized by the structure of the
dormant microsporidian ribosome [more info...]
Chain information for Rib_Vnec.cif #2
---
Chain | Description
L50 | 23S rRNA
L70 | 5S rRNA
LA0 | uL2
LAA | uL15
LB0 | uL3
LBB | eL29
LC0 | uL4
LCC | eL30
LD0 | uL18
LDD | eL31
LE0 | eL6
LEE | eL32
LF0 | uL30
LFF | eL33
LG0 | eL8
LGG | eL34
LH0 | uL6
LHH | uL29
LI0 | uL16
LII | eL36
LJ0 | uL5
LJJ | eL37
LL0 | eL13
LLL | eL39
LM0 | eL14
LMM | eL40
LN0 | eL15
LNN | MDF2
LO0 | uL13
LOO | eL42
LP0 | uL22
LPP | eL43
LQ0 | eL18
LR0 | eL19
LS0 | eL20
LT0 | eL21
LU0 | eL22
LV0 | uL14
LW0 | eL24
LX0 | uL23
LXX | msL1
LY0 | uL24
LZ0 | eL27
S60 | 16S rRNA
SA0 | uS2
SAA | eS26
SB0 | eS1
SBB | eS27
SC0 | uS5
SCC | eS28
SD0 | uS3
SDD | uS14
SE0 | eS4
SEE | eS30
SF0 | uS7
SFF | eS31
SG0 | eS6
SGG | RACK1
SH0 | eS7
SI0 | eS8
SJ0 | uS4
SK0 | eS10
SL0 | uS17
SM0 | eS12
SN0 | uS15
SNN | MDF1
SO0 | uS11
SP0 | uS19
SQ0 | uS9
SR0 | eS17
SS0 | uS13
ST0 | eS19
SU0 | uS10
SV0 | eS21
SW0 | uS8
SX0 | uS12
SY0 | eS24
SZ0 | eS25
Non-standard residues in Rib_Vnec.cif #2
---
MG — magnesium ion
ZN — zinc ion
> open Rib_Palo.cif
Rib_Palo.cif title:
Structure of the Paranosema locustae ribosome in complex with Lso2 [more
info...]
Chain information for Rib_Palo.cif #3
---
Chain | Description
L50 | 25S rRNA
L70 | 5S rRNA
LA0 | uL2
LAA | uL15
LB0 | uL3
LBB | eL29
LC0 | uL4
LCC | eL30
LD0 | uL18
LDD | eL31
LE0 | eL6
LEE | eL32
LF0 | uL30
LFF | eL33
LG0 | eL8
LGG | eL34
LH0 | uL6
LHH | uL29
LI0 | uL16
LII | eL36
LJ0 | uL5
LJJ | eL37
LL0 | eL13
LLL | eL39
LM0 | eL14
LMM | eL40
LN0 | eL15
LNN | Lso2
LO0 | uL13
LOO | eL42
LP0 | uL22
LPP | eL43
LQ0 | eL18
LR0 | eL19
LS0 | eL20
LT0 | eL21
LU0 | eL22
LV0 | uL14
LW0 | eL24
LX0 | uL23
LY0 | uL24
LZ0 | eL27
S60 | 18S rRNA
SA0 | uS2
SAA | eS26
SB0 | eS1
SBB | eS27
SC0 | uS5
SCC | eS28
SD0 | uS3
SDD | uS14
SE0 | eS4
SEE | eS30
SF0 | uS7
SG0 | eS6
SGG | RACK1
SH0 | eS7
SI0 | eS8
SJ0 | uS4
SK0 | eS10
SL0 | uS17
SN0 | uS15
SO0 | uS11
SP0 | uS19
SQ0 | uS9
SR0 | eS17
SS0 | uS13
ST0 | eS19
SU0 | uS10
SV0 | eS21
SW0 | uS8
SX0 | uS12
SY0 | eS24
SZ0 | eS25
Non-standard residues in Rib_Palo.cif #3
---
AMP — adenosine monophosphate
MG — magnesium ion
ZN — zinc ion
> open Sc_v2.pdb
Summary of feedback from opening Sc_v2.pdb
---
warnings | Duplicate atom serial number found: 99999
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TER 103123 HIS i 100
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TER 106522 LEU k 78
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TER 108071 ALA L 195
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TER 109568 ALA M 138
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TER 119277 VAL Q 186
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TER 120356 UNK q 221
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TER 121878 ALA R 189
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TER 128850 ILE X 142
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TER 184437 GLU G 218
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TER 186880 ASN g 319
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TER 188372 SER H 187
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TER 192061 GLU K 84
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Duplicate atom serial number found: 99999
1187 messages similar to the above omitted
Ignored bad PDB record found on line 192336
TER 195374 ASN N 151
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
944 messages similar to the above omitted
Ignored bad PDB record found on line 193286
TER 196324 LEU O 137
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
1034 messages similar to the above omitted
