Opened 3 years ago

Closed 3 years ago

#8622 closed defect (nonchimerax)

Graphics crash, macOS 13.2.1, Intel Iris Plus Graphics 640

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

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
  "uptime" : 14000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro14,1",
  "coalitionID" : 1762,
  "osVersion" : {
    "train" : "macOS 13.2.1",
    "build" : "22D68",
    "releaseType" : "User"
  },
  "captureTime" : "2023-03-09 15:50:21.6567 +0900",
  "incident" : "B329984D-17E7-46B5-AC21-F7E7AFD3142C",
  "pid" : 4258,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-03-09 15:10:32.3413 +0900",
  "procStartAbsTime" : 11673169941231,
  "procExitAbsTime" : 14062336914015,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"859EF5D9-1082-58C2-87EF-FC86A6996A31","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "63C4051F-E77D-88FE-6025-9A942AD279BE",
  "throttleTimeout" : 2147483647,
  "wakeTime" : 4126,
  "sleepWakeUUID" : "2F1AB5EF-7D3F-4DE7-BF13-FC3318159E5A",
  "sip" : "enabled",
  "exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
  "asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000002\n"],
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  "faultingThread" : 0,
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===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309
> 田中先生/cryosparc_P14_J41_map.mrc"

Opened cryosparc_P14_J41_map.mrc as #1, grid size 600,600,600, pixel 1.18,
shown at level 0.186, step 4, values float32  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309
> 田中先生/cryosparc_P14_J41_map.mrc"

Opened cryosparc_P14_J41_map.mrc as #2, grid size 600,600,600, pixel 1.18,
shown at level 0.186, step 4, values float32  

> hide #!1 models

> show #!1 models

> hide #!2 models

> close

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/チノリモ PBS.map" format ccp4

Opened チノリモ PBS.map as #1, grid size 560,560,560, pixel 1.09, shown at level
0.0214, step 4, values float32  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309
> 田中先生/cryosparc_P14_J41_map.mrc"

Opened cryosparc_P14_J41_map.mrc as #2, grid size 600,600,600, pixel 1.18,
shown at level 0.186, step 4, values float32  

> hide #!2 models

> volume #1 level 0.02551

> volume #1 level 0.01381

> volume #1 step 2

> show #!2 models

> volume #2 level 0.1145

> volume #2 step 2

> show #!1 models

> select add #1

2 models selected  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx.cif"

6kgx.cif title:  
Structure of the phycobilisome from the red alga Porphyridium purpureum [more
info...]  
  
Chain information for 6kgx.cif #3  
---  
Chain | Description | UniProt  
11 14 A5 AC B1 B3 B4 B5 BC BD BE BG C5 C9 CC CJ D1 D3 D4 D8 DA DD DE DG E9 EJ
F1 F3 F4 F5 F8 FA FC FD FE FG G5 G9 GC GJ H1 H3 H4 H5 H8 HA HC HD HE HG I5 I9
IC IJ J1 J3 J4 J8 JA JD JE JG K5 K9 KC KJ L1 L3 L4 L5 L8 LA LC LD LE LG M9 MJ
N3 N8 NA ND NE NG O1 O4 O9 OJ P2 P3 P6 P7 P8 PA PB PD PE PF PG PI Q1 Q4 Q9 QJ
R2 R3 R6 R7 R8 RA RB RD RE RF RG RI S1 S4 S9 SJ T2 T3 T6 T7 T8 TA TB TD TE TF
TG TI U1 U4 U9 UJ V2 V3 V6 V7 V8 VA VB VD VE VF VG VI W1 W4 W9 WJ X3 X8 XA XD
XE XG Y1 Y2 Y4 Y6 Y7 Y9 YB YF YI YJ Z1 Z4 Z8 ZA ZE ZG a1 a2 a4 a6 a7 aB aF aI
bE bG c2 c6 c7 c8 cA cB cF cI d1 d4 dE dG e2 e6 e7 e8 eA eB eF eI f1 f4 fE fG
g2 g6 g7 g8 gA gB gF gI h1 h4 hE hG i2 i6 i7 i8 iA iB iF iI j1 j4 jE jG k2 k6
k7 k8 kA kB kF kI l1 l4 lE lG m2 m6 m7 m8 mA mB mF mI n1 n4 nE nG pE pG q1 q4
rE rG s1 s4 tE tG u1 u4 vE vG w1 w4 y1 y4 | B-phycoerythrin beta chain |
PHEB_PORPP  
1H YH | Phycobilisome linker polypeptide | W0RZJ2_PORPP  
21 24 M1 M4 | LR7 |  
2H ZH | LRC4 |  
31 34 | LR9 |  
3H aH | LRC5 |  
4H bH | LRC6 |  
A1 A3 A4 AD AE AG B9 BJ C1 C3 C4 C8 CA CD CE CG D9 DJ E1 E3 E4 E8 EA ED EE EG
F9 FJ G1 G3 G4 G8 GA GD GE GG H9 HJ I1 I3 I4 I8 IA ID IE IG J5 J9 JC JJ K1 K3
K4 K8 KA KD KE KG L9 LJ M3 M8 MA MD ME MG N1 N4 N9 NJ O2 O3 O6 O7 O8 OA OB OD
OE OF OG OI P1 P4 P9 PJ Q2 Q3 Q6 Q7 Q8 QA QB QD QE QF QG QI R1 R4 R9 RJ S2 S3
S6 S7 S8 SA SB SD SE SF SG SI T1 T4 T9 TJ U2 U3 U6 U7 U8 UA UB UD UE UF UG UI
V1 V4 V9 VJ W2 W3 W6 W7 W8 WA WB WD WE WF WG WI X1 X4 X9 XJ Y8 YA YE YG Z2 Z6
Z7 ZB ZF ZI a8 aA aE aG b2 b6 b7 bB bF bI c1 c4 cE cG d2 d6 d7 d8 dA dB dF dI
e1 e4 eE eG f2 f6 f7 f8 fA fB fF fI g1 g4 gE gG h2 h6 h7 h8 hA hB hF hI i1 i4
iE iG j2 j6 j7 j8 jA jB jF jI k1 k4 kE kG l2 l6 l7 l8 lA lB lF lI m1 m4 mE mG
oE oG p1 p4 qE qG r1 r4 sE sG t1 t4 uE uG v1 v4 x1 x4 z1 z4 | Phycoerythrin
alpha subunit | E2IH77_PORPP  
A2 A6 A7 A9 AB AF AI AJ Y3 YD | LR4 |  
A8 AA wE wG xE xG | LR5 |  
AH CH EH GH JH KH NH PH RH TH cH eH gH iH lH mH pH rH tH vH | Allophycocyanin
alpha subunit | W0RYM0_PORPP  
B2 B6 B7 BB BF BI | Phycobilisome rod-core linker polypeptide | W0RZ90_PORPP  
B8 BA yE yG | LR8 |  
BH DH FH HH IH LH MH OH QH SH UH dH fH hH jH kH nH oH qH sH uH wH |
Allophycocyanin beta subunit | W0S279_PORPP  
C2 C6 C7 CB CF CI E2 E6 E7 EB EF EI G2 G6 G7 GB GF GI I2 I6 I7 IB IF II K2 K6
K7 KB KF KI M2 M6 M7 MB MF MI | C-phycocyanin alpha subunit | W0RYI4_PORPP  
D2 D6 D7 DB DF DI F2 F6 F7 FB FF FI H2 H6 H7 HB HF HI J2 J6 J7 JB JF JI L2 L6
L7 LB LF LI N2 N6 N7 NB NF NI | C-phycocyanin beta subunit | W0RZB2_PORPP  
VH xH | Allophycocyanin gamma subunit | W0S1U6_PORPP  
WH yH | Allophycocyanin beta 18 subunit | W0RZE2_PORPP  
X2 X6 X7 XB XF XI | LR1 |  
XH zH | LC |  
b1 b4 o1 o4 | LR2_Hb |  
b8 bA | LRC2 |  
d9 dJ | LR3 |  
e3 eD | LR2 |  
zE zG | LRC3 |  
  
Non-standard residues in 6kgx.cif #3  
---  
CYC — phycocyanobilin  
PEB — phycoerythrobilin  
PUB — phycourobilin  
  

> hide #!1 models

> close #1

> select add #2

2 models selected  

> transparency sel 50

> log metadata #3

Metadata for 6kgx.cif #3  
---  
Title | Structure of the phycobilisome from the red alga Porphyridium
purpureum  
Citation | Ma, J.F., You, X., Sun, S., Wang, X.X., Qin, S., Sui, S.F. (2020).
Structural basis of energy transfer in Porphyridium purpureum phycobilisome.
Nature, 579, 146-151. PMID: 32076272. DOI: 10.1038/s41586-020-2020-7  
Non-standard residues | CYC — phycocyanobilin  
PEB — phycoerythrobilin  
PUB — phycourobilin  
Source (natural) | Porphyridium purpureum (red alga)  
CryoEM Map | EMDB 9976 — open map  
Experimental method | Electron microscopy  
Resolution | 2.8Å  
  
> log chains #3

Chain information for 6kgx.cif #3  
---  
Chain | Description | UniProt  
11 14 A5 AC B1 B3 B4 B5 BC BD BE BG C5 C9 CC CJ D1 D3 D4 D8 DA DD DE DG E9 EJ
F1 F3 F4 F5 F8 FA FC FD FE FG G5 G9 GC GJ H1 H3 H4 H5 H8 HA HC HD HE HG I5 I9
IC IJ J1 J3 J4 J8 JA JD JE JG K5 K9 KC KJ L1 L3 L4 L5 L8 LA LC LD LE LG M9 MJ
N3 N8 NA ND NE NG O1 O4 O9 OJ P2 P3 P6 P7 P8 PA PB PD PE PF PG PI Q1 Q4 Q9 QJ
R2 R3 R6 R7 R8 RA RB RD RE RF RG RI S1 S4 S9 SJ T2 T3 T6 T7 T8 TA TB TD TE TF
TG TI U1 U4 U9 UJ V2 V3 V6 V7 V8 VA VB VD VE VF VG VI W1 W4 W9 WJ X3 X8 XA XD
XE XG Y1 Y2 Y4 Y6 Y7 Y9 YB YF YI YJ Z1 Z4 Z8 ZA ZE ZG a1 a2 a4 a6 a7 aB aF aI
bE bG c2 c6 c7 c8 cA cB cF cI d1 d4 dE dG e2 e6 e7 e8 eA eB eF eI f1 f4 fE fG
g2 g6 g7 g8 gA gB gF gI h1 h4 hE hG i2 i6 i7 i8 iA iB iF iI j1 j4 jE jG k2 k6
k7 k8 kA kB kF kI l1 l4 lE lG m2 m6 m7 m8 mA mB mF mI n1 n4 nE nG pE pG q1 q4
rE rG s1 s4 tE tG u1 u4 vE vG w1 w4 y1 y4 | B-phycoerythrin beta chain |
PHEB_PORPP  
1H YH | Phycobilisome linker polypeptide | W0RZJ2_PORPP  
21 24 M1 M4 | LR7 |  
2H ZH | LRC4 |  
31 34 | LR9 |  
3H aH | LRC5 |  
4H bH | LRC6 |  
A1 A3 A4 AD AE AG B9 BJ C1 C3 C4 C8 CA CD CE CG D9 DJ E1 E3 E4 E8 EA ED EE EG
F9 FJ G1 G3 G4 G8 GA GD GE GG H9 HJ I1 I3 I4 I8 IA ID IE IG J5 J9 JC JJ K1 K3
K4 K8 KA KD KE KG L9 LJ M3 M8 MA MD ME MG N1 N4 N9 NJ O2 O3 O6 O7 O8 OA OB OD
OE OF OG OI P1 P4 P9 PJ Q2 Q3 Q6 Q7 Q8 QA QB QD QE QF QG QI R1 R4 R9 RJ S2 S3
S6 S7 S8 SA SB SD SE SF SG SI T1 T4 T9 TJ U2 U3 U6 U7 U8 UA UB UD UE UF UG UI
V1 V4 V9 VJ W2 W3 W6 W7 W8 WA WB WD WE WF WG WI X1 X4 X9 XJ Y8 YA YE YG Z2 Z6
Z7 ZB ZF ZI a8 aA aE aG b2 b6 b7 bB bF bI c1 c4 cE cG d2 d6 d7 d8 dA dB dF dI
e1 e4 eE eG f2 f6 f7 f8 fA fB fF fI g1 g4 gE gG h2 h6 h7 h8 hA hB hF hI i1 i4
iE iG j2 j6 j7 j8 jA jB jF jI k1 k4 kE kG l2 l6 l7 l8 lA lB lF lI m1 m4 mE mG
oE oG p1 p4 qE qG r1 r4 sE sG t1 t4 uE uG v1 v4 x1 x4 z1 z4 | Phycoerythrin
alpha subunit | E2IH77_PORPP  
A2 A6 A7 A9 AB AF AI AJ Y3 YD | LR4 |  
A8 AA wE wG xE xG | LR5 |  
AH CH EH GH JH KH NH PH RH TH cH eH gH iH lH mH pH rH tH vH | Allophycocyanin
alpha subunit | W0RYM0_PORPP  
B2 B6 B7 BB BF BI | Phycobilisome rod-core linker polypeptide | W0RZ90_PORPP  
B8 BA yE yG | LR8 |  
BH DH FH HH IH LH MH OH QH SH UH dH fH hH jH kH nH oH qH sH uH wH |
Allophycocyanin beta subunit | W0S279_PORPP  
C2 C6 C7 CB CF CI E2 E6 E7 EB EF EI G2 G6 G7 GB GF GI I2 I6 I7 IB IF II K2 K6
K7 KB KF KI M2 M6 M7 MB MF MI | C-phycocyanin alpha subunit | W0RYI4_PORPP  
D2 D6 D7 DB DF DI F2 F6 F7 FB FF FI H2 H6 H7 HB HF HI J2 J6 J7 JB JF JI L2 L6
L7 LB LF LI N2 N6 N7 NB NF NI | C-phycocyanin beta subunit | W0RZB2_PORPP  
VH xH | Allophycocyanin gamma subunit | W0S1U6_PORPP  
WH yH | Allophycocyanin beta 18 subunit | W0RZE2_PORPP  
X2 X6 X7 XB XF XI | LR1 |  
XH zH | LC |  
b1 b4 o1 o4 | LR2_Hb |  
b8 bA | LRC2 |  
d9 dJ | LR3 |  
e3 eD | LR2 |  
zE zG | LRC3 |  
  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-69.154,0,1,0,-30.402,0,0,1,-26.313

> view matrix models #2,1,0,0,-58.589,0,1,0,-35.554,0,0,1,-47.627

> view matrix models #2,1,0,0,-50.689,0,1,0,-36.529,0,0,1,-59.77

> view matrix models #2,1,0,0,-77.255,0,1,0,-54.657,0,0,1,-45.124

> view matrix models #2,1,0,0,-44.258,0,1,0,-43.603,0,0,1,-49.119

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.98892,-0.14524,0.030589,0.28873,0.14479,0.98932,0.016624,-97.073,-0.032677,-0.012011,0.99939,-33.058

> volume #2 step 4

> color #2 #95fff2ff models

> color #2 #fb8dedff models

> color #3 #65e1e0ff

> ui tool show Angles/Torsions

> ui mousemode right "translate selected models"

> ui tool show "Side View"

> ui tool show "Fit in Map"

> select subtract #2

Nothing selected  

> fitmap #3 inMap #2

Fit molecule 6kgx.cif (#3) to map cryosparc_P14_J41_map.mrc (#2) using 1013398
atoms  
average map value = 0.109, steps = 120  
shifted from previous position = 11.2  
rotated from previous position = 2.48 degrees  
atoms outside contour = 771596, contour level = 0.11453  
  
Position of 6kgx.cif (#3) relative to cryosparc_P14_J41_map.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.98534503 0.17057309 -0.00003566 1.50097440  
-0.17057309 0.98534503 0.00001086 105.69904189  
0.00003699 -0.00000462 1.00000000 57.27121156  
Axis -0.00004535 -0.00021296 -0.99999998  
Axis point 615.80765974 44.12342660 0.00000000  
Rotation angle (degrees) 9.82114140  
Shift along axis -57.29378787  
  

> fitmap #3 inMap #2

Fit molecule 6kgx.cif (#3) to map cryosparc_P14_J41_map.mrc (#2) using 1013398
atoms  
average map value = 0.1091, steps = 40  
shifted from previous position = 0.0198  
rotated from previous position = 0.00148 degrees  
atoms outside contour = 771518, contour level = 0.11453  
  
Position of 6kgx.cif (#3) relative to cryosparc_P14_J41_map.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.98534752 0.17055867 -0.00005502 1.50384534  
-0.17055867 0.98534752 0.00001961 105.69300222  
0.00005756 -0.00000994 1.00000000 57.24801158  
Axis -0.00008662 -0.00033006 -0.99999994  
Axis point 615.78651004 44.11335413 0.00000000  
Rotation angle (degrees) 9.82030326  
Shift along axis -57.28302317  
  

> fitmap #3 inMap #2

Fit molecule 6kgx.cif (#3) to map cryosparc_P14_J41_map.mrc (#2) using 1013398
atoms  
average map value = 0.109, steps = 44  
shifted from previous position = 0.0193  
rotated from previous position = 0.00134 degrees  
atoms outside contour = 771579, contour level = 0.11453  
  
Position of 6kgx.cif (#3) relative to cryosparc_P14_J41_map.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.98534719 0.17056060 -0.00003172 1.49713685  
-0.17056060 0.98534719 0.00001762 105.69383362  
0.00003426 -0.00001195 1.00000000 57.27501867  
Axis -0.00008667 -0.00019344 -0.99999998  
Axis point 615.82644757 44.15684784 0.00000000  
Rotation angle (degrees) 9.82041536  
Shift along axis -57.29559245  
  

> volume #2 level 0.09346

> fitmap #3 inMap #2

Fit molecule 6kgx.cif (#3) to map cryosparc_P14_J41_map.mrc (#2) using 1013398
atoms  
average map value = 0.1091, steps = 44  
shifted from previous position = 0.0186  
rotated from previous position = 0.000464 degrees  
atoms outside contour = 706022, contour level = 0.093461  
  
Position of 6kgx.cif (#3) relative to cryosparc_P14_J41_map.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.98534737 0.17055958 -0.00002374 1.49537016  
-0.17055958 0.98534737 0.00001842 105.69084184  
0.00002653 -0.00001410 1.00000000 57.25964023  
Axis -0.00009533 -0.00014738 -0.99999998  
Axis point 615.82702399 44.16977691 0.00000000  
Rotation angle (degrees) 9.82035584  
Shift along axis -57.27535823  
  

> hide #!3 models

> show #!3 models

> hide #!3 models

> volume gaussian #1 sDev 5

> show #!3 models

> show target m

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle1.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle1.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle1.pdb #1  
---  
Chain | Description  
0 B D F H J L O Q S U W Y d f h j l n q s u w y | No description available  
1 M | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 8 | No description available  
7 9 | No description available  
A C E G I K N P R T V X c e g i k m p r t v x z | No description available  
Z a | No description available  
b | No description available  
o | No description available  
  

> close #1

> hide atoms

> show cartoons

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle1.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle1.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle1.pdb #1  
---  
Chain | Description  
0 B D F H J L O Q S U W Y d f h j l n q s u w y | No description available  
1 M | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 8 | No description available  
7 9 | No description available  
A C E G I K N P R T V X c e g i k m p r t v x z | No description available  
Z a | No description available  
b | No description available  
o | No description available  
  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle2.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle2.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle2.pdb #4  
---  
Chain | Description  
0 2 4 7 9 J L N P R T V X Z b d f i k m o q s u w y | No description available  
1 3 6 8 I K M O Q S U W Y a c e h j l n p r t v x z | No description available  
5 | No description available  
A C E G | No description available  
B D F H | No description available  
g | No description available  
  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle3.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle3.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle3.pdb #5  
---  
Chain | Description  
0 1 2 3 4 8 V W z | No description available  
5 7 B D F H K M O Q S U Z b d f h j m o q s u w | No description available  
6 A C E G J L N P R T Y a c e g i l n p r t v | No description available  
9 | No description available  
I x | No description available  
X | No description available  
k | No description available  
y | No description available  
  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle4.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle4.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle4.pdb #6  
---  
Chain | Description  
0 D F H J L N q s u w y | No description available  
1 3 5 7 9 O Q S U W Y a c e g i k | No description available  
2 4 6 8 P R T V X Z b d f h j l | No description available  
A n | No description available  
B | No description available  
C E G I K M p r t v x z | No description available  
m | No description available  
o | No description available  
  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle5.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle5.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle5.pdb #7  
---  
Chain | Description  
0 4 6 8 B D F H J L N S U W Y a c e g i k m o q s u w y | No description
available  
1 5 7 9 A C E G I K M O T V X Z b d f h j l n p r t v x z | No description
available  
2 | No description available  
3 | No description available  
P | No description available  
Q | No description available  
R | No description available  
  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle6.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle6.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle6.pdb #8  
---  
Chain | Description  
0 2 4 B D F H J L N P R W Y a c e g i k m o q s u w y | No description
available  
1 3 A C E G I K M O Q V X Z b d f h j l n p r t v x z | No description
available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
S | No description available  
T | No description available  
U | No description available  
  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle7.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle7.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle7.pdb #9  
---  
Chain | Description  
0 2 4 6 8 L N P R T V X Z b d f h q u w y | No description available  
1 3 5 7 9 K M O Q S U W Y a c e g p t v x z | No description available  
A C E G I | No description available  
B D F H J | No description available  
i j k l m n r | No description available  
o | No description available  
s | No description available  
  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle8.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle8.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle8.pdb #10  
---  
Chain | Description  
0 2 B D F I K M O Q S U W Y a c e g i k m o q s u w y | No description
available  
1 3 A C E G J L N P R T V X Z b d f h j l n p r t v x z | No description
available  
4 5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
H | No description available  
  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle9.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle9.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle9.pdb #11  
---  
Chain | Description  
0 2 4 6 8 O Q S U W Y a c e g i k m o q s u w y | No description available  
1 3 5 7 9 N P R T V X Z b d f h j l n p r t v x z | No description available  
A | No description available  
B D F H J L | No description available  
C E G I K M | No description available  
  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle10.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle10.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle10.pdb #12  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 5 7 9 b d f h k l o q s u | No description available  
4 6 8 c e g i j m n p r t v | No description available  
A C E G I K M O Q S U W | No description available  
B D F H J L N P R T V | No description available  
X Y | No description available  
Z | No description available  
a | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle11.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle11.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle11.pdb #13  
---  
Chain | Description  
0 2 4 6 k m o q s u w y | No description available  
1 3 5 7 l n p r t v x z | No description available  
8 | No description available  
9 | No description available  
A B E F H J L N | No description available  
C D G I K M | 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 a c e g i | No description available  
Z b d f h j | No description available  
  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle12.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle12.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle12.pdb #14  
---  
Chain | Description  
A C E G I K M O Q S U W | No description available  
B D F H J L N P R T V X | No description available  
  

> color #3 #e50f10ff

> color #2 #09f1e4ff models

> select

2026796 atoms, 2068256 bonds, 4 pseudobonds, 254226 residues, 18 models
selected  

> select subtract #2

2026796 atoms, 2068256 bonds, 4 pseudobonds, 254226 residues, 16 models
selected  

> select subtract #3

1013398 atoms, 1031635 bonds, 2 pseudobonds, 127113 residues, 14 models
selected  

> hide #!2 models

> hide sel atoms

> show sel cartoons

> view

> view orient

> select subtract #1

922484 atoms, 939033 bonds, 2 pseudobonds, 115715 residues, 13 models selected  

> select subtract #4

836212 atoms, 851218 bonds, 2 pseudobonds, 104880 residues, 12 models selected  

> select subtract #5

747625 atoms, 761022 bonds, 2 pseudobonds, 93771 residues, 11 models selected  

> select subtract #6

659852 atoms, 671656 bonds, 2 pseudobonds, 82718 residues, 10 models selected  

> select subtract #7

569845 atoms, 580025 bonds, 2 pseudobonds, 71430 residues, 9 models selected  

> select subtract #8

479076 atoms, 487590 bonds, 2 pseudobonds, 60058 residues, 8 models selected  

> select subtract #9

394865 atoms, 401901 bonds, 2 pseudobonds, 49469 residues, 7 models selected  

> select subtract #10

303226 atoms, 308570 bonds, 2 pseudobonds, 38011 residues, 6 models selected  

> select subtract #11

218026 atoms, 221860 bonds, 2 pseudobonds, 27292 residues, 5 models selected  

> select subtract #12

125989 atoms, 128240 bonds, 1 pseudobond, 15812 residues, 3 models selected  

> select subtract #13

33108 atoms, 33696 bonds, 4152 residues, 1 model selected  

> select subtract #14

Nothing selected  

> select down

Nothing selected  

> hide #4 models

> hide #5 models

> hide #6 models

> hide #7 models

> hide #8 models

> hide #9 models

> hide #10 models

> hide #11 models

> hide #!12 models

> hide #!13 models

> hide #14 models

> hide #!3 models

> show #!2 models

> fitmap #1 inMap #2

Fit molecule 6kgx-pdb-bundle1.pdb (#1) to map cryosparc_P14_J41_map.mrc (#2)
using 90914 atoms  
average map value = 0.07354, steps = 160  
shifted from previous position = 11  
rotated from previous position = 2.31 degrees  
atoms outside contour = 74154, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle1.pdb (#1) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98964122 0.14094326 -0.02729944 18.27956381  
-0.14019313 0.98973698 0.02768764 84.42226986  
0.03092165 -0.02357364 0.99924378 52.43017931  
Axis -0.17576778 -0.19963202 -0.96397756  
Axis point 501.98887356 -4.74646467 0.00000000  
Rotation angle (degrees) 8.38482590  
Shift along axis -70.60786309  
  

> fitmap #4 inMap #2

Fit molecule 6kgx-pdb-bundle2.pdb (#4) to map cryosparc_P14_J41_map.mrc (#2)
using 86272 atoms  
average map value = 0.1382, steps = 188  
shifted from previous position = 12  
rotated from previous position = 2.67 degrees  
atoms outside contour = 56742, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle2.pdb (#4) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98334724 0.18167009 -0.00491778 0.48642804  
-0.18171141 0.98330156 -0.00994989 113.12999527  
0.00302806 0.01067781 0.99993841 52.15486534  
Axis 0.05666121 -0.02182603 -0.99815486  
Axis point 612.68149302 36.48569757 0.00000000  
Rotation angle (degrees) 10.48782653  
Shift along axis -54.50024921  
  

> show #4 models

> show #5 models

> fitmap #5 inMap #2

Fit molecule 6kgx-pdb-bundle3.pdb (#5) to map cryosparc_P14_J41_map.mrc (#2)
using 88587 atoms  
average map value = 0.06532, steps = 156  
shifted from previous position = 12.9  
rotated from previous position = 3.44 degrees  
atoms outside contour = 73534, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle3.pdb (#5) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98978213 0.14018698 0.02605669 0.62054514  
-0.13957590 0.98992142 -0.02396155 103.92298262  
-0.02915317 0.02007983 0.99937325 57.71038547  
Axis 0.15263551 0.19134249 -0.96958262  
Axis point 792.85576827 14.19270752 0.00000000  
Rotation angle (degrees) 8.29499432  
Shift along axis -35.97538685  
  

> fitmap #6 inMap #2

Fit molecule 6kgx-pdb-bundle4.pdb (#6) to map cryosparc_P14_J41_map.mrc (#2)
using 87773 atoms  
average map value = 0.04756, steps = 84  
shifted from previous position = 5.24  
rotated from previous position = 1.5 degrees  
atoms outside contour = 65309, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle4.pdb (#6) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.99088008 0.13438991 -0.00979861 6.27372621  
-0.13444560 0.99090700 -0.00526283 94.46244110  
0.00900224 0.00653222 0.99993814 45.76846826  
Axis 0.04372583 -0.06969730 -0.99660942  
Axis point 676.88334144 -17.64247857 0.00000000  
Rotation angle (degrees) 7.75139535  
Shift along axis -51.92273990  
  

> show #6 models

> show #7 models

> fitmap #7 inMap #2

Fit molecule 6kgx-pdb-bundle5.pdb (#7) to map cryosparc_P14_J41_map.mrc (#2)
using 90007 atoms  
average map value = 0.1155, steps = 196  
shifted from previous position = 8.69  
rotated from previous position = 2.74 degrees  
atoms outside contour = 62637, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle5.pdb (#7) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98467660 0.17437786 -0.00208775 0.60281478  
-0.17434872 0.98463254 0.01006365 104.77750186  
0.00381055 -0.00954544 0.99994718 58.75566475  
Axis -0.05613388 -0.01688475 -0.99828047  
Axis point 589.13630612 67.77510316 0.00000000  
Rotation angle (degrees) 10.05908385  
Shift along axis -60.45761278  
  

> show #8 models

> fitmap #8 inMap #2

Fit molecule 6kgx-pdb-bundle6.pdb (#8) to map cryosparc_P14_J41_map.mrc (#2)
using 90769 atoms  
average map value = 0.1174, steps = 156  
shifted from previous position = 15.7  
rotated from previous position = 3 degrees  
atoms outside contour = 64917, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle6.pdb (#8) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98473122 0.17377278 0.01036530 -1.22861424  
-0.17372181 0.98477863 -0.00563706 108.20523438  
-0.01118709 0.00375031 0.99993039 58.45317613  
Axis 0.02695285 0.06188080 -0.99771956  
Axis point 636.44828132 54.98037793 0.00000000  
Rotation angle (degrees) 10.02887232  
Shift along axis -51.65716520  
  

> show #9 models

> fitmap #11 inMap #2

Fit molecule 6kgx-pdb-bundle9.pdb (#11) to map cryosparc_P14_J41_map.mrc (#2)
using 85200 atoms  
average map value = 0.1572, steps = 160  
shifted from previous position = 7.19  
rotated from previous position = 2.1 degrees  
atoms outside contour = 52114, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle9.pdb (#11) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98632513 0.16470273 -0.00597929 4.61711112  
-0.16468444 0.98634032 0.00343685 102.67745715  
0.00646367 -0.00240516 0.99997622 56.40715032  
Axis -0.01772056 -0.03774325 -0.99913034  
Axis point 607.26155745 28.87586516 0.00000000  
Rotation angle (degrees) 9.48776196  
Shift along axis -60.31529387  
  

> show #10 models

> fitmap #12 inMap #2

Fit molecule 6kgx-pdb-bundle10.pdb (#12) to map cryosparc_P14_J41_map.mrc (#2)
using 92037 atoms  
average map value = 0.1689, steps = 140  
shifted from previous position = 11.5  
rotated from previous position = 2.46 degrees  
atoms outside contour = 59280, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle10.pdb (#12) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98529117 0.17088339 0.00041946 1.42416716  
-0.17088012 0.98528269 -0.00424251 106.84324051  
-0.00113826 0.00410843 0.99999091 56.71682889  
Axis 0.02442730 0.00455648 -0.99969123  
Axis point 623.53749976 37.30655282 0.00000000  
Rotation angle (degrees) 9.84215939  
Shift along axis -56.17769806  
  

> show #11 models

> fitmap #13 inMap #2

Fit molecule 6kgx-pdb-bundle11.pdb (#13) to map cryosparc_P14_J41_map.mrc (#2)
using 92881 atoms  
average map value = 0.2155, steps = 196  
shifted from previous position = 14.6  
rotated from previous position = 2.84 degrees  
atoms outside contour = 52178, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle11.pdb (#13) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98378615 0.17934518 0.00034989 -0.87804214  
-0.17934532 0.98378610 0.00041203 108.33156747  
-0.00027032 -0.00046810 0.99999985 57.21941675  
Axis -0.00245374 0.00172910 -0.99999549  
Axis point 599.17846641 59.84531789 0.00000000  
Rotation angle (degrees) 10.33167169  
Shift along axis -57.02968863  
  

> show #!12 models

> fitmap #14 inMap #2

Fit molecule 6kgx-pdb-bundle12.pdb (#14) to map cryosparc_P14_J41_map.mrc (#2)
using 33108 atoms  
average map value = 0.02906, steps = 100  
shifted from previous position = 6.21  
rotated from previous position = 6.38 degrees  
atoms outside contour = 28882, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle12.pdb (#14) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.99554242 0.09279711 0.01685217 11.37798697  
-0.09074443 0.99113804 -0.09700945 119.67635637  
-0.02570502 0.09504779 0.99514078 26.95347377  
Axis 0.71385106 0.15817937 -0.68219935  
Axis point 0.00000000 -282.10509727 1245.29878467  
Rotation angle (degrees) 7.73097618  
Shift along axis 8.66487654  
  

> show #!13 models

> fitmap #13 inMap #2

Fit molecule 6kgx-pdb-bundle11.pdb (#13) to map cryosparc_P14_J41_map.mrc (#2)
using 92881 atoms  
average map value = 0.2155, steps = 44  
shifted from previous position = 0.0188  
rotated from previous position = 0.00516 degrees  
atoms outside contour = 52194, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle11.pdb (#13) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98378837 0.17933313 0.00026161 -0.86688873  
-0.17933323 0.98378831 0.00039969 108.32742079  
-0.00018569 -0.00044012 0.99999989 57.19899267  
Axis -0.00234146 0.00124710 -0.99999648  
Axis point 599.05354873 59.73313575 0.00000000  
Rotation angle (degrees) 10.33095868  
Shift along axis -57.06166656  
  

> show #14 models

> fitmap #14 inMap #2

Fit molecule 6kgx-pdb-bundle12.pdb (#14) to map cryosparc_P14_J41_map.mrc (#2)
using 33108 atoms  
average map value = 0.02906, steps = 80  
shifted from previous position = 0.0212  
rotated from previous position = 0.00911 degrees  
atoms outside contour = 28882, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle12.pdb (#14) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.99553317 0.09288190 0.01693076 11.32176997  
-0.09081853 0.99112053 -0.09711897 119.76771574  
-0.02580102 0.09514753 0.99512876 26.96131356  
Axis 0.71387151 0.15865997 -0.68206633  
Axis point 0.00000000 -281.96646356 1244.78096060  
Rotation angle (degrees) 7.73922805  
Shift along axis 8.69522752  
  

> fitmap #14 inMap #2

Fit molecule 6kgx-pdb-bundle12.pdb (#14) to map cryosparc_P14_J41_map.mrc (#2)
using 33108 atoms  
average map value = 0.02906, steps = 48  
shifted from previous position = 0.0255  
rotated from previous position = 0.00515 degrees  
atoms outside contour = 28881, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle12.pdb (#14) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.99553752 0.09285058 0.01684677 11.36278802  
-0.09079551 0.99112324 -0.09711284 119.73941791  
-0.02571420 0.09514986 0.99513079 26.92201788  
Axis 0.71403458 0.15806500 -0.68203378  
Axis point 0.00000000 -281.45833009 1244.59467326  
Rotation angle (degrees) 7.73729596  
Shift along axis 8.67830907  
  

> fitmap #14 inMap #2

Fit molecule 6kgx-pdb-bundle12.pdb (#14) to map cryosparc_P14_J41_map.mrc (#2)
using 33108 atoms  
average map value = 0.02906, steps = 48  
shifted from previous position = 0.00496  
rotated from previous position = 0.0132 degrees  
atoms outside contour = 28882, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle12.pdb (#14) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.99553199 0.09293636 0.01670023 11.40618008  
-0.09089085 0.99109923 -0.09726855 119.84425639  
-0.02559137 0.09531605 0.99511805 26.83862425  
Axis 0.71440492 0.15688339 -0.68191878  
Axis point 0.00000000 -279.74563858 1243.74642494  
Rotation angle (degrees) 7.74628766  
Shift along axis 8.64844254  
  

> fitmap #13 inMap #2

Fit molecule 6kgx-pdb-bundle11.pdb (#13) to map cryosparc_P14_J41_map.mrc (#2)
using 92881 atoms  
average map value = 0.2155, steps = 48  
shifted from previous position = 0.0063  
rotated from previous position = 0.00468 degrees  
atoms outside contour = 52186, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle11.pdb (#13) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98380104 0.17926363 0.00026851 -0.85741507  
-0.17926372 0.98380099 0.00035936 108.32116872  
-0.00019974 -0.00040167 0.99999990 57.19200411  
Axis -0.00212264 0.00130601 -0.99999689  
Axis point 599.28477492 59.61220782 0.00000000  
Rotation angle (degrees) 10.32690613  
Shift along axis -57.04853793  
  

> fitmap #12 inMap #2

Fit molecule 6kgx-pdb-bundle10.pdb (#12) to map cryosparc_P14_J41_map.mrc (#2)
using 92037 atoms  
average map value = 0.1689, steps = 84  
shifted from previous position = 0.00485  
rotated from previous position = 0.000885 degrees  
atoms outside contour = 59279, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle10.pdb (#12) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98529232 0.17087673 0.00042547 1.42398769  
-0.17087345 0.98528390 -0.00423000 106.83497629  
-0.00114202 0.00409508 0.99999096 56.72514417  
Axis 0.02435264 0.00458525 -0.99969292  
Axis point 623.52155847 37.32724501 0.00000000  
Rotation angle (degrees) 9.84175494  
Shift along axis -56.18318192  
  

> fitmap #11 inMap #2

Fit molecule 6kgx-pdb-bundle9.pdb (#11) to map cryosparc_P14_J41_map.mrc (#2)
using 85200 atoms  
average map value = 0.1572, steps = 48  
shifted from previous position = 0.0184  
rotated from previous position = 0.00734 degrees  
atoms outside contour = 52106, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle9.pdb (#11) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98632378 0.16471116 -0.00596934 4.60273859  
-0.16469206 0.98633859 0.00356429 102.64068135  
0.00647486 -0.00253244 0.99997583 56.43223541  
Axis -0.01849204 -0.03774463 -0.99911630  
Axis point 606.97406987 29.22820187 0.00000000  
Rotation angle (degrees) 9.48836311  
Shift along axis -60.34161488  
  

> fitmap #11 inMap #2

Fit molecule 6kgx-pdb-bundle9.pdb (#11) to map cryosparc_P14_J41_map.mrc (#2)
using 85200 atoms  
average map value = 0.1572, steps = 116  
shifted from previous position = 0.0188  
rotated from previous position = 0.00721 degrees  
atoms outside contour = 52124, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle9.pdb (#11) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98631473 0.16476857 -0.00587919 4.58438250  
-0.16475012 0.98632913 0.00349872 102.68411071  
0.00637530 -0.00248224 0.99997660 56.44931471  
Axis -0.01813509 -0.03715726 -0.99914486  
Axis point 607.24490410 29.24990518 0.00000000  
Rotation angle (degrees) 9.49144596  
Shift along axis -60.29964130  
  

> fitmap #10 inMap #2

Fit molecule 6kgx-pdb-bundle8.pdb (#10) to map cryosparc_P14_J41_map.mrc (#2)
using 91639 atoms  
average map value = 0.1524, steps = 116  
shifted from previous position = 8.01  
rotated from previous position = 3.37 degrees  
atoms outside contour = 61669, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle8.pdb (#10) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98349966 0.18053856 0.01158673 -6.02798063  
-0.18057452 0.98355900 0.00212814 108.86319606  
-0.01101202 -0.00418530 0.99993061 62.65192945  
Axis -0.01744648 0.06244913 -0.99789565  
Axis point 613.47120494 94.83169659 0.00000000  
Rotation angle (degrees) 10.42435947  
Shift along axis -55.61650861  
  

> fitmap #10 inMap #2

Fit molecule 6kgx-pdb-bundle8.pdb (#10) to map cryosparc_P14_J41_map.mrc (#2)
using 91639 atoms  
average map value = 0.1524, steps = 48  
shifted from previous position = 0.0198  
rotated from previous position = 0.00148 degrees  
atoms outside contour = 61680, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle8.pdb (#10) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98350426 0.18051361 0.01158501 -6.00199034  
-0.18054952 0.98356360 0.00212383 108.85462295  
-0.01101122 -0.00418046 0.99993064 62.65942003  
Axis -0.01742362 0.06245082 -0.99789594  
Axis point 613.52797889 94.68415167 0.00000000  
Rotation angle (degrees) 10.42289802  
Shift along axis -55.62494461  
  

> fitmap #9 inMap #2

Fit molecule 6kgx-pdb-bundle7.pdb (#9) to map cryosparc_P14_J41_map.mrc (#2)
using 84211 atoms  
average map value = 0.0671, steps = 184  
shifted from previous position = 8.64  
rotated from previous position = 1.66 degrees  
atoms outside contour = 62252, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle7.pdb (#9) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98732362 0.15802111 -0.01487967 7.01902774  
-0.15793568 0.98742627 0.00675869 96.75987533  
0.01576060 -0.00432299 0.99986645 50.79538780  
Axis -0.03488838 -0.09646457 -0.99472478  
Axis point 574.75090048 14.95840131 0.00000000  
Rotation angle (degrees) 9.13818986  
Shift along axis -60.10621296  
  

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

Mismatch between Cocoa '\x0' and Carbon 'k' for virtual key 40 with
QFlags(NoModifier)  

Mismatch between Cocoa '\x0' and Carbon 'K' for virtual key 40 with
QFlags(ShiftModifier)  

Mismatch between Cocoa '\x0' and Carbon 'k' for virtual key 40 with
QFlags(ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon 'k' for virtual key 40 with
QFlags(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\u02da' for virtual key 40 with
QFlags(AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\uf8ff' for virtual key 40 with
QFlags(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\u02da' for virtual key 40 with
QFlags(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\uf8ff' for virtual key 40 with
QFlags(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xb' for virtual key 40 with
QFlags(MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xb' for virtual key 40 with
QFlags(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xb' for virtual key 40 with
QFlags(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xb' for virtual key 40 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xb' for virtual key 40 with
QFlags(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xb' for virtual key 40 with
QFlags(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xb' for virtual key 40 with
QFlags(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xb' for virtual key 40 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> save "/Users/yamadakouseki/Desktop/PBS cryo-EM/チノリモPDBとダルスを重ねたもの.cxs"
> includeMaps true

> hide #!3 models

> hide #!2 models

> save "/Users/yamadakouseki/Desktop/PBS cryo-EM/fit01.pdb" models #1 relModel
> #2

> save "/Users/yamadakouseki/Desktop/PBS cryo-EM/fit/fit02.pdb" models #4
> relModel #2

> save "/Users/yamadakouseki/Desktop/PBS cryo-EM/fit/fit03.pdb" models #5
> relModel #2

> save "/Users/yamadakouseki/Desktop/PBS cryo-EM/fit/fit04.pdb" models #6
> relModel #2

> save "/Users/yamadakouseki/Desktop/PBS cryo-EM/fit/fit05.pdb" models #7
> relModel #2

> save "/Users/yamadakouseki/Desktop/PBS cryo-EM/fit/fit06.pdb" relModel #2


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/チノリモPDBとダルスを重ねたもの.cxs"

Opened cryosparc_P14_J41_map.mrc as #2, grid size 600,600,600, pixel 1.18,
shown at level 0.0935, step 4, values float32  
Log from Thu Mar 9 16:33:29 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309
> 田中先生/cryosparc_P14_J41_map.mrc"

Opened cryosparc_P14_J41_map.mrc as #1, grid size 600,600,600, pixel 1.18,
shown at level 0.186, step 4, values float32  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309
> 田中先生/cryosparc_P14_J41_map.mrc"

Opened cryosparc_P14_J41_map.mrc as #2, grid size 600,600,600, pixel 1.18,
shown at level 0.186, step 4, values float32  

> hide #!1 models

> show #!1 models

> hide #!2 models

> close

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/チノリモ PBS.map" format ccp4

Opened チノリモ PBS.map as #1, grid size 560,560,560, pixel 1.09, shown at level
0.0214, step 4, values float32  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309
> 田中先生/cryosparc_P14_J41_map.mrc"

Opened cryosparc_P14_J41_map.mrc as #2, grid size 600,600,600, pixel 1.18,
shown at level 0.186, step 4, values float32  

> hide #!2 models

> volume #1 level 0.02551

> volume #1 level 0.01381

> volume #1 step 2

> show #!2 models

> volume #2 level 0.1145

> volume #2 step 2

> show #!1 models

> select add #1

2 models selected  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx.cif"

6kgx.cif title:  
Structure of the phycobilisome from the red alga Porphyridium purpureum [more
info...]  
  
Chain information for 6kgx.cif #3  
---  
Chain | Description | UniProt  
11 14 A5 AC B1 B3 B4 B5 BC BD BE BG C5 C9 CC CJ D1 D3 D4 D8 DA DD DE DG E9 EJ
F1 F3 F4 F5 F8 FA FC FD FE FG G5 G9 GC GJ H1 H3 H4 H5 H8 HA HC HD HE HG I5 I9
IC IJ J1 J3 J4 J8 JA JD JE JG K5 K9 KC KJ L1 L3 L4 L5 L8 LA LC LD LE LG M9 MJ
N3 N8 NA ND NE NG O1 O4 O9 OJ P2 P3 P6 P7 P8 PA PB PD PE PF PG PI Q1 Q4 Q9 QJ
R2 R3 R6 R7 R8 RA RB RD RE RF RG RI S1 S4 S9 SJ T2 T3 T6 T7 T8 TA TB TD TE TF
TG TI U1 U4 U9 UJ V2 V3 V6 V7 V8 VA VB VD VE VF VG VI W1 W4 W9 WJ X3 X8 XA XD
XE XG Y1 Y2 Y4 Y6 Y7 Y9 YB YF YI YJ Z1 Z4 Z8 ZA ZE ZG a1 a2 a4 a6 a7 aB aF aI
bE bG c2 c6 c7 c8 cA cB cF cI d1 d4 dE dG e2 e6 e7 e8 eA eB eF eI f1 f4 fE fG
g2 g6 g7 g8 gA gB gF gI h1 h4 hE hG i2 i6 i7 i8 iA iB iF iI j1 j4 jE jG k2 k6
k7 k8 kA kB kF kI l1 l4 lE lG m2 m6 m7 m8 mA mB mF mI n1 n4 nE nG pE pG q1 q4
rE rG s1 s4 tE tG u1 u4 vE vG w1 w4 y1 y4 | B-phycoerythrin beta chain |
PHEB_PORPP  
1H YH | Phycobilisome linker polypeptide | W0RZJ2_PORPP  
21 24 M1 M4 | LR7 |  
2H ZH | LRC4 |  
31 34 | LR9 |  
3H aH | LRC5 |  
4H bH | LRC6 |  
A1 A3 A4 AD AE AG B9 BJ C1 C3 C4 C8 CA CD CE CG D9 DJ E1 E3 E4 E8 EA ED EE EG
F9 FJ G1 G3 G4 G8 GA GD GE GG H9 HJ I1 I3 I4 I8 IA ID IE IG J5 J9 JC JJ K1 K3
K4 K8 KA KD KE KG L9 LJ M3 M8 MA MD ME MG N1 N4 N9 NJ O2 O3 O6 O7 O8 OA OB OD
OE OF OG OI P1 P4 P9 PJ Q2 Q3 Q6 Q7 Q8 QA QB QD QE QF QG QI R1 R4 R9 RJ S2 S3
S6 S7 S8 SA SB SD SE SF SG SI T1 T4 T9 TJ U2 U3 U6 U7 U8 UA UB UD UE UF UG UI
V1 V4 V9 VJ W2 W3 W6 W7 W8 WA WB WD WE WF WG WI X1 X4 X9 XJ Y8 YA YE YG Z2 Z6
Z7 ZB ZF ZI a8 aA aE aG b2 b6 b7 bB bF bI c1 c4 cE cG d2 d6 d7 d8 dA dB dF dI
e1 e4 eE eG f2 f6 f7 f8 fA fB fF fI g1 g4 gE gG h2 h6 h7 h8 hA hB hF hI i1 i4
iE iG j2 j6 j7 j8 jA jB jF jI k1 k4 kE kG l2 l6 l7 l8 lA lB lF lI m1 m4 mE mG
oE oG p1 p4 qE qG r1 r4 sE sG t1 t4 uE uG v1 v4 x1 x4 z1 z4 | Phycoerythrin
alpha subunit | E2IH77_PORPP  
A2 A6 A7 A9 AB AF AI AJ Y3 YD | LR4 |  
A8 AA wE wG xE xG | LR5 |  
AH CH EH GH JH KH NH PH RH TH cH eH gH iH lH mH pH rH tH vH | Allophycocyanin
alpha subunit | W0RYM0_PORPP  
B2 B6 B7 BB BF BI | Phycobilisome rod-core linker polypeptide | W0RZ90_PORPP  
B8 BA yE yG | LR8 |  
BH DH FH HH IH LH MH OH QH SH UH dH fH hH jH kH nH oH qH sH uH wH |
Allophycocyanin beta subunit | W0S279_PORPP  
C2 C6 C7 CB CF CI E2 E6 E7 EB EF EI G2 G6 G7 GB GF GI I2 I6 I7 IB IF II K2 K6
K7 KB KF KI M2 M6 M7 MB MF MI | C-phycocyanin alpha subunit | W0RYI4_PORPP  
D2 D6 D7 DB DF DI F2 F6 F7 FB FF FI H2 H6 H7 HB HF HI J2 J6 J7 JB JF JI L2 L6
L7 LB LF LI N2 N6 N7 NB NF NI | C-phycocyanin beta subunit | W0RZB2_PORPP  
VH xH | Allophycocyanin gamma subunit | W0S1U6_PORPP  
WH yH | Allophycocyanin beta 18 subunit | W0RZE2_PORPP  
X2 X6 X7 XB XF XI | LR1 |  
XH zH | LC |  
b1 b4 o1 o4 | LR2_Hb |  
b8 bA | LRC2 |  
d9 dJ | LR3 |  
e3 eD | LR2 |  
zE zG | LRC3 |  
  
Non-standard residues in 6kgx.cif #3  
---  
CYC — phycocyanobilin  
PEB — phycoerythrobilin  
PUB — phycourobilin  
  

> hide #!1 models

> close #1

> select add #2

2 models selected  

> transparency sel 50

> log metadata #3

Metadata for 6kgx.cif #3  
---  
Title | Structure of the phycobilisome from the red alga Porphyridium
purpureum  
Citation | Ma, J.F., You, X., Sun, S., Wang, X.X., Qin, S., Sui, S.F. (2020).
Structural basis of energy transfer in Porphyridium purpureum phycobilisome.
Nature, 579, 146-151. PMID: 32076272. DOI: 10.1038/s41586-020-2020-7  
Non-standard residues | CYC — phycocyanobilin  
PEB — phycoerythrobilin  
PUB — phycourobilin  
Source (natural) | Porphyridium purpureum (red alga)  
CryoEM Map | EMDB 9976 — open map  
Experimental method | Electron microscopy  
Resolution | 2.8Å  
  
> log chains #3

Chain information for 6kgx.cif #3  
---  
Chain | Description | UniProt  
11 14 A5 AC B1 B3 B4 B5 BC BD BE BG C5 C9 CC CJ D1 D3 D4 D8 DA DD DE DG E9 EJ
F1 F3 F4 F5 F8 FA FC FD FE FG G5 G9 GC GJ H1 H3 H4 H5 H8 HA HC HD HE HG I5 I9
IC IJ J1 J3 J4 J8 JA JD JE JG K5 K9 KC KJ L1 L3 L4 L5 L8 LA LC LD LE LG M9 MJ
N3 N8 NA ND NE NG O1 O4 O9 OJ P2 P3 P6 P7 P8 PA PB PD PE PF PG PI Q1 Q4 Q9 QJ
R2 R3 R6 R7 R8 RA RB RD RE RF RG RI S1 S4 S9 SJ T2 T3 T6 T7 T8 TA TB TD TE TF
TG TI U1 U4 U9 UJ V2 V3 V6 V7 V8 VA VB VD VE VF VG VI W1 W4 W9 WJ X3 X8 XA XD
XE XG Y1 Y2 Y4 Y6 Y7 Y9 YB YF YI YJ Z1 Z4 Z8 ZA ZE ZG a1 a2 a4 a6 a7 aB aF aI
bE bG c2 c6 c7 c8 cA cB cF cI d1 d4 dE dG e2 e6 e7 e8 eA eB eF eI f1 f4 fE fG
g2 g6 g7 g8 gA gB gF gI h1 h4 hE hG i2 i6 i7 i8 iA iB iF iI j1 j4 jE jG k2 k6
k7 k8 kA kB kF kI l1 l4 lE lG m2 m6 m7 m8 mA mB mF mI n1 n4 nE nG pE pG q1 q4
rE rG s1 s4 tE tG u1 u4 vE vG w1 w4 y1 y4 | B-phycoerythrin beta chain |
PHEB_PORPP  
1H YH | Phycobilisome linker polypeptide | W0RZJ2_PORPP  
21 24 M1 M4 | LR7 |  
2H ZH | LRC4 |  
31 34 | LR9 |  
3H aH | LRC5 |  
4H bH | LRC6 |  
A1 A3 A4 AD AE AG B9 BJ C1 C3 C4 C8 CA CD CE CG D9 DJ E1 E3 E4 E8 EA ED EE EG
F9 FJ G1 G3 G4 G8 GA GD GE GG H9 HJ I1 I3 I4 I8 IA ID IE IG J5 J9 JC JJ K1 K3
K4 K8 KA KD KE KG L9 LJ M3 M8 MA MD ME MG N1 N4 N9 NJ O2 O3 O6 O7 O8 OA OB OD
OE OF OG OI P1 P4 P9 PJ Q2 Q3 Q6 Q7 Q8 QA QB QD QE QF QG QI R1 R4 R9 RJ S2 S3
S6 S7 S8 SA SB SD SE SF SG SI T1 T4 T9 TJ U2 U3 U6 U7 U8 UA UB UD UE UF UG UI
V1 V4 V9 VJ W2 W3 W6 W7 W8 WA WB WD WE WF WG WI X1 X4 X9 XJ Y8 YA YE YG Z2 Z6
Z7 ZB ZF ZI a8 aA aE aG b2 b6 b7 bB bF bI c1 c4 cE cG d2 d6 d7 d8 dA dB dF dI
e1 e4 eE eG f2 f6 f7 f8 fA fB fF fI g1 g4 gE gG h2 h6 h7 h8 hA hB hF hI i1 i4
iE iG j2 j6 j7 j8 jA jB jF jI k1 k4 kE kG l2 l6 l7 l8 lA lB lF lI m1 m4 mE mG
oE oG p1 p4 qE qG r1 r4 sE sG t1 t4 uE uG v1 v4 x1 x4 z1 z4 | Phycoerythrin
alpha subunit | E2IH77_PORPP  
A2 A6 A7 A9 AB AF AI AJ Y3 YD | LR4 |  
A8 AA wE wG xE xG | LR5 |  
AH CH EH GH JH KH NH PH RH TH cH eH gH iH lH mH pH rH tH vH | Allophycocyanin
alpha subunit | W0RYM0_PORPP  
B2 B6 B7 BB BF BI | Phycobilisome rod-core linker polypeptide | W0RZ90_PORPP  
B8 BA yE yG | LR8 |  
BH DH FH HH IH LH MH OH QH SH UH dH fH hH jH kH nH oH qH sH uH wH |
Allophycocyanin beta subunit | W0S279_PORPP  
C2 C6 C7 CB CF CI E2 E6 E7 EB EF EI G2 G6 G7 GB GF GI I2 I6 I7 IB IF II K2 K6
K7 KB KF KI M2 M6 M7 MB MF MI | C-phycocyanin alpha subunit | W0RYI4_PORPP  
D2 D6 D7 DB DF DI F2 F6 F7 FB FF FI H2 H6 H7 HB HF HI J2 J6 J7 JB JF JI L2 L6
L7 LB LF LI N2 N6 N7 NB NF NI | C-phycocyanin beta subunit | W0RZB2_PORPP  
VH xH | Allophycocyanin gamma subunit | W0S1U6_PORPP  
WH yH | Allophycocyanin beta 18 subunit | W0RZE2_PORPP  
X2 X6 X7 XB XF XI | LR1 |  
XH zH | LC |  
b1 b4 o1 o4 | LR2_Hb |  
b8 bA | LRC2 |  
d9 dJ | LR3 |  
e3 eD | LR2 |  
zE zG | LRC3 |  
  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-69.154,0,1,0,-30.402,0,0,1,-26.313

> view matrix models #2,1,0,0,-58.589,0,1,0,-35.554,0,0,1,-47.627

> view matrix models #2,1,0,0,-50.689,0,1,0,-36.529,0,0,1,-59.77

> view matrix models #2,1,0,0,-77.255,0,1,0,-54.657,0,0,1,-45.124

> view matrix models #2,1,0,0,-44.258,0,1,0,-43.603,0,0,1,-49.119

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.98892,-0.14524,0.030589,0.28873,0.14479,0.98932,0.016624,-97.073,-0.032677,-0.012011,0.99939,-33.058

> volume #2 step 4

> color #2 #95fff2ff models

> color #2 #fb8dedff models

> color #3 #65e1e0ff

> ui tool show Angles/Torsions

> ui mousemode right "translate selected models"

> ui tool show "Side View"

> ui tool show "Fit in Map"

> select subtract #2

Nothing selected  

> fitmap #3 inMap #2

Fit molecule 6kgx.cif (#3) to map cryosparc_P14_J41_map.mrc (#2) using 1013398
atoms  
average map value = 0.109, steps = 120  
shifted from previous position = 11.2  
rotated from previous position = 2.48 degrees  
atoms outside contour = 771596, contour level = 0.11453  
  
Position of 6kgx.cif (#3) relative to cryosparc_P14_J41_map.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.98534503 0.17057309 -0.00003566 1.50097440  
-0.17057309 0.98534503 0.00001086 105.69904189  
0.00003699 -0.00000462 1.00000000 57.27121156  
Axis -0.00004535 -0.00021296 -0.99999998  
Axis point 615.80765974 44.12342660 0.00000000  
Rotation angle (degrees) 9.82114140  
Shift along axis -57.29378787  
  

> fitmap #3 inMap #2

Fit molecule 6kgx.cif (#3) to map cryosparc_P14_J41_map.mrc (#2) using 1013398
atoms  
average map value = 0.1091, steps = 40  
shifted from previous position = 0.0198  
rotated from previous position = 0.00148 degrees  
atoms outside contour = 771518, contour level = 0.11453  
  
Position of 6kgx.cif (#3) relative to cryosparc_P14_J41_map.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.98534752 0.17055867 -0.00005502 1.50384534  
-0.17055867 0.98534752 0.00001961 105.69300222  
0.00005756 -0.00000994 1.00000000 57.24801158  
Axis -0.00008662 -0.00033006 -0.99999994  
Axis point 615.78651004 44.11335413 0.00000000  
Rotation angle (degrees) 9.82030326  
Shift along axis -57.28302317  
  

> fitmap #3 inMap #2

Fit molecule 6kgx.cif (#3) to map cryosparc_P14_J41_map.mrc (#2) using 1013398
atoms  
average map value = 0.109, steps = 44  
shifted from previous position = 0.0193  
rotated from previous position = 0.00134 degrees  
atoms outside contour = 771579, contour level = 0.11453  
  
Position of 6kgx.cif (#3) relative to cryosparc_P14_J41_map.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.98534719 0.17056060 -0.00003172 1.49713685  
-0.17056060 0.98534719 0.00001762 105.69383362  
0.00003426 -0.00001195 1.00000000 57.27501867  
Axis -0.00008667 -0.00019344 -0.99999998  
Axis point 615.82644757 44.15684784 0.00000000  
Rotation angle (degrees) 9.82041536  
Shift along axis -57.29559245  
  

> volume #2 level 0.09346

> fitmap #3 inMap #2

Fit molecule 6kgx.cif (#3) to map cryosparc_P14_J41_map.mrc (#2) using 1013398
atoms  
average map value = 0.1091, steps = 44  
shifted from previous position = 0.0186  
rotated from previous position = 0.000464 degrees  
atoms outside contour = 706022, contour level = 0.093461  
  
Position of 6kgx.cif (#3) relative to cryosparc_P14_J41_map.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.98534737 0.17055958 -0.00002374 1.49537016  
-0.17055958 0.98534737 0.00001842 105.69084184  
0.00002653 -0.00001410 1.00000000 57.25964023  
Axis -0.00009533 -0.00014738 -0.99999998  
Axis point 615.82702399 44.16977691 0.00000000  
Rotation angle (degrees) 9.82035584  
Shift along axis -57.27535823  
  

> hide #!3 models

> show #!3 models

> hide #!3 models

> volume gaussian #1 sDev 5

[Repeated 1 time(s)]

> show #!3 models

> show target m

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle1.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle1.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle1.pdb #1  
---  
Chain | Description  
0 B D F H J L O Q S U W Y d f h j l n q s u w y | No description available  
1 M | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 8 | No description available  
7 9 | No description available  
A C E G I K N P R T V X c e g i k m p r t v x z | No description available  
Z a | No description available  
b | No description available  
o | No description available  
  

> close #1

> hide atoms

> show cartoons

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle1.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle1.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle1.pdb #1  
---  
Chain | Description  
0 B D F H J L O Q S U W Y d f h j l n q s u w y | No description available  
1 M | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 8 | No description available  
7 9 | No description available  
A C E G I K N P R T V X c e g i k m p r t v x z | No description available  
Z a | No description available  
b | No description available  
o | No description available  
  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle2.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle2.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle2.pdb #4  
---  
Chain | Description  
0 2 4 7 9 J L N P R T V X Z b d f i k m o q s u w y | No description available  
1 3 6 8 I K M O Q S U W Y a c e h j l n p r t v x z | No description available  
5 | No description available  
A C E G | No description available  
B D F H | No description available  
g | No description available  
  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle3.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle3.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle3.pdb #5  
---  
Chain | Description  
0 1 2 3 4 8 V W z | No description available  
5 7 B D F H K M O Q S U Z b d f h j m o q s u w | No description available  
6 A C E G J L N P R T Y a c e g i l n p r t v | No description available  
9 | No description available  
I x | No description available  
X | No description available  
k | No description available  
y | No description available  
  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle4.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle4.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle4.pdb #6  
---  
Chain | Description  
0 D F H J L N q s u w y | No description available  
1 3 5 7 9 O Q S U W Y a c e g i k | No description available  
2 4 6 8 P R T V X Z b d f h j l | No description available  
A n | No description available  
B | No description available  
C E G I K M p r t v x z | No description available  
m | No description available  
o | No description available  
  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle5.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle5.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle5.pdb #7  
---  
Chain | Description  
0 4 6 8 B D F H J L N S U W Y a c e g i k m o q s u w y | No description
available  
1 5 7 9 A C E G I K M O T V X Z b d f h j l n p r t v x z | No description
available  
2 | No description available  
3 | No description available  
P | No description available  
Q | No description available  
R | No description available  
  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle6.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle6.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle6.pdb #8  
---  
Chain | Description  
0 2 4 B D F H J L N P R W Y a c e g i k m o q s u w y | No description
available  
1 3 A C E G I K M O Q V X Z b d f h j l n p r t v x z | No description
available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
S | No description available  
T | No description available  
U | No description available  
  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle7.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle7.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle7.pdb #9  
---  
Chain | Description  
0 2 4 6 8 L N P R T V X Z b d f h q u w y | No description available  
1 3 5 7 9 K M O Q S U W Y a c e g p t v x z | No description available  
A C E G I | No description available  
B D F H J | No description available  
i j k l m n r | No description available  
o | No description available  
s | No description available  
  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle8.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle8.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle8.pdb #10  
---  
Chain | Description  
0 2 B D F I K M O Q S U W Y a c e g i k m o q s u w y | No description
available  
1 3 A C E G J L N P R T V X Z b d f h j l n p r t v x z | No description
available  
4 5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
H | No description available  
  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle9.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle9.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle9.pdb #11  
---  
Chain | Description  
0 2 4 6 8 O Q S U W Y a c e g i k m o q s u w y | No description available  
1 3 5 7 9 N P R T V X Z b d f h j l n p r t v x z | No description available  
A | No description available  
B D F H J L | No description available  
C E G I K M | No description available  
  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle10.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle10.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle10.pdb #12  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 5 7 9 b d f h k l o q s u | No description available  
4 6 8 c e g i j m n p r t v | No description available  
A C E G I K M O Q S U W | No description available  
B D F H J L N P R T V | No description available  
X Y | No description available  
Z | No description available  
a | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle11.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle11.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle11.pdb #13  
---  
Chain | Description  
0 2 4 6 k m o q s u w y | No description available  
1 3 5 7 l n p r t v x z | No description available  
8 | No description available  
9 | No description available  
A B E F H J L N | No description available  
C D G I K M | 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 a c e g i | No description available  
Z b d f h j | No description available  
  

> open "/Users/yamadakouseki/Desktop/PBS cryo-EM/230309 田中先生/6kgx-pdb-
> bundle/6kgx-pdb-bundle12.pdb"

Summary of feedback from opening /Users/yamadakouseki/Desktop/PBS cryo-
EM/230309 田中先生/6kgx-pdb-bundle/6kgx-pdb-bundle12.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER PHOTOSYNTHESIS 2019-07-12 XXXX  
  
Chain information for 6kgx-pdb-bundle12.pdb #14  
---  
Chain | Description  
A C E G I K M O Q S U W | No description available  
B D F H J L N P R T V X | No description available  
  

> color #3 #e50f10ff

> color #2 #09f1e4ff models

> select

2026796 atoms, 2068256 bonds, 4 pseudobonds, 254226 residues, 18 models
selected  

> select subtract #2

2026796 atoms, 2068256 bonds, 4 pseudobonds, 254226 residues, 16 models
selected  

> select subtract #3

1013398 atoms, 1031635 bonds, 2 pseudobonds, 127113 residues, 14 models
selected  

> hide #!2 models

> hide sel atoms

[Repeated 1 time(s)]

> show sel cartoons

[Repeated 1 time(s)]

> view

[Repeated 1 time(s)]

> view orient

[Repeated 1 time(s)]

> select subtract #1

922484 atoms, 939033 bonds, 2 pseudobonds, 115715 residues, 13 models selected  

> select subtract #4

836212 atoms, 851218 bonds, 2 pseudobonds, 104880 residues, 12 models selected  

> select subtract #5

747625 atoms, 761022 bonds, 2 pseudobonds, 93771 residues, 11 models selected  

> select subtract #6

659852 atoms, 671656 bonds, 2 pseudobonds, 82718 residues, 10 models selected  

> select subtract #7

569845 atoms, 580025 bonds, 2 pseudobonds, 71430 residues, 9 models selected  

> select subtract #8

479076 atoms, 487590 bonds, 2 pseudobonds, 60058 residues, 8 models selected  

> select subtract #9

394865 atoms, 401901 bonds, 2 pseudobonds, 49469 residues, 7 models selected  

> select subtract #10

303226 atoms, 308570 bonds, 2 pseudobonds, 38011 residues, 6 models selected  

> select subtract #11

218026 atoms, 221860 bonds, 2 pseudobonds, 27292 residues, 5 models selected  

> select subtract #12

125989 atoms, 128240 bonds, 1 pseudobond, 15812 residues, 3 models selected  

> select subtract #13

33108 atoms, 33696 bonds, 4152 residues, 1 model selected  

> select subtract #14

Nothing selected  

> select down

Nothing selected  

> hide #4 models

> hide #5 models

> hide #6 models

> hide #7 models

> hide #8 models

> hide #9 models

> hide #10 models

> hide #11 models

> hide #!12 models

> hide #!13 models

> hide #14 models

> hide #!3 models

> show #!2 models

> fitmap #1 inMap #2

Fit molecule 6kgx-pdb-bundle1.pdb (#1) to map cryosparc_P14_J41_map.mrc (#2)
using 90914 atoms  
average map value = 0.07354, steps = 160  
shifted from previous position = 11  
rotated from previous position = 2.31 degrees  
atoms outside contour = 74154, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle1.pdb (#1) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98964122 0.14094326 -0.02729944 18.27956381  
-0.14019313 0.98973698 0.02768764 84.42226986  
0.03092165 -0.02357364 0.99924378 52.43017931  
Axis -0.17576778 -0.19963202 -0.96397756  
Axis point 501.98887356 -4.74646467 0.00000000  
Rotation angle (degrees) 8.38482590  
Shift along axis -70.60786309  
  

> fitmap #4 inMap #2

Fit molecule 6kgx-pdb-bundle2.pdb (#4) to map cryosparc_P14_J41_map.mrc (#2)
using 86272 atoms  
average map value = 0.1382, steps = 188  
shifted from previous position = 12  
rotated from previous position = 2.67 degrees  
atoms outside contour = 56742, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle2.pdb (#4) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98334724 0.18167009 -0.00491778 0.48642804  
-0.18171141 0.98330156 -0.00994989 113.12999527  
0.00302806 0.01067781 0.99993841 52.15486534  
Axis 0.05666121 -0.02182603 -0.99815486  
Axis point 612.68149302 36.48569757 0.00000000  
Rotation angle (degrees) 10.48782653  
Shift along axis -54.50024921  
  

> show #4 models

> show #5 models

> fitmap #5 inMap #2

Fit molecule 6kgx-pdb-bundle3.pdb (#5) to map cryosparc_P14_J41_map.mrc (#2)
using 88587 atoms  
average map value = 0.06532, steps = 156  
shifted from previous position = 12.9  
rotated from previous position = 3.44 degrees  
atoms outside contour = 73534, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle3.pdb (#5) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98978213 0.14018698 0.02605669 0.62054514  
-0.13957590 0.98992142 -0.02396155 103.92298262  
-0.02915317 0.02007983 0.99937325 57.71038547  
Axis 0.15263551 0.19134249 -0.96958262  
Axis point 792.85576827 14.19270752 0.00000000  
Rotation angle (degrees) 8.29499432  
Shift along axis -35.97538685  
  

> fitmap #6 inMap #2

Fit molecule 6kgx-pdb-bundle4.pdb (#6) to map cryosparc_P14_J41_map.mrc (#2)
using 87773 atoms  
average map value = 0.04756, steps = 84  
shifted from previous position = 5.24  
rotated from previous position = 1.5 degrees  
atoms outside contour = 65309, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle4.pdb (#6) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.99088008 0.13438991 -0.00979861 6.27372621  
-0.13444560 0.99090700 -0.00526283 94.46244110  
0.00900224 0.00653222 0.99993814 45.76846826  
Axis 0.04372583 -0.06969730 -0.99660942  
Axis point 676.88334144 -17.64247857 0.00000000  
Rotation angle (degrees) 7.75139535  
Shift along axis -51.92273990  
  

> show #6 models

> show #7 models

> fitmap #7 inMap #2

Fit molecule 6kgx-pdb-bundle5.pdb (#7) to map cryosparc_P14_J41_map.mrc (#2)
using 90007 atoms  
average map value = 0.1155, steps = 196  
shifted from previous position = 8.69  
rotated from previous position = 2.74 degrees  
atoms outside contour = 62637, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle5.pdb (#7) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98467660 0.17437786 -0.00208775 0.60281478  
-0.17434872 0.98463254 0.01006365 104.77750186  
0.00381055 -0.00954544 0.99994718 58.75566475  
Axis -0.05613388 -0.01688475 -0.99828047  
Axis point 589.13630612 67.77510316 0.00000000  
Rotation angle (degrees) 10.05908385  
Shift along axis -60.45761278  
  

> show #8 models

> fitmap #8 inMap #2

Fit molecule 6kgx-pdb-bundle6.pdb (#8) to map cryosparc_P14_J41_map.mrc (#2)
using 90769 atoms  
average map value = 0.1174, steps = 156  
shifted from previous position = 15.7  
rotated from previous position = 3 degrees  
atoms outside contour = 64917, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle6.pdb (#8) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98473122 0.17377278 0.01036530 -1.22861424  
-0.17372181 0.98477863 -0.00563706 108.20523438  
-0.01118709 0.00375031 0.99993039 58.45317613  
Axis 0.02695285 0.06188080 -0.99771956  
Axis point 636.44828132 54.98037793 0.00000000  
Rotation angle (degrees) 10.02887232  
Shift along axis -51.65716520  
  

> show #9 models

> fitmap #11 inMap #2

Fit molecule 6kgx-pdb-bundle9.pdb (#11) to map cryosparc_P14_J41_map.mrc (#2)
using 85200 atoms  
average map value = 0.1572, steps = 160  
shifted from previous position = 7.19  
rotated from previous position = 2.1 degrees  
atoms outside contour = 52114, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle9.pdb (#11) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98632513 0.16470273 -0.00597929 4.61711112  
-0.16468444 0.98634032 0.00343685 102.67745715  
0.00646367 -0.00240516 0.99997622 56.40715032  
Axis -0.01772056 -0.03774325 -0.99913034  
Axis point 607.26155745 28.87586516 0.00000000  
Rotation angle (degrees) 9.48776196  
Shift along axis -60.31529387  
  

> show #10 models

> fitmap #12 inMap #2

Fit molecule 6kgx-pdb-bundle10.pdb (#12) to map cryosparc_P14_J41_map.mrc (#2)
using 92037 atoms  
average map value = 0.1689, steps = 140  
shifted from previous position = 11.5  
rotated from previous position = 2.46 degrees  
atoms outside contour = 59280, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle10.pdb (#12) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98529117 0.17088339 0.00041946 1.42416716  
-0.17088012 0.98528269 -0.00424251 106.84324051  
-0.00113826 0.00410843 0.99999091 56.71682889  
Axis 0.02442730 0.00455648 -0.99969123  
Axis point 623.53749976 37.30655282 0.00000000  
Rotation angle (degrees) 9.84215939  
Shift along axis -56.17769806  
  

> show #11 models

> fitmap #13 inMap #2

Fit molecule 6kgx-pdb-bundle11.pdb (#13) to map cryosparc_P14_J41_map.mrc (#2)
using 92881 atoms  
average map value = 0.2155, steps = 196  
shifted from previous position = 14.6  
rotated from previous position = 2.84 degrees  
atoms outside contour = 52178, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle11.pdb (#13) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98378615 0.17934518 0.00034989 -0.87804214  
-0.17934532 0.98378610 0.00041203 108.33156747  
-0.00027032 -0.00046810 0.99999985 57.21941675  
Axis -0.00245374 0.00172910 -0.99999549  
Axis point 599.17846641 59.84531789 0.00000000  
Rotation angle (degrees) 10.33167169  
Shift along axis -57.02968863  
  

> show #!12 models

> fitmap #14 inMap #2

Fit molecule 6kgx-pdb-bundle12.pdb (#14) to map cryosparc_P14_J41_map.mrc (#2)
using 33108 atoms  
average map value = 0.02906, steps = 100  
shifted from previous position = 6.21  
rotated from previous position = 6.38 degrees  
atoms outside contour = 28882, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle12.pdb (#14) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.99554242 0.09279711 0.01685217 11.37798697  
-0.09074443 0.99113804 -0.09700945 119.67635637  
-0.02570502 0.09504779 0.99514078 26.95347377  
Axis 0.71385106 0.15817937 -0.68219935  
Axis point 0.00000000 -282.10509727 1245.29878467  
Rotation angle (degrees) 7.73097618  
Shift along axis 8.66487654  
  

> show #!13 models

> fitmap #13 inMap #2

Fit molecule 6kgx-pdb-bundle11.pdb (#13) to map cryosparc_P14_J41_map.mrc (#2)
using 92881 atoms  
average map value = 0.2155, steps = 44  
shifted from previous position = 0.0188  
rotated from previous position = 0.00516 degrees  
atoms outside contour = 52194, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle11.pdb (#13) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98378837 0.17933313 0.00026161 -0.86688873  
-0.17933323 0.98378831 0.00039969 108.32742079  
-0.00018569 -0.00044012 0.99999989 57.19899267  
Axis -0.00234146 0.00124710 -0.99999648  
Axis point 599.05354873 59.73313575 0.00000000  
Rotation angle (degrees) 10.33095868  
Shift along axis -57.06166656  
  

> show #14 models

> fitmap #14 inMap #2

Fit molecule 6kgx-pdb-bundle12.pdb (#14) to map cryosparc_P14_J41_map.mrc (#2)
using 33108 atoms  
average map value = 0.02906, steps = 80  
shifted from previous position = 0.0212  
rotated from previous position = 0.00911 degrees  
atoms outside contour = 28882, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle12.pdb (#14) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.99553317 0.09288190 0.01693076 11.32176997  
-0.09081853 0.99112053 -0.09711897 119.76771574  
-0.02580102 0.09514753 0.99512876 26.96131356  
Axis 0.71387151 0.15865997 -0.68206633  
Axis point 0.00000000 -281.96646356 1244.78096060  
Rotation angle (degrees) 7.73922805  
Shift along axis 8.69522752  
  

> fitmap #14 inMap #2

Fit molecule 6kgx-pdb-bundle12.pdb (#14) to map cryosparc_P14_J41_map.mrc (#2)
using 33108 atoms  
average map value = 0.02906, steps = 48  
shifted from previous position = 0.0255  
rotated from previous position = 0.00515 degrees  
atoms outside contour = 28881, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle12.pdb (#14) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.99553752 0.09285058 0.01684677 11.36278802  
-0.09079551 0.99112324 -0.09711284 119.73941791  
-0.02571420 0.09514986 0.99513079 26.92201788  
Axis 0.71403458 0.15806500 -0.68203378  
Axis point 0.00000000 -281.45833009 1244.59467326  
Rotation angle (degrees) 7.73729596  
Shift along axis 8.67830907  
  

> fitmap #14 inMap #2

Fit molecule 6kgx-pdb-bundle12.pdb (#14) to map cryosparc_P14_J41_map.mrc (#2)
using 33108 atoms  
average map value = 0.02906, steps = 48  
shifted from previous position = 0.00496  
rotated from previous position = 0.0132 degrees  
atoms outside contour = 28882, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle12.pdb (#14) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.99553199 0.09293636 0.01670023 11.40618008  
-0.09089085 0.99109923 -0.09726855 119.84425639  
-0.02559137 0.09531605 0.99511805 26.83862425  
Axis 0.71440492 0.15688339 -0.68191878  
Axis point 0.00000000 -279.74563858 1243.74642494  
Rotation angle (degrees) 7.74628766  
Shift along axis 8.64844254  
  

> fitmap #13 inMap #2

Fit molecule 6kgx-pdb-bundle11.pdb (#13) to map cryosparc_P14_J41_map.mrc (#2)
using 92881 atoms  
average map value = 0.2155, steps = 48  
shifted from previous position = 0.0063  
rotated from previous position = 0.00468 degrees  
atoms outside contour = 52186, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle11.pdb (#13) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98380104 0.17926363 0.00026851 -0.85741507  
-0.17926372 0.98380099 0.00035936 108.32116872  
-0.00019974 -0.00040167 0.99999990 57.19200411  
Axis -0.00212264 0.00130601 -0.99999689  
Axis point 599.28477492 59.61220782 0.00000000  
Rotation angle (degrees) 10.32690613  
Shift along axis -57.04853793  
  

> fitmap #12 inMap #2

Fit molecule 6kgx-pdb-bundle10.pdb (#12) to map cryosparc_P14_J41_map.mrc (#2)
using 92037 atoms  
average map value = 0.1689, steps = 84  
shifted from previous position = 0.00485  
rotated from previous position = 0.000885 degrees  
atoms outside contour = 59279, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle10.pdb (#12) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98529232 0.17087673 0.00042547 1.42398769  
-0.17087345 0.98528390 -0.00423000 106.83497629  
-0.00114202 0.00409508 0.99999096 56.72514417  
Axis 0.02435264 0.00458525 -0.99969292  
Axis point 623.52155847 37.32724501 0.00000000  
Rotation angle (degrees) 9.84175494  
Shift along axis -56.18318192  
  

> fitmap #11 inMap #2

Fit molecule 6kgx-pdb-bundle9.pdb (#11) to map cryosparc_P14_J41_map.mrc (#2)
using 85200 atoms  
average map value = 0.1572, steps = 48  
shifted from previous position = 0.0184  
rotated from previous position = 0.00734 degrees  
atoms outside contour = 52106, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle9.pdb (#11) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98632378 0.16471116 -0.00596934 4.60273859  
-0.16469206 0.98633859 0.00356429 102.64068135  
0.00647486 -0.00253244 0.99997583 56.43223541  
Axis -0.01849204 -0.03774463 -0.99911630  
Axis point 606.97406987 29.22820187 0.00000000  
Rotation angle (degrees) 9.48836311  
Shift along axis -60.34161488  
  

> fitmap #11 inMap #2

Fit molecule 6kgx-pdb-bundle9.pdb (#11) to map cryosparc_P14_J41_map.mrc (#2)
using 85200 atoms  
average map value = 0.1572, steps = 116  
shifted from previous position = 0.0188  
rotated from previous position = 0.00721 degrees  
atoms outside contour = 52124, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle9.pdb (#11) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98631473 0.16476857 -0.00587919 4.58438250  
-0.16475012 0.98632913 0.00349872 102.68411071  
0.00637530 -0.00248224 0.99997660 56.44931471  
Axis -0.01813509 -0.03715726 -0.99914486  
Axis point 607.24490410 29.24990518 0.00000000  
Rotation angle (degrees) 9.49144596  
Shift along axis -60.29964130  
  

> fitmap #10 inMap #2

Fit molecule 6kgx-pdb-bundle8.pdb (#10) to map cryosparc_P14_J41_map.mrc (#2)
using 91639 atoms  
average map value = 0.1524, steps = 116  
shifted from previous position = 8.01  
rotated from previous position = 3.37 degrees  
atoms outside contour = 61669, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle8.pdb (#10) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98349966 0.18053856 0.01158673 -6.02798063  
-0.18057452 0.98355900 0.00212814 108.86319606  
-0.01101202 -0.00418530 0.99993061 62.65192945  
Axis -0.01744648 0.06244913 -0.99789565  
Axis point 613.47120494 94.83169659 0.00000000  
Rotation angle (degrees) 10.42435947  
Shift along axis -55.61650861  
  

> fitmap #10 inMap #2

Fit molecule 6kgx-pdb-bundle8.pdb (#10) to map cryosparc_P14_J41_map.mrc (#2)
using 91639 atoms  
average map value = 0.1524, steps = 48  
shifted from previous position = 0.0198  
rotated from previous position = 0.00148 degrees  
atoms outside contour = 61680, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle8.pdb (#10) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98350426 0.18051361 0.01158501 -6.00199034  
-0.18054952 0.98356360 0.00212383 108.85462295  
-0.01101122 -0.00418046 0.99993064 62.65942003  
Axis -0.01742362 0.06245082 -0.99789594  
Axis point 613.52797889 94.68415167 0.00000000  
Rotation angle (degrees) 10.42289802  
Shift along axis -55.62494461  
  

> fitmap #9 inMap #2

Fit molecule 6kgx-pdb-bundle7.pdb (#9) to map cryosparc_P14_J41_map.mrc (#2)
using 84211 atoms  
average map value = 0.0671, steps = 184  
shifted from previous position = 8.64  
rotated from previous position = 1.66 degrees  
atoms outside contour = 62252, contour level = 0.093461  
  
Position of 6kgx-pdb-bundle7.pdb (#9) relative to cryosparc_P14_J41_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.98732362 0.15802111 -0.01487967 7.01902774  
-0.15793568 0.98742627 0.00675869 96.75987533  
0.01576060 -0.00432299 0.99986645 50.79538780  
Axis -0.03488838 -0.09646457 -0.99472478  
Axis point 574.75090048 14.95840131 0.00000000  
Rotation angle (degrees) 9.13818986  
Shift along axis -60.10621296  
  

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

Mismatch between Cocoa '\x0' and Carbon 'k' for virtual key 40 with
QFlags<Qt::KeyboardModifier>(NoModifier)  

Mismatch between Cocoa '\x0' and Carbon 'K' for virtual key 40 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)  

Mismatch between Cocoa '\x0' and Carbon 'k' for virtual key 40 with
QFlags<Qt::KeyboardModifier>(ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon 'k' for virtual key 40 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\u02da' for virtual key 40 with
QFlags<Qt::KeyboardModifier>(AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\uf8ff' for virtual key 40 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\u02da' for virtual key 40 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\uf8ff' for virtual key 40 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xb' for virtual key 40 with
QFlags<Qt::KeyboardModifier>(MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xb' for virtual key 40 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xb' for virtual key 40 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xb' for virtual key 40 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xb' for virtual key 40 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xb' for virtual key 40 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xb' for virtual key 40 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xb' for virtual key 40 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> save "/Users/yamadakouseki/Desktop/PBS cryo-EM/チノリモPDBとダルスを重ねたもの.cxs"
> includeMaps true

——— End of log from Thu Mar 9 16:33:29 2023 ———

opened ChimeraX session  




OpenGL version: 4.1 INTEL-20.2.50
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,1
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 499.40.2.0.0
      OS Loader Version: 564.40.4~66
      SMC Version (system): 2.43f11

Software:

    System Software Overview:

      System Version: macOS 13.2.1 (22D68)
      Kernel Version: Darwin 22.3.0
      Time since boot: 8時間 4分

Graphics/Displays:

    Intel Iris Plus Graphics 640:

      Chipset Model: Intel Iris Plus Graphics 640
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x5926
      Revision ID: 0x0006
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

Change History (2)

comment:1 by pett, 3 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Graphics hardware encountered an error and was reset

comment:2 by Tom Goddard, 3 years ago

Resolution: → nonchimerax
Status: assigned → closed
Summary: Graphics hardware encountered an error and was reset → Graphics crash, macOS 13.2.1, Intel Iris Plus Graphics 640

Apple Intel graphics crash.

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