Opened 7 months ago

Last modified 7 months ago

#17222 assigned defect

ISOLDE: ResidueStepper's 'positions' attribute is None

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

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        macOS-15.0.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/Manuscript/figures/figureA/supercomplexMapcoloredView1.cxs"

Opened cryosparc_P43_J450_008_volume_map_sharp.mrc as #2, grid size
500,500,500, pixel 1.21, shown at level 0.192, step 1, values float32  
Opened superComplexConsolidatedV1.cif map 3.5 as #4, grid size 226,226,275,
pixel 1.17, shown at level 0.106, step 1, values float32  
Opened volume difference as #5, grid size 500,500,500, pixel 1.21, shown at
level 0.185, step 1, values float32  
Opened cryosparc_P43_J450_008_volume_map_sharp.mrc as #1.1.1.1, grid size
500,500,500, pixel 1.21, shown at level 0.203, step 1, values float32  
Opened cryosparc_P43_J436_002_volume_map_sharp.mrc as #10, grid size
500,500,500, pixel 1.21, shown at level 0.131, step 1, values float32  
Opened cryosparc_P43_J450_008_volume_map_sharp.mrc as #11, grid size
500,500,500, pixel 1.21, shown at level 0.131, step 1, values float32  
Opened lipidLayer.mrc as #12, grid size 500,500,500, pixel 1.21, shown at
level 0.0696, step 1, values float32  
Restoring stepper: combination  
Log from Thu Mar 6 18:11:35 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J450_008_volume_map_sharp_NOSEQ/superComplexConsolidation/superComplexConsolidatedV8.cxs"

Opened cryosparc_P43_J450_008_volume_map_sharp.mrc as #2, grid size
500,500,500, pixel 1.21, shown at level 0.296, step 1, values float32  
Opened superComplexConsolidatedV1.cif map 3.5 as #4, grid size 226,226,275,
pixel 1.17, shown at level 0.106, step 1, values float32  
Opened volume difference as #5, grid size 500,500,500, pixel 1.21, shown at
level 0.185, step 1, values float32  
Opened cryosparc_P43_J450_008_volume_map_sharp.mrc as #1.1.1.1, grid size
500,500,500, pixel 1.21, shown at level 0.203, step 1, values float32  
Restoring stepper: combination  
Log from Thu Mar 6 15:08:05 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J450_008_volume_map_sharp_NOSEQ/superComplexConsolidation/superComplexConsolidatedV6.cxs"

Opened cryosparc_P43_J450_008_volume_map_sharp.mrc as #1.1.1.1, grid size
500,500,500, pixel 1.21, shown at level 0.335, step 1, values float32  
Opened cryosparc_P43_J450_008_volume_map_sharp.mrc as #2, grid size
500,500,500, pixel 1.21, shown at level 0.296, step 1, values float32  
Opened superComplexConsolidatedV1.cif map 3.5 as #4, grid size 226,226,275,
pixel 1.17, shown at level 0.106, step 1, values float32  
Opened volume difference as #5, grid size 500,500,500, pixel 1.21, shown at
level 0.185, step 1, values float32  
Restoring stepper: superComplexConsolidatedV1.cif  
Log from Thu Jan 16 15:16:15 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J450_008_volume_map_sharp_NOSEQ/superComplexConsolidation/superComplexConsolidatedV6.cxs"

Opened cryosparc_P43_J450_008_volume_map_sharp.mrc as #1.1.1.1, grid size
500,500,500, pixel 1.21, shown at level 0.255, step 1, values float32  
Opened cryosparc_P43_J450_008_volume_map_sharp.mrc as #2, grid size
500,500,500, pixel 1.21, shown at level 0.296, step 1, values float32  
Opened superComplexConsolidatedV1.cif map 3.5 as #4, grid size 226,226,275,
pixel 1.17, shown at level 0.106, step 1, values float32  
Opened volume difference as #5, grid size 500,500,500, pixel 1.21, shown at
level 0.255, step 1, values float32  
Restoring stepper: superComplexConsolidatedV1.cif  
Log from Wed Jan 15 18:19:59 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J450_008_volume_map_sharp_NOSEQ/superComplexConsolidation/superComplexConsolidatedV5.cxs"

Opened cryosparc_P43_J450_008_volume_map_sharp.mrc as #1.1.1.1, grid size
500,500,500, pixel 1.21, shown at level 0.255, step 1, values float32  
Opened cryosparc_P43_J450_008_volume_map_sharp.mrc as #2, grid size
500,500,500, pixel 1.21, shown at level 0.296, step 1, values float32  
Opened superComplexConsolidatedV1.cif map 3.5 as #4, grid size 226,226,275,
pixel 1.17, shown at level 0.106, step 1, values float32  
Opened volume difference as #5, grid size 500,500,500, pixel 1.21, shown at
level 0.255, step 1, values float32  
Restoring stepper: superComplexConsolidatedV1.cif  
Log from Wed Jan 15 18:04:27 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J450_008_volume_map_sharp_NOSEQ/superComplexConsolidation/superComplexConsolidatedV1.cxs"

Opened cryosparc_P43_J450_008_volume_map_sharp.mrc as #5, grid size
500,500,500, pixel 1.21, shown at level 0.118, step 2, values float32  
Log from Tue Jan 14 10:38:39 2025

> set selectionWidth 4

Done loading forcefield  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-IV2-II/cryosparc_P43_J454_map_sharp-
> EMHanced.mrc"

Opened cryosparc_P43_J454_map_sharp-EMHanced.mrc as #1, grid size 500,500,500,
pixel 1.21, shown at level 0.000679, step 2, values float32  

> volume #1 level 0.01917

> volume #1 step 1

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-IV2-II/cryosparc_P43_J453_map_sharp-
> EMHanced.mrc"

Opened cryosparc_P43_J453_map_sharp-EMHanced.mrc as #2, grid size 500,500,500,
pixel 1.21, shown at level 0.00075, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.01913

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J450_008_volume_map_sharp.mrc"

Opened cryosparc_P43_J450_008_volume_map_sharp.mrc as #3, grid size
500,500,500, pixel 1.21, shown at level 0.118, step 2, values float32  