Ignored bad PDB record found on line 194326
TER 197364 PHE P 138
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
1106 messages similar to the above omitted
Ignored bad PDB record found on line 195438
TER 198476 ARG Q 143
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
731 messages similar to the above omitted
Ignored bad PDB record found on line 196175
TER 199213 ALA R 90
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
165 messages similar to the above omitted
Ignored bad PDB record found on line 196346
TER 199384 ILE R 122
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
1187 messages similar to the above omitted
Ignored bad PDB record found on line 197539
TER 200577 ALA S 146
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
1107 messages similar to the above omitted
Ignored bad PDB record found on line 198652
TER 201690 GLU T 144
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
877 messages similar to the above omitted
Ignored bad PDB record found on line 199535
TER 202573 ASN U 121
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
679 messages similar to the above omitted
Ignored bad PDB record found on line 200220
TER 203258 ARG V 87
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
1016 messages similar to the above omitted
Ignored bad PDB record found on line 201242
TER 204280 TYR W 130
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
1116 messages similar to the above omitted
Ignored bad PDB record found on line 202364
TER 205402 SER X 145
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
1068 messages similar to the above omitted
Ignored bad PDB record found on line 203438
TER 206476 ASP Y 135
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
553 messages similar to the above omitted
Chain information for Sc_v2.pdb #4
---
Chain | Description
5 | No description available
6 | No description available
7 | No description available
8 | 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
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
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
> matchmaker #1 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Sc_v2.pdb, chain B (#4) with Rib_Encu.cif, chain L3 (#1), sequence
alignment score = 1068.1
RMSD between 301 pruned atom pairs is 1.132 angstroms; (across all 361 pairs:
2.358)
> matchmaker #2 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Sc_v2.pdb, chain B (#4) with Rib_Vnec.cif, chain LB0 (#2), sequence
alignment score = 1086.1
RMSD between 252 pruned atom pairs is 1.274 angstroms; (across all 365 pairs:
3.072)
> matchmaker #3 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Sc_v2.pdb, chain B (#4) with Rib_Palo.cif, chain LB0 (#3), sequence
alignment score = 1052.3
RMSD between 336 pruned atom pairs is 0.844 angstroms; (across all 362 pairs:
1.618)
> hide #1 #2 #3 #4 atoms
> cartoon style #1/MS #2/LXX modeHelix tube width 4 thickness 2
> cartoon style #1/1:1153-1164 #2/L50:1189-1206 #3/L50:1233-1264
> #4/5:1537-1584 xsection oval width 1 thickness 1.6
> set bgColor white
> set silhouettes true
> set silhouetteWidth 3.5
> lighting soft
> lighting shadows false
> lighting depthCueStart 0.4
> lighting depthCueEnd 1
> show #1/1:1153-1164 cartoons,surfaces
> show #1/MS cartoons
> color #1/MS #00FF00
> color #1/1:1153-1164 #0C0786 cartoons,surfaces
> surface #1/1:1153-1164 resolution 8
1 Gaussian surfaces, threshold level 0.104
> transparency #1/1:1153-1164 40 surfaces
> color #1/1:85-104 #CA4678
> show #1/1:85-104 cartoons,surfaces
> transparency #1/1:85-104 40 surfaces
> show #2/L50:1189-1206 cartoons,surfaces
> show #2/LXX cartoons
> color #2/LXX #00FA9A
> color #2/L50:1189-1206 #0C0786 cartoons,surfaces
> surface #2/L50:1189-1206 resolution 8
1 Gaussian surfaces, threshold level 0.105
> transparency #2/L50:1189-1206 40 surfaces
> color #2/L50:80-105 #CA4678
> show #2/L50:80-105 cartoons,surfaces
> transparency #2/L50:80-105 40 surfaces
> show #3/L50:1233-1264 cartoons,surfaces
> color #3/L50:1233-1264 #0C0786 cartoons,surfaces
> surface #3/L50:1233-1264 resolution 8
1 Gaussian surfaces, threshold level 0.104
> transparency #3/L50:1233-1264 40 surfaces
> color #3/L50:95-113 #CA4678
> show #3/L50:95-113 cartoons,surfaces
> transparency #3/L50:95-113 40 surfaces
> show #4/5:1537-1584 cartoons,surfaces
> show #4/5:3-10/8:146-158 cartoons,surfaces
> color #4/5:1537-1584 #0C0786 cartoons,surfaces
> color #4/5:3-10/8:146-158 #D7566C
> surface #4/5:1537-1584/5:3-10/8:146-158 resolution 8
2 Gaussian surfaces, threshold level 0.105
> transparency #4/5:1537-1584/5:3-10/8:146-158 40 surfaces
> cd /Users/ljs/Desktop/Figures/Figure2/msL1
Current working directory is: /Users/ljs/Desktop/Figures/Figure2/msL1
> view matrix camera
> -0.42439,0.71378,0.55715,507.89,-0.8611,-0.50842,-0.004568,228.47,0.28001,-0.4817,0.83041,623.52
> hide #1 #2 #3 #4 target m
> show #1 target m
> save F2_Encu_msL1.png width 1000 height 1000
> hide #1/1:1153-1164 cartoons,surfaces
> hide #1/1:85-104 cartoons,surfaces
> show #2 target m
> hide #2/LXX cartoons
> save F2_Vane_msL1.png width 1000 height 1000
> hide #2 target m
> show #3 target m
> save F2_Palo_msL1.png width 1000 height 1000
> hide #3 target m
> show #4 target m
> save F2_Sace_msL1.png width 1000 height 1000
> hide #4 target m
[Repeated 1 time(s)]
> cd /Users/ljs/Desktop/Figures/Figure2/msL2
Current working directory is: /Users/ljs/Desktop/Figures/Figure2/msL2
> show #1 #2 target m
> show #1/1:1153-1164 cartoons,surfaces
> show #1/1:85-104 cartoons,surfaces
> show #2/LXX cartoons
> hide #1/MS cartoons
> hide #2/L50:1189-1206 cartoons,surfaces
> hide #2/L50:80-105 cartoons,surfaces
> save F2_Encu_msL2.png width 1000 height 1000
> hide #1/1:1153-1164 surfaces
> hide #1/1:85-104 cartoons,surfaces
> show #2/L50:1189-1206 surfaces
> show #2/L50:80-105 cartoons,surfaces
> save F2_Vane_msL2.png width 1000 height 1000
> hide #2/L50:1189-1206 surfaces
> hide #2/L50:80-105 cartoons,surfaces
> show #3 target m
> save F2_Palo_msL2.png width 1000 height 1000
> hide #3 target m
> show #4 target m
> save F2_Sace_msL2.png width 1000 height 1000
> hide #!2 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
> show #3 target m
Alignment identifier is 1/RA
Alignment identifier is 1/1
Alignment identifier is 1/2
Alignment identifier is 1/3
Alignment identifier is 1/C0
Alignment identifier is 1/C1
Alignment identifier is 1/C2
Alignment identifier is 1/C3
Alignment identifier is 1/C4
Alignment identifier is 1/C5
Alignment identifier is 1/C6
Alignment identifier is 1/C7
Alignment identifier is 1/C8
Alignment identifier is 1/C9
Alignment identifier is 1/D0
Alignment identifier is 1/D1
Alignment identifier is 1/D2
Alignment identifier is 1/D3
Alignment identifier is 1/D4
Alignment identifier is 1/D5
Alignment identifier is 1/D6
Alignment identifier is 1/D7
Alignment identifier is 1/D8
Alignment identifier is 1/D9
Alignment identifier is 1/E1
Alignment identifier is 1/L1
Alignment identifier is 1/L2
Alignment identifier is 1/L3
Alignment identifier is 1/L4
Alignment identifier is 1/L5
Alignment identifier is 1/L6
Alignment identifier is 1/L7
Alignment identifier is 1/L8
Alignment identifier is 1/L9
Alignment identifier is 1/M0
Alignment identifier is 1/M1
Alignment identifier is 1/M3
Alignment identifier is 1/M4
Alignment identifier is 1/M5
Alignment identifier is 1/M6
Alignment identifier is 1/M7
Alignment identifier is 1/M8
Alignment identifier is 1/M9
Alignment identifier is 1/MD
Alignment identifier is 1/MS
Alignment identifier is 1/N0
Alignment identifier is 1/N1
Alignment identifier is 1/N2
Alignment identifier is 1/N3
Alignment identifier is 1/N4
Alignment identifier is 1/N5
Alignment identifier is 1/N6
Alignment identifier is 1/N7
Alignment identifier is 1/N8
Alignment identifier is 1/N9
Alignment identifier is 1/O0
Alignment identifier is 1/O1
Alignment identifier is 1/O2
Alignment identifier is 1/O3
Alignment identifier is 1/O4
Alignment identifier is 1/O5
Alignment identifier is 1/O6
Alignment identifier is 1/O7
Alignment identifier is 1/O9
Alignment identifier is 1/P0
Alignment identifier is 1/P2
Alignment identifier is 1/P3
Alignment identifier is 1/S0
Alignment identifier is 1/S1
Alignment identifier is 1/S2
Alignment identifier is 1/S3
Alignment identifier is 1/S4
Alignment identifier is 1/S5
Alignment identifier is 1/S6
Alignment identifier is 1/S7
Alignment identifier is 1/S8
Alignment identifier is 1/S9
Alignment identifier is 2/S60
Alignment identifier is 2/L70
Alignment identifier is 2/LA0
Alignment identifier is 2/SA0
Alignment identifier is 2/LAA
Alignment identifier is 2/SAA
Alignment identifier is 2/LB0
Alignment identifier is 2/SB0
Alignment identifier is 2/LBB
Alignment identifier is 2/SBB
Alignment identifier is 2/LC0
Alignment identifier is 2/SC0
Alignment identifier is 2/LCC
Alignment identifier is 2/SCC
Alignment identifier is 2/LD0
Alignment identifier is 2/SD0
Alignment identifier is 2/LDD
Alignment identifier is 2/SDD
Alignment identifier is 2/LE0
Alignment identifier is 2/SE0
Alignment identifier is 2/LEE
Alignment identifier is 2/SEE
Alignment identifier is 2/LF0
Alignment identifier is 2/SF0
Alignment identifier is 2/LFF
Alignment identifier is 2/SFF
Alignment identifier is 2/LG0
Alignment identifier is 2/SG0
Alignment identifier is 2/LGG
Alignment identifier is 2/SGG
Alignment identifier is 2/LH0
Alignment identifier is 2/SH0
Alignment identifier is 2/LHH
Alignment identifier is 2/LI0
Alignment identifier is 2/SI0
Alignment identifier is 2/LII
Alignment identifier is 2/LJ0
Alignment identifier is 2/SJ0
Alignment identifier is 2/LJJ
Alignment identifier is 2/LL0
Alignment identifier is 2/SL0
Alignment identifier is 2/LLL
Alignment identifier is 2/LM0
Alignment identifier is 2/LMM
Alignment identifier is 2/SM0
Alignment identifier is 2/LN0
Alignment identifier is 2/SN0
Alignment identifier is 2/LNN
Alignment identifier is 2/SNN
Alignment identifier is 2/LO0
Alignment identifier is 2/SO0
Alignment identifier is 2/LOO
Alignment identifier is 2/LP0
Alignment identifier is 2/SP0
Alignment identifier is 2/LPP
Alignment identifier is 2/LQ0
Alignment identifier is 2/SQ0
Alignment identifier is 2/LR0
Alignment identifier is 2/SR0
Alignment identifier is 2/LS0
Alignment identifier is 2/SS0
Alignment identifier is 2/LT0
Alignment identifier is 2/ST0
Alignment identifier is 2/LU0
Alignment identifier is 2/SU0
Alignment identifier is 2/LV0
Alignment identifier is 2/SV0
Alignment identifier is 2/LW0
Alignment identifier is 2/SW0
Alignment identifier is 2/LX0
Alignment identifier is 2/SX0
Alignment identifier is 2/LXX
Alignment identifier is 2/LY0
Alignment identifier is 2/SY0
Alignment identifier is 2/LZ0
Alignment identifier is 2/SZ0
Alignment identifier is 2/SK0
Alignment identifier is 2/L50
Alignment identifier is 3/L50
Alignment identifier is 3/L70
Alignment identifier is 3/LA0
Alignment identifier is 3/LAA
Alignment identifier is 3/LB0
Alignment identifier is 3/LBB
Alignment identifier is 3/LC0
Alignment identifier is 3/LCC
Alignment identifier is 3/LD0
Alignment identifier is 3/LDD
Alignment identifier is 3/LE0
Alignment identifier is 3/LEE
Alignment identifier is 3/LF0
Alignment identifier is 3/LFF
Alignment identifier is 3/LG0
Alignment identifier is 3/LGG
Alignment identifier is 3/LH0
Alignment identifier is 3/LHH
Alignment identifier is 3/LI0
Alignment identifier is 3/LII
Alignment identifier is 3/LJ0
Alignment identifier is 3/LJJ
Alignment identifier is 3/LL0
Alignment identifier is 3/LLL
Alignment identifier is 3/LM0
Alignment identifier is 3/LMM
Alignment identifier is 3/LN0
Alignment identifier is 3/LNN
Alignment identifier is 3/LO0
Alignment identifier is 3/LOO
Alignment identifier is 3/LP0
Alignment identifier is 3/LPP
Alignment identifier is 3/LQ0
Alignment identifier is 3/LR0
Alignment identifier is 3/LS0
Alignment identifier is 3/LT0
Alignment identifier is 3/LU0
Alignment identifier is 3/LV0
Alignment identifier is 3/LW0
Alignment identifier is 3/LX0
Alignment identifier is 3/LY0
Alignment identifier is 3/LZ0
Alignment identifier is 3/S60
Alignment identifier is 3/SA0
Alignment identifier is 3/SAA
Alignment identifier is 3/SB0
Alignment identifier is 3/SBB
Alignment identifier is 3/SC0
Alignment identifier is 3/SCC
Alignment identifier is 3/SD0
Alignment identifier is 3/SDD
Alignment identifier is 3/SE0
Alignment identifier is 3/SEE
Alignment identifier is 3/SF0
Alignment identifier is 3/SG0
Alignment identifier is 3/SGG
Alignment identifier is 3/SH0
Alignment identifier is 3/SI0
Alignment identifier is 3/SJ0
Alignment identifier is 3/SK0
Alignment identifier is 3/SL0
Alignment identifier is 3/SN0
Alignment identifier is 3/SO0
Alignment identifier is 3/SP0
Alignment identifier is 3/SQ0
Alignment identifier is 3/SR0
Alignment identifier is 3/SS0
Alignment identifier is 3/ST0
Alignment identifier is 3/SU0
Alignment identifier is 3/SV0
Alignment identifier is 3/SW0
Alignment identifier is 3/SX0
Alignment identifier is 3/SY0
Alignment identifier is 3/SZ0
Alignment identifier is 4/5
Alignment identifier is 4/7
Alignment identifier is 4/8
Alignment identifier is 4/A
Alignment identifier is 4/a
Alignment identifier is 4/B
Alignment identifier is 4/b
Alignment identifier is 4/C
Alignment identifier is 4/c
Alignment identifier is 4/D
Alignment identifier is 4/d
Alignment identifier is 4/E
Alignment identifier is 4/e
Alignment identifier is 4/F
Alignment identifier is 4/f
Alignment identifier is 4/G
Alignment identifier is 4/g
Alignment identifier is 4/H
Alignment identifier is 4/h
Alignment identifier is 4/I
Alignment identifier is 4/i
Alignment identifier is 4/J
Alignment identifier is 4/j
Alignment identifier is 4/K
Alignment identifier is 4/k
Alignment identifier is 4/L
Alignment identifier is 4/l
Alignment identifier is 4/M
Alignment identifier is 4/m
Alignment identifier is 4/N
Alignment identifier is 4/n
Alignment identifier is 4/O
Alignment identifier is 4/o
Alignment identifier is 4/P
Alignment identifier is 4/p
Alignment identifier is 4/Q
Alignment identifier is 4/q
Alignment identifier is 4/R
Alignment identifier is 4/r
Alignment identifier is 4/S
Alignment identifier is 4/s
Alignment identifier is 4/T
Alignment identifier is 4/U
Alignment identifier is 4/V
Alignment identifier is 4/W
Alignment identifier is 4/X
Alignment identifier is 4/Y
Alignment identifier is 4/Z
Alignment identifier is 4/6
An OpenGL graphics error occurred. Most often this is caused by a graphics
driver bug. The only way to fix such bugs is to update your graphics driver.
Redrawing graphics is now stopped to avoid a continuous stream of error
messages. To restart graphics use the command "graphics restart" after
changing the settings that caused the error.
Texture size (1344,16438) exceeds OpenGL driver maximum 16384
Traceback (most recent call last):
File
"/Users/ljs/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame
view.draw(check_for_changes = False)
File
"/Users/ljs/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 165, in draw
self._draw_scene(camera, drawings)
File
"/Users/ljs/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 214, in _draw_scene
silhouette.start_silhouette_drawing(r)
File
"/Users/ljs/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1757, in start_silhouette_drawing
fb = self._silhouette_framebuffer(r)
File
"/Users/ljs/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1793, in _silhouette_framebuffer
dt.initialize_depth(size, depth_compare_mode=False)
File
"/Users/ljs/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 2916, in initialize_depth
self.initialize_texture(size, format, iformat, tdtype, ncomp,
File
"/Users/ljs/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 2925, in initialize_texture
self._check_maximum_texture_size(size)
File
"/Users/ljs/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 2998, in
_check_maximum_texture_size
raise OpenGLError('Texture size (%s) exceeds OpenGL driver maximum %d' %
chimerax.graphics.opengl.OpenGLError: Texture size (1344,16438) exceeds OpenGL
driver maximum 16384
Exception ignored in: <function Texture.__del__ at 0x7ff4189dbf70>
Traceback (most recent call last):
File
"/Users/ljs/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 3003, in __del__
raise OpenGLError('OpenGL texture was not deleted before graphics.Texture
destroyed')
chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before
graphics.Texture destroyed
Failed to create NSOpenGLContext
No statusbar messages will be shown due to inadequate OpenGL
Failed to create NSOpenGLContext
No statusbar messages will be shown due to inadequate OpenGL
Failed to create NSOpenGLContext
No statusbar messages will be shown due to inadequate OpenGL
Failed to create NSOpenGLContext
No statusbar messages will be shown due to inadequate OpenGL
Failed to create NSOpenGLContext
No statusbar messages will be shown due to inadequate OpenGL
Reformatting alignment; please wait...
Alignment reformatted
Reformatting alignment; please wait...
Alignment reformatted
Reformatting alignment; please wait...
Alignment reformatted
Reformatting alignment; please wait...
Alignment reformatted
Reformatting alignment; please wait...
Alignment reformatted
Window position QRect(910,8944 100x30) outside any known screen, using primary
screen
OpenGL version: 4.1 Metal - 76.1
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:
Hardware Overview:
Model Name: Mac mini
Model Identifier: Macmini9,1
Processor Name: Unknown
Processor Speed: 2,4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache: 8 MB
Memory: 16 GB
Software:
System Software Overview:
System Version: macOS 12.0.1 (21A559)
Kernel Version: Darwin 21.1.0
Time since boot: 2 days 2:26
Graphics/Displays:
Apple G13G:
Chipset Model: Apple G13G
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
C27F390:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Somehow the graphics window was resized to 16438 pixels tall, larger than the OpenGL 16K limit, leading to an OpenGL error when it tried to make a texture for silhouette edges.
I don't think the user made their ChimeraX window that large, instead some tool did it. I'm guessing sequence viewer based on the logged messages before and after this error.
Alignment identifier is 1/RA
Alignment identifier is 1/1
Alignment identifier is 1/2
Alignment identifier is 1/3
Alignment identifier is 1/C0
Reformatting alignment; please wait...
Alignment reformatted
Reformatting alignment; please wait...
Alignment reformatted
Probably that tool should do something to avoid making its gui 16000 pixels tall.