> volume #3 step 1

> volume #3 level 0.1415

> volume #3 level 0.1934

> show #!1 models

> volume #1 level -0.00379

> volume #1 level 0.023

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J436_002_volume_map_sharp_NOSEQ/ligandsDetection/manualRefinementStep8WithLigs.cif"

Summary of feedback from opening
/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
Computer/supercomplex/supercomplexV-
IV2-II/cryosparc_P43_J436_002_volume_map_sharp_NOSEQ/ligandsDetection/manualRefinementStep8WithLigs.cif  
---  
warnings | Unknown polymer entity '1' on line 281  
Unknown polymer entity '2' on line 3139  
Unknown polymer entity '3' on line 4765  
Unknown polymer entity '4' on line 6243  
Unknown polymer entity '5' on line 10007  
37 messages similar to the above omitted  
Atom HN3 is not in the residue template for 3PE /LG:1000  
Atom HN3 is not in the residue template for 3PE /LO:1000  
Atom HN3 is not in the residue template for 3PE /Np:1001  
Atom HN3 is not in the residue template for 3PE /t7:1001  
Atom HN3 is not in the residue template for 3PE /tb:1001  
Atom OMA is not in the residue template for HEM /HM:1  
Atom HO11 is not in the residue template for HEA /HN:3  
Atom HO11 is not in the residue template for HEA /HN:4  
Atom C13 is not in the residue template for HE9 /HM:1  
Atom HO11 is not in the residue template for HEA /HM:2  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for manualRefinementStep8WithLigs.cif #4  
---  
Chain | Description  
AG t3 | No description available  
Ar t4 | No description available  
CS | No description available  
I0 tb | No description available  
I2 | No description available  
Ii | No description available  
Il td | No description available  
Ix t9 | No description available  
Iy tc | No description available  
J4 | No description available  
J6 t1 | No description available  
JI | No description available  
JJ t6 | No description available  
JN tf | No description available  
Jw t8 | No description available  
Jx | No description available  
K5 | No description available  
KI t5 | No description available  
Ke | No description available  
Kp | No description available  
Ks te | No description available  
L3 | No description available  
LG | No description available  
LO t2 | No description available  
LR | No description available  
LY tg | No description available  
Lb | No description available  
Lr | No description available  
M | No description available  
MC | No description available  
Mg | No description available  
Mh | No description available  
Ml | No description available  
Mq | No description available  
Mr t0 | No description available  
Mw | No description available  
Mx | No description available  
NF | No description available  
NM | No description available  
Np t7 | No description available  
TB | No description available  
Y ta | No description available  
  

> select add #4

166871 atoms, 169315 bonds, 40 pseudobonds, 10067 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> hide #!1 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #!1 models

> hide #!1 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/CV-Full/cryosparc_P31_J281_004_volume_map_sharp--VC-
> Conf1/complexVconsolidation/complexVconsolidatedV29.cif"

Summary of feedback from opening
/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
Computer/supercomplex/CV-Full/cryosparc_P31_J281_004_volume_map_sharp--VC-
Conf1/complexVconsolidation/complexVconsolidatedV29.cif  
---  
warnings | Unknown polymer entity '1' on line 202  
Unknown polymer entity '2' on line 1252  
Unknown polymer entity '3' on line 6584  
Unknown polymer entity '4' on line 13903  
Unknown polymer entity '5' on line 22164  
33 messages similar to the above omitted  
Atom HA2 is not in the residue template for GLU /A:176  
Atom H5' is not in the residue template for ATP /AU:2000  
Atom H is not in the residue template for ALA /B:23  
Atom H is not in the residue template for SER /C:85  
Atom H is not in the residue template for ILE /C0:33  
Atom H is not in the residue template for ILE /C1:33  
Atom H is not in the residue template for ILE /C2:33  
2 messages similar to the above omitted  
Too many hydrogens missing from residue template(s) to warn about  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for complexVconsolidatedV29.cif #5  
---  
Chain | Description  
A | No description available  
A0 | No description available  
AU | No description available  
Ab | No description available  
Aj | No description available  
Aq | No description available  
B | No description available  
BI | No description available  
BK | No description available  
BP | No description available  
C | No description available  
C0 C1 C2 C3 C5 C6 C7 C8 C9 | No description available  
C4 | No description available  
D | No description available  
D6 | No description available  
E | No description available  
E1 | No description available  
E4 | No description available  
Eg | No description available  
Ek | No description available  
Eq | No description available  
Es | No description available  
Ev | No description available  
F9 | No description available  
FF | No description available  
FH | No description available  
FL | No description available  
FO | No description available  
Fy | No description available  
Fz | No description available  
GT | No description available  
IE | No description available  
IY | No description available  
JC | No description available  
P | No description available  
R | No description available  
S | No description available  
a | No description available  
  

> select add #5

292434 atoms, 297470 bonds, 52 pseudobonds, 17932 residues, 5 models selected  

> select subtract #4

125563 atoms, 128155 bonds, 12 pseudobonds, 7865 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> hide #!3 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> align #5/E4:137-156@CA #4/MC:137-156@CA

Missing required "to_atoms" argument  

> align #5/E4:137-156@CA toAtoms #4/MC:137-156@CA

RMSD between 20 atom pairs is 2.087 angstroms  

> color #5@C blue

> color #5@C mediumorchid

> select clear

> color #4@C mediumturquoise

> align #5/Ev:138-148@CA toAtoms #4/Lr:138-148@CA

RMSD between 11 atom pairs is 0.742 angstroms  

> show #!3 models

> hide #!3 models

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J450_008_volume_map_sharp_NOSEQ/cryosparc_P43_J450_008_volume_map_sharp_NOSEQ.cif"

Summary of feedback from opening
/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
Computer/supercomplex/supercomplexV-
IV2-II/cryosparc_P43_J450_008_volume_map_sharp_NOSEQ/cryosparc_P43_J450_008_volume_map_sharp_NOSEQ.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for cryosparc_P43_J450_008_volume_map_sharp_NOSEQ.cif #6  
---  
Chain | Description  
1 CY | No description available  
3 | No description available  
6 | No description available  
8 | No description available  
9 Au | No description available  
A | No description available  
A3 DB | No description available  
A4 | No description available  
A6 | No description available  
A8 | No description available  
A9 | No description available  
AA | No description available  
AB | No description available  
AD | No description available  
AE | No description available  
AF | No description available  
AG AJ EH | No description available  
AH | No description available  
AK | No description available  
AL | No description available  
AN Fo | No description available  
AO | No description available  
AP | No description available  
AQ | No description available  
AR BH DP EC | No description available  
AS CS | No description available  
AV | No description available  
AZ Bz CJ CP CZ Cr t | No description available  
Aa | No description available  
Ab | No description available  
Ad | No description available  
Ae | No description available  
Am M | No description available  
An | No description available  
Ao | No description available  
Aq | No description available  
Ar | No description available  
As BB Bn | No description available  
Ax | No description available  
Ay BK | No description available  
Az | No description available  
B1 | No description available  
B2 | No description available  
B3 | No description available  
B5 | No description available  
B9 | No description available  
BC EV | No description available  
BJ | No description available  
BL | No description available  
BO | No description available  
BP | No description available  
BQ | No description available  
BW | No description available  
BY C u | No description available  
Bb o | No description available  
Bd | No description available  
Bf | No description available  
Bg Ce | No description available  
Bp | No description available  
Bq | No description available  
Bt | No description available  
Bv | No description available  
Bw | No description available  
By w | No description available  
C2 | No description available  
C3 | No description available  
C4 | No description available  
C7 | No description available  
CA | No description available  
CE Ca | No description available  
CG | No description available  
CQ p | No description available  
CR | No description available  
Cg EY | No description available  
Cv | No description available  
Cz | No description available  
D | No description available  
D3 | No description available  
DI | No description available  
DZ | No description available  
Di | No description available  
Dr | No description available  
E | No description available  
E0 | No description available  
E1 | No description available  
E2 | No description available  
E3 | No description available  
E4 | No description available  
E5 | No description available  
E6 | No description available  
E7 | No description available  
E8 | No description available  
E9 | No description available  
EJ | No description available  
EK | No description available  
Ec | No description available  
Ef | No description available  
Eg | No description available  
Eh | No description available  
Ei | No description available  
Ej | No description available  
Ek | No description available  
El | No description available  
Em | No description available  
En | No description available  
Eo | No description available  
Ep | No description available  
Eq | No description available  
Er | No description available  
Es | No description available  
Et | No description available  
Eu | No description available  
Ev | No description available  
Ew | No description available  
Ex | No description available  
Ey | No description available  
Ez | No description available  
F0 | No description available  
F1 | No description available  
F2 Fq | No description available  
F3 | No description available  
F4 | No description available  
F5 | No description available  
F6 | No description available  
F7 | No description available  
F8 | No description available  
F9 | No description available  
FA | No description available  
FB | No description available  
FC | No description available  
FD | No description available  
FE | No description available  
FF | No description available  
FG | No description available  
FH | No description available  
FI | No description available  
FJ | No description available  
FK | No description available  
FL | No description available  
FM | No description available  
FN | No description available  
FO | No description available  
FP | No description available  
FQ | No description available  
FR | No description available  
FS | No description available  
FT | No description available  
FU | No description available  
FV | No description available  
FW | No description available  
FX | No description available  
FY | No description available  
FZ | No description available  
Fa | No description available  
Fb | No description available  
Fc | No description available  
Fd | No description available  
Fe | No description available  
Ff GH | No description available  
Fg | No description available  
Fh | No description available  
Fi | No description available  
Fj | No description available  
Fk | No description available  
Fl | No description available  
Fm | No description available  
Fn | No description available  
Fp | No description available  
Fr | No description available  
Fs | No description available  
Ft | No description available  
Fu | No description available  
Fv | No description available  
Fw | No description available  
Fx | No description available  
Fy | No description available  
Fz | No description available  
G X | No description available  
GA | No description available  
GB | No description available  
GC | No description available  
GD | No description available  
GE | No description available  
GF | No description available  
GG | No description available  
GI | No description available  
GJ | No description available  
GK | No description available  
GL | No description available  
GM | No description available  
GN | No description available  
GO | No description available  
GP | No description available  
GQ | No description available  
GR | No description available  
GS | No description available  
GT | No description available  
J | No description available  
L | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
Y | No description available  
Z | No description available  
a | No description available  
c | No description available  
d | No description available  
e | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
l | No description available  
m | No description available  
n | No description available  
q | No description available  
r | No description available  
v | No description available  
x | No description available  
y | No description available  
  

> select add #6

26819 atoms, 27073 bonds, 3296 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

Computing secondary structure  

> color #6@C greenyellow

> select clear

> show #!3 models

> volume #3 level 0.1367

> hide #!5 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #6 models

> show #6 models

> show #!5 models

> hide #6 models

> show #6 models

> hide #!4 models

> show #!4 models

> hide #!5 models

> show #!5 models

> hide #6 models

> combine #4,5

> hide #!5 models

> hide #!4 models

> select #7MC

Expected an objects specifier or a keyword  

> select #7/MC

1871 atoms, 1890 bonds, 1 pseudobond, 110 residues, 2 models selected  

> delete #3/MC

> close #1

> close #3

> close #2

> rename #7 id #3

> delete #3/MC

> delete #3/I2

> select #3/Lr

5619 atoms, 5702 bonds, 2 pseudobonds, 344 residues, 2 models selected  

> delete #3/Lr

> delete #3/Mw

Undo failed, probably because structures have been modified.  

> select #3/Mh

1043 atoms, 1067 bonds, 59 residues, 1 model selected  

> delete #3/Mh

> select #3/Mx

727 atoms, 736 bonds, 42 residues, 1 model selected  

> delete #3/Mx

> select #3/Ii

1448 atoms, 1472 bonds, 2 pseudobonds, 87 residues, 2 models selected  

> delete #3/Ii

> select #3/Lb

1851 atoms, 1883 bonds, 115 residues, 1 model selected  

> delete #3/Lb

> select #3/Mi

Nothing selected  

> select #3/Ml

1230 atoms, 1245 bonds, 71 residues, 1 model selected  

> delete #3/Ml

> select #3/J4

1544 atoms, 1569 bonds, 1 pseudobond, 95 residues, 2 models selected  

> delete #3/J4

> select #3/CS

1478 atoms, 1496 bonds, 1 pseudobond, 89 residues, 2 models selected  

> delete #3/CS

> select #3/P

162 atoms, 162 bonds, 10 residues, 1 model selected  

> select #3/Eg

327 atoms, 334 bonds, 21 residues, 1 model selected  

> show #!4 models

> hide #!4 models

> delete #3/P

> delete #3/Eg

> delete #3/S

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J450_008_volume_map_sharp.mrc"

Opened cryosparc_P43_J450_008_volume_map_sharp.mrc as #1, grid size
500,500,500, pixel 1.21, shown at level 0.118, step 2, values float32  

> close #1

> rename #4 id #1

> rename #5 id #2

> rename #6 id #4

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J450_008_volume_map_sharp.mrc"

Opened cryosparc_P43_J450_008_volume_map_sharp.mrc as #5, grid size
500,500,500, pixel 1.21, shown at level 0.118, step 2, values float32  

> save /Users/rafaelrocha/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J450_008_volume_map_sharp_NOSEQ/superComplexConsolidation/superComplexConsolidatedV1.cxs

——— End of log from Tue Jan 14 10:38:39 2025 ———

opened ChimeraX session  

> close #4

> close #5

> close #2

> close #1

> delete #3@H*

> rename #3 id #1

> cd "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J450_008_volume_map_sharp_NOSEQ/superComplexConsolidation"

Current working directory is:
/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
Computer/supercomplex/supercomplexV-
IV2-II/cryosparc_P43_J450_008_volume_map_sharp_NOSEQ/superComplexConsolidation  

> runscript /Users/rafaelrocha/Library/CloudStorage/OneDrive-
> Personal/GitHub/KRSPs/modelangeloScripts/correctStructureSequences.py False

> info #1 saveFile chainsInfoTMP.txt

> select #1/AG

1430 atoms, 1462 bonds, 179 residues, 1 model selected  

> save chainsTMP/AG_uu.pdb format pdb models #1/AG selectedOnly true

> open chainsTMP/AG_uu_Mod.pdb

Chain information for AG_uu_Mod.pdb #2  
---  
Chain | Description  
AG | No description available  
  

> select #1/Ar

831 atoms, 860 bonds, 96 residues, 1 model selected  

> save chainsTMP/Ar_ul.pdb format pdb models #1/Ar selectedOnly true

> open chainsTMP/Ar_ul_Mod.pdb

Chain information for Ar_ul_Mod.pdb #3  
---  
Chain | Description  
Ar | No description available  
  

> select #1/I0

1884 atoms, 1936 bonds, 225 residues, 1 model selected  

> save chainsTMP/I0_un.pdb format pdb models #1/I0 selectedOnly true

> open chainsTMP/I0_un_Mod.pdb

Chain information for I0_un_Mod.pdb #4  
---  
Chain | Description  
I0 | No description available  
  

> select #1/Il

664 atoms, 688 bonds, 79 residues, 1 model selected  

> save chainsTMP/Il_ul.pdb format pdb models #1/Il selectedOnly true

> open chainsTMP/Il_ul_Mod.pdb

Chain information for Il_ul_Mod.pdb #5  
---  
Chain | Description  
Il | No description available  
  

> select #1/Ix

1101 atoms, 1145 bonds, 128 residues, 1 model selected  

> save chainsTMP/Ix_ul.pdb format pdb models #1/Ix selectedOnly true

> open chainsTMP/Ix_ul_Mod.pdb

Chain information for Ix_ul_Mod.pdb #6  
---  
Chain | Description  
Ix | No description available  
  

> select #1/Iy

751 atoms, 763 bonds, 94 residues, 1 model selected  

> save chainsTMP/Iy_ul.pdb format pdb models #1/Iy selectedOnly true

> open chainsTMP/Iy_ul_Mod.pdb

Chain information for Iy_ul_Mod.pdb #7  
---  
Chain | Description  
Iy | No description available  
  

> select #1/J6

1621 atoms, 1663 bonds, 198 residues, 1 model selected  

> save chainsTMP/J6_un.pdb format pdb models #1/J6 selectedOnly true

> open chainsTMP/J6_un_Mod.pdb

Chain information for J6_un_Mod.pdb #8  
---  
Chain | Description  
J6 | No description available  
  

> select #1/JI

3646 atoms, 3705 bonds, 1 pseudobond, 475 residues, 2 models selected  

> save chainsTMP/JI_uu.pdb format pdb models #1/JI selectedOnly true

> open chainsTMP/JI_uu_Mod.pdb

Chain information for JI_uu_Mod.pdb #9  
---  
Chain | Description  
JI | No description available  
  

> select #1/JJ

4683 atoms, 4842 bonds, 552 residues, 1 model selected  

> save chainsTMP/JJ_uu.pdb format pdb models #1/JJ selectedOnly true

> open chainsTMP/JJ_uu_Mod.pdb

Chain information for JJ_uu_Mod.pdb #10  
---  
Chain | Description  
JJ | No description available  
  

> select #1/JN

870 atoms, 900 bonds, 107 residues, 1 model selected  

> save chainsTMP/JN_uu.pdb format pdb models #1/JN selectedOnly true

> open chainsTMP/JN_uu_Mod.pdb

Chain information for JN_uu_Mod.pdb #11  
---  
Chain | Description  
JN | No description available  
  

> select #1/Jw

1146 atoms, 1193 bonds, 125 residues, 1 model selected  

> save chainsTMP/Jw_ul.pdb format pdb models #1/Jw selectedOnly true

> open chainsTMP/Jw_ul_Mod.pdb

Chain information for Jw_ul_Mod.pdb #12  
---  
Chain | Description  
Jw | No description available  
  

> select #1/Jx

948 atoms, 976 bonds, 114 residues, 1 model selected  

> save chainsTMP/Jx_ul.pdb format pdb models #1/Jx selectedOnly true

> open chainsTMP/Jx_ul_Mod.pdb

Chain information for Jx_ul_Mod.pdb #13  
---  
Chain | Description  
Jx | No description available  
  

> select #1/K5

3795 atoms, 3864 bonds, 6 pseudobonds, 498 residues, 2 models selected  

> save chainsTMP/K5_un.pdb format pdb models #1/K5 selectedOnly true

> open chainsTMP/K5_un_Mod.pdb

Chain information for K5_un_Mod.pdb #14  
---  
Chain | Description  
K5 | No description available  
  

> select #1/KI

1666 atoms, 1730 bonds, 201 residues, 1 model selected  

> save chainsTMP/KI_uu.pdb format pdb models #1/KI selectedOnly true

> open chainsTMP/KI_uu_Mod.pdb

Chain information for KI_uu_Mod.pdb #15  
---  
Chain | Description  
KI | No description available  
  

> select #1/Ke

741 atoms, 764 bonds, 95 residues, 1 model selected  

> save chainsTMP/Ke_ul.pdb format pdb models #1/Ke selectedOnly true

> open chainsTMP/Ke_ul_Mod.pdb

Chain information for Ke_ul_Mod.pdb #16  
---  
Chain | Description  
Ke | No description available  
  

> select #1/Kp

1379 atoms, 1414 bonds, 172 residues, 1 model selected  

> save chainsTMP/Kp_ul.pdb format pdb models #1/Kp selectedOnly true

> open chainsTMP/Kp_ul_Mod.pdb

Chain information for Kp_ul_Mod.pdb #17  
---  
Chain | Description  
Kp | No description available  
  

> select #1/Ks

1327 atoms, 1375 bonds, 153 residues, 1 model selected  

> save chainsTMP/Ks_ul.pdb format pdb models #1/Ks selectedOnly true

> open chainsTMP/Ks_ul_Mod.pdb

Chain information for Ks_ul_Mod.pdb #18  
---  
Chain | Description  
Ks | No description available  
  

> select #1/L3

1230 atoms, 1253 bonds, 3 pseudobonds, 157 residues, 2 models selected  

> save chainsTMP/L3_un.pdb format pdb models #1/L3 selectedOnly true

> open chainsTMP/L3_un_Mod.pdb

Chain information for L3_un_Mod.pdb #19  
---  
Chain | Description  
L3 | No description available  
  

> select #1/LG

932 atoms, 954 bonds, 105 residues, 1 model selected  

> save chainsTMP/LG_uu.pdb format pdb models #1/LG selectedOnly true

> open chainsTMP/LG_uu_Mod.pdb

Chain information for LG_uu_Mod.pdb #20  
---  
Chain | Description  
LG | No description available  
  

> select #1/LO

2582 atoms, 2626 bonds, 308 residues, 1 model selected  

> save chainsTMP/LO_uu.pdb format pdb models #1/LO selectedOnly true

> open chainsTMP/LO_uu_Mod.pdb

Chain information for LO_uu_Mod.pdb #21  
---  
Chain | Description  
LO | No description available  
  

> select #1/LR

554 atoms, 561 bonds, 71 residues, 1 model selected  

> save chainsTMP/LR_uu.pdb format pdb models #1/LR selectedOnly true

> open chainsTMP/LR_uu_Mod.pdb

Chain information for LR_uu_Mod.pdb #22  
---  
Chain | Description  
LR | No description available  
  

> select #1/LY

1390 atoms, 1441 bonds, 165 residues, 1 model selected  

> save chainsTMP/LY_uu.pdb format pdb models #1/LY selectedOnly true

> open chainsTMP/LY_uu_Mod.pdb

Chain information for LY_uu_Mod.pdb #23  
---  
Chain | Description  
LY | No description available  
  

> select #1/M

819 atoms, 841 bonds, 102 residues, 1 model selected  

> save chainsTMP/M_u.pdb format pdb models #1/M selectedOnly true

> open chainsTMP/M_u_Mod.pdb

Chain information for M_u_Mod.pdb #24  
---  
Chain | Description  
M | No description available  
  

> select #1/Mg

1821 atoms, 1875 bonds, 215 residues, 1 model selected  

> save chainsTMP/Mg_ul.pdb format pdb models #1/Mg selectedOnly true

> open chainsTMP/Mg_ul_Mod.pdb

Chain information for Mg_ul_Mod.pdb #25  
---  
Chain | Description  
Mg | No description available  
  

> select #1/Mq

474 atoms, 492 bonds, 57 residues, 1 model selected  

> save chainsTMP/Mq_ul.pdb format pdb models #1/Mq selectedOnly true

> open chainsTMP/Mq_ul_Mod.pdb

Chain information for Mq_ul_Mod.pdb #26  
---  
Chain | Description  
Mq | No description available  
  

> select #1/Mr

852 atoms, 882 bonds, 110 residues, 1 model selected  

> save chainsTMP/Mr_ul.pdb format pdb models #1/Mr selectedOnly true

> open chainsTMP/Mr_ul_Mod.pdb

Chain information for Mr_ul_Mod.pdb #27  
---  
Chain | Description  
Mr | No description available  
  

> select #1/NF

1651 atoms, 1677 bonds, 1 pseudobond, 212 residues, 2 models selected  

> save chainsTMP/NF_uu.pdb format pdb models #1/NF selectedOnly true

> open chainsTMP/NF_uu_Mod.pdb

Chain information for NF_uu_Mod.pdb #28  
---  
Chain | Description  
NF | No description available  
  

> select #1/NM

504 atoms, 518 bonds, 63 residues, 1 model selected  

> save chainsTMP/NM_uu.pdb format pdb models #1/NM selectedOnly true

> open chainsTMP/NM_uu_Mod.pdb

Chain information for NM_uu_Mod.pdb #29  
---  
Chain | Description  
NM | No description available  
  

> select #1/Np

2489 atoms, 2578 bonds, 285 residues, 1 model selected  

> save chainsTMP/Np_ul.pdb format pdb models #1/Np selectedOnly true

> open chainsTMP/Np_ul_Mod.pdb

Chain information for Np_ul_Mod.pdb #30  
---  
Chain | Description  
Np | No description available  
  

> select #1/TB

479 atoms, 485 bonds, 64 residues, 1 model selected  

> save chainsTMP/TB_uu.pdb format pdb models #1/TB selectedOnly true

> open chainsTMP/TB_uu_Mod.pdb

Chain information for TB_uu_Mod.pdb #31  
---  
Chain | Description  
TB | No description available  
  

> select #1/Y

1742 atoms, 1789 bonds, 211 residues, 1 model selected  

> save chainsTMP/Y_u.pdb format pdb models #1/Y selectedOnly true

> open chainsTMP/Y_u_Mod.pdb

Chain information for Y_u_Mod.pdb #32  
---  
Chain | Description  
Y | No description available  
  

> select #1/t0

853 atoms, 883 bonds, 110 residues, 1 model selected  

> save chainsTMP/t0_ln.pdb format pdb models #1/t0 selectedOnly true

> open chainsTMP/t0_ln_Mod.pdb

Chain information for t0_ln_Mod.pdb #33  
---  
Chain | Description  
t0 | No description available  
  

> select #1/t1

1621 atoms, 1663 bonds, 198 residues, 1 model selected  

> save chainsTMP/t1_ln.pdb format pdb models #1/t1 selectedOnly true

> open chainsTMP/t1_ln_Mod.pdb

Chain information for t1_ln_Mod.pdb #34  
---  
Chain | Description  
t1 | No description available  
  

> select #1/t2

2478 atoms, 2524 bonds, 306 residues, 1 model selected  

> save chainsTMP/t2_ln.pdb format pdb models #1/t2 selectedOnly true

> open chainsTMP/t2_ln_Mod.pdb

Chain information for t2_ln_Mod.pdb #35  
---  
Chain | Description  
t2 | No description available  
  

> select #1/t3

1430 atoms, 1462 bonds, 179 residues, 1 model selected  

> save chainsTMP/t3_ln.pdb format pdb models #1/t3 selectedOnly true

> open chainsTMP/t3_ln_Mod.pdb

Chain information for t3_ln_Mod.pdb #36  
---  
Chain | Description  
t3 | No description available  
  

> select #1/t4

831 atoms, 860 bonds, 96 residues, 1 model selected  

> save chainsTMP/t4_ln.pdb format pdb models #1/t4 selectedOnly true

> open chainsTMP/t4_ln_Mod.pdb

Chain information for t4_ln_Mod.pdb #37  
---  
Chain | Description  
t4 | No description available  
  

> select #1/t5

1666 atoms, 1730 bonds, 201 residues, 1 model selected  

> save chainsTMP/t5_ln.pdb format pdb models #1/t5 selectedOnly true

> open chainsTMP/t5_ln_Mod.pdb

Chain information for t5_ln_Mod.pdb #38  
---  
Chain | Description  
t5 | No description available  
  

> select #1/t6

4626 atoms, 4785 bonds, 552 residues, 1 model selected  

> save chainsTMP/t6_ln.pdb format pdb models #1/t6 selectedOnly true

> open chainsTMP/t6_ln_Mod.pdb

Chain information for t6_ln_Mod.pdb #39  
---  
Chain | Description  
t6 | No description available  
  

> select #1/t7

2489 atoms, 2579 bonds, 285 residues, 1 model selected  

> save chainsTMP/t7_ln.pdb format pdb models #1/t7 selectedOnly true

> open chainsTMP/t7_ln_Mod.pdb

Chain information for t7_ln_Mod.pdb #40  
---  
Chain | Description  
t7 | No description available  
  

> select #1/t8

1146 atoms, 1193 bonds, 125 residues, 1 model selected  

> save chainsTMP/t8_ln.pdb format pdb models #1/t8 selectedOnly true

> open chainsTMP/t8_ln_Mod.pdb

Chain information for t8_ln_Mod.pdb #41  
---  
Chain | Description  
t8 | No description available  
  

> select #1/t9

1102 atoms, 1146 bonds, 128 residues, 1 model selected  

> save chainsTMP/t9_ln.pdb format pdb models #1/t9 selectedOnly true

> open chainsTMP/t9_ln_Mod.pdb

Chain information for t9_ln_Mod.pdb #42  
---  
Chain | Description  
t9 | No description available  
  

> select #1/ta

1688 atoms, 1736 bonds, 210 residues, 1 model selected  

> save chainsTMP/ta_ll.pdb format pdb models #1/ta selectedOnly true

> open chainsTMP/ta_ll_Mod.pdb

Chain information for ta_ll_Mod.pdb #43  
---  
Chain | Description  
ta | No description available  
  

> select #1/tb

2045 atoms, 2095 bonds, 227 residues, 1 model selected  

> save chainsTMP/tb_ll.pdb format pdb models #1/tb selectedOnly true

> open chainsTMP/tb_ll_Mod.pdb

Chain information for tb_ll_Mod.pdb #44  
---  
Chain | Description  
tb | No description available  
  

> select #1/tc

751 atoms, 763 bonds, 94 residues, 1 model selected  

> save chainsTMP/tc_ll.pdb format pdb models #1/tc selectedOnly true

> open chainsTMP/tc_ll_Mod.pdb

Chain information for tc_ll_Mod.pdb #45  
---  
Chain | Description  
tc | No description available  
  

> select #1/td

664 atoms, 688 bonds, 79 residues, 1 model selected  

> save chainsTMP/td_ll.pdb format pdb models #1/td selectedOnly true

> open chainsTMP/td_ll_Mod.pdb

Chain information for td_ll_Mod.pdb #46  
---  
Chain | Description  
td | No description available  
  

> select #1/te

1327 atoms, 1375 bonds, 153 residues, 1 model selected  

> save chainsTMP/te_ll.pdb format pdb models #1/te selectedOnly true

> open chainsTMP/te_ll_Mod.pdb

Chain information for te_ll_Mod.pdb #47  
---  
Chain | Description  
te | No description available  
  

> select #1/tf

870 atoms, 900 bonds, 107 residues, 1 model selected  

> save chainsTMP/tf_ll.pdb format pdb models #1/tf selectedOnly true

> open chainsTMP/tf_ll_Mod.pdb

Chain information for tf_ll_Mod.pdb #48  
---  
Chain | Description  
tf | No description available  
  

> select #1/tg

1347 atoms, 1399 bonds, 164 residues, 1 model selected  

> save chainsTMP/tg_ll.pdb format pdb models #1/tg selectedOnly true

> open chainsTMP/tg_ll_Mod.pdb

Chain information for tg_ll_Mod.pdb #49  
---  
Chain | Description  
tg | No description available  
  

> select #1/FD

53 atoms, 58 bonds, 1 residue, 1 model selected  

> save chainsTMP/FD_uu.pdb format pdb models #1/FD selectedOnly true

> open chainsTMP/FD_uu_Mod.pdb

> select #1/HM

120 atoms, 125 bonds, 8 pseudobonds, 3 residues, 2 models selected  

> save chainsTMP/HM_uu.pdb format pdb models #1/HM selectedOnly true

> open chainsTMP/HM_uu_Mod.pdb

> select #1/HN

120 atoms, 126 bonds, 8 pseudobonds, 2 residues, 2 models selected  

> save chainsTMP/HN_uu.pdb format pdb models #1/HN selectedOnly true

> open chainsTMP/HN_uu_Mod.pdb

> select #1/FS

19 atoms, 25 bonds, 3 residues, 1 model selected  

> save chainsTMP/FS_uu.pdb format pdb models #1/FS selectedOnly true

> open chainsTMP/FS_uu_Mod.pdb

> select #1/HO

43 atoms, 46 bonds, 4 pseudobonds, 1 residue, 2 models selected  

> save chainsTMP/HO_uu.pdb format pdb models #1/HO selectedOnly true

> open chainsTMP/HO_uu_Mod.pdb

> select #1/R

540 atoms, 564 bonds, 62 residues, 1 model selected  

> save chainsTMP/R_u.pdb format pdb models #1/R selectedOnly true

> open chainsTMP/R_u_Mod.pdb

Chain information for R_u_Mod.pdb #55  
---  
Chain | Description  
R | No description available  
  

> select #1/A

2659 atoms, 2704 bonds, 324 residues, 1 model selected  

> save chainsTMP/A_u.pdb format pdb models #1/A selectedOnly true

> open chainsTMP/A_u_Mod.pdb

Chain information for A_u_Mod.pdb #56  
---  
Chain | Description  
A | No description available  
  

> select #1/A0

3641 atoms, 3696 bonds, 482 residues, 1 model selected  

> save chainsTMP/A0_un.pdb format pdb models #1/A0 selectedOnly true

> open chainsTMP/A0_un_Mod.pdb

Chain information for A0_un_Mod.pdb #57  
---  
Chain | Description  
A0 | No description available  
  

> select #1/AU

4069 atoms, 4141 bonds, 2 pseudobonds, 525 residues, 2 models selected  

> save chainsTMP/AU_uu.pdb format pdb models #1/AU selectedOnly true

> open chainsTMP/AU_uu_Mod.pdb

Chain information for AU_uu_Mod.pdb #58  
---  
Chain | Description  
AU | No description available  
  

> select #1/Ab

3641 atoms, 3693 bonds, 1 pseudobond, 480 residues, 2 models selected  

> save chainsTMP/Ab_ul.pdb format pdb models #1/Ab selectedOnly true

> open chainsTMP/Ab_ul_Mod.pdb

Chain information for Ab_ul_Mod.pdb #59  
---  
Chain | Description  
Ab | No description available  
  

> select #1/Aj

3647 atoms, 3701 bonds, 483 residues, 1 model selected  

> save chainsTMP/Aj_ul.pdb format pdb models #1/Aj selectedOnly true

> open chainsTMP/Aj_ul_Mod.pdb

Chain information for Aj_ul_Mod.pdb #60  
---  
Chain | Description  
Aj | No description available  
  

> select #1/Aq

1320 atoms, 1347 bonds, 163 residues, 1 model selected  

> save chainsTMP/Aq_ul.pdb format pdb models #1/Aq selectedOnly true

> open chainsTMP/Aq_ul_Mod.pdb

Chain information for Aq_ul_Mod.pdb #61  
---  
Chain | Description  
Aq | No description available  
  

> select #1/B

1080 atoms, 1097 bonds, 138 residues, 1 model selected  

> save chainsTMP/B_u.pdb format pdb models #1/B selectedOnly true

> open chainsTMP/B_u_Mod.pdb

Chain information for B_u_Mod.pdb #62  
---  
Chain | Description  
B | No description available  
  

> select #1/BI

1334 atoms, 1361 bonds, 165 residues, 1 model selected  

> save chainsTMP/BI_uu.pdb format pdb models #1/BI selectedOnly true

> open chainsTMP/BI_uu_Mod.pdb

Chain information for BI_uu_Mod.pdb #63  
---  
Chain | Description  
BI | No description available  
  

> select #1/BK

4007 atoms, 4077 bonds, 2 pseudobonds, 520 residues, 2 models selected  

> save chainsTMP/BK_uu.pdb format pdb models #1/BK selectedOnly true

> open chainsTMP/BK_uu_Mod.pdb

Chain information for BK_uu_Mod.pdb #64  
---  
Chain | Description  
BK | No description available  
  

> select #1/BP

1338 atoms, 1365 bonds, 166 residues, 1 model selected  

> save chainsTMP/BP_uu.pdb format pdb models #1/BP selectedOnly true

> open chainsTMP/BP_uu_Mod.pdb

Chain information for BP_uu_Mod.pdb #65  
---  
Chain | Description  
BP | No description available  
  

> select #1/C

1907 atoms, 1933 bonds, 265 residues, 1 model selected  

> save chainsTMP/C_u.pdb format pdb models #1/C selectedOnly true

> open chainsTMP/C_u_Mod.pdb

Chain information for C_u_Mod.pdb #66  
---  
Chain | Description  
C | No description available  
  

> select #1/C0

538 atoms, 547 bonds, 74 residues, 1 model selected  

> save chainsTMP/C0_un.pdb format pdb models #1/C0 selectedOnly true

> open chainsTMP/C0_un_Mod.pdb

Chain information for C0_un_Mod.pdb #67  
---  
Chain | Description  
C0 | No description available  
  

> select #1/C1

538 atoms, 547 bonds, 74 residues, 1 model selected  

> save chainsTMP/C1_un.pdb format pdb models #1/C1 selectedOnly true

> open chainsTMP/C1_un_Mod.pdb

Chain information for C1_un_Mod.pdb #68  
---  
Chain | Description  
C1 | No description available  
  

> select #1/C2

538 atoms, 547 bonds, 74 residues, 1 model selected  

> save chainsTMP/C2_un.pdb format pdb models #1/C2 selectedOnly true

> open chainsTMP/C2_un_Mod.pdb

Chain information for C2_un_Mod.pdb #69  
---  
Chain | Description  
C2 | No description available  
  

> select #1/C3

538 atoms, 547 bonds, 74 residues, 1 model selected  

> save chainsTMP/C3_un.pdb format pdb models #1/C3 selectedOnly true

> open chainsTMP/C3_un_Mod.pdb

Chain information for C3_un_Mod.pdb #70  
---  
Chain | Description  
C3 | No description available  
  

> select #1/C4

530 atoms, 539 bonds, 73 residues, 1 model selected  

> save chainsTMP/C4_un.pdb format pdb models #1/C4 selectedOnly true

> open chainsTMP/C4_un_Mod.pdb

Chain information for C4_un_Mod.pdb #71  
---  
Chain | Description  
C4 | No description available  
  

> select #1/C5

538 atoms, 547 bonds, 74 residues, 1 model selected  

> save chainsTMP/C5_un.pdb format pdb models #1/C5 selectedOnly true

> open chainsTMP/C5_un_Mod.pdb

Chain information for C5_un_Mod.pdb #72  
---  
Chain | Description  
C5 | No description available  
  

> select #1/C6

538 atoms, 547 bonds, 74 residues, 1 model selected  

> save chainsTMP/C6_un.pdb format pdb models #1/C6 selectedOnly true

> open chainsTMP/C6_un_Mod.pdb

Chain information for C6_un_Mod.pdb #73  
---  
Chain | Description  
C6 | No description available  
  

> select #1/C7

538 atoms, 547 bonds, 74 residues, 1 model selected  

> save chainsTMP/C7_un.pdb format pdb models #1/C7 selectedOnly true

> open chainsTMP/C7_un_Mod.pdb

Chain information for C7_un_Mod.pdb #74  
---  
Chain | Description  
C7 | No description available  
  

> select #1/C8

538 atoms, 547 bonds, 74 residues, 1 model selected  

> save chainsTMP/C8_un.pdb format pdb models #1/C8 selectedOnly true

> open chainsTMP/C8_un_Mod.pdb

Chain information for C8_un_Mod.pdb #75  
---  
Chain | Description  
C8 | No description available  
  

> select #1/C9

538 atoms, 547 bonds, 74 residues, 1 model selected  

> save chainsTMP/C9_un.pdb format pdb models #1/C9 selectedOnly true

> open chainsTMP/C9_un_Mod.pdb

Chain information for C9_un_Mod.pdb #76  
---  
Chain | Description  
C9 | No description available  
  

> select #1/D

1695 atoms, 1727 bonds, 1 pseudobond, 214 residues, 2 models selected  

> save chainsTMP/D_u.pdb format pdb models #1/D selectedOnly true

> open chainsTMP/D_u_Mod.pdb

Chain information for D_u_Mod.pdb #77  
---  
Chain | Description  
D | No description available  
  

> select #1/D6

437 atoms, 447 bonds, 1 pseudobond, 54 residues, 2 models selected  

> save chainsTMP/D6_un.pdb format pdb models #1/D6 selectedOnly true

> open chainsTMP/D6_un_Mod.pdb

Chain information for D6_un_Mod.pdb #78  
---  
Chain | Description  
D6 | No description available  
  

> select #1/E

4072 atoms, 4145 bonds, 2 pseudobonds, 526 residues, 2 models selected  

> save chainsTMP/E_u.pdb format pdb models #1/E selectedOnly true

> open chainsTMP/E_u_Mod.pdb

Chain information for E_u_Mod.pdb #79  
---  
Chain | Description  
E | No description available  
  

> select #1/E1

608 atoms, 625 bonds, 1 pseudobond, 80 residues, 2 models selected  

> save chainsTMP/E1_un.pdb format pdb models #1/E1 selectedOnly true

> open chainsTMP/E1_un_Mod.pdb

Chain information for E1_un_Mod.pdb #80  
---  
Chain | Description  
E1 | No description available  
  

> select #1/E4

1397 atoms, 1429 bonds, 169 residues, 1 model selected  

> save chainsTMP/E4_un.pdb format pdb models #1/E4 selectedOnly true

> open chainsTMP/E4_un_Mod.pdb

Chain information for E4_un_Mod.pdb #81  
---  
Chain | Description  
E4 | No description available  
  

> select #1/Ek

670 atoms, 695 bonds, 78 residues, 1 model selected  

> save chainsTMP/Ek_ul.pdb format pdb models #1/Ek selectedOnly true

> open chainsTMP/Ek_ul_Mod.pdb

Chain information for Ek_ul_Mod.pdb #82  
---  
Chain | Description  
Ek | No description available  
  

> select #1/Eq

772 atoms, 805 bonds, 84 residues, 1 model selected  

> save chainsTMP/Eq_ul.pdb format pdb models #1/Eq selectedOnly true

> open chainsTMP/Eq_ul_Mod.pdb

Chain information for Eq_ul_Mod.pdb #83  
---  
Chain | Description  
Eq | No description available  
  

> select #1/Es

1117 atoms, 1156 bonds, 135 residues, 1 model selected  

> save chainsTMP/Es_ul.pdb format pdb models #1/Es selectedOnly true

> open chainsTMP/Es_ul_Mod.pdb

Chain information for Es_ul_Mod.pdb #84  
---  
Chain | Description  
Es | No description available  
  

> select #1/Ev

3194 atoms, 3290 bonds, 384 residues, 1 model selected  

> save chainsTMP/Ev_ul.pdb format pdb models #1/Ev selectedOnly true

> open chainsTMP/Ev_ul_Mod.pdb

Chain information for Ev_ul_Mod.pdb #85  
---  
Chain | Description  
Ev | No description available  
  

> select #1/F9

595 atoms, 621 bonds, 67 residues, 1 model selected  

> save chainsTMP/F9_un.pdb format pdb models #1/F9 selectedOnly true

> open chainsTMP/F9_un_Mod.pdb

Chain information for F9_un_Mod.pdb #86  
---  
Chain | Description  
F9 | No description available  
  

> select #1/FF

596 atoms, 618 bonds, 1 pseudobond, 72 residues, 2 models selected  

> save chainsTMP/FF_uu.pdb format pdb models #1/FF selectedOnly true

> open chainsTMP/FF_uu_Mod.pdb

Chain information for FF_uu_Mod.pdb #87  
---  
Chain | Description  
FF | No description available  
  

> select #1/FH

1138 atoms, 1176 bonds, 140 residues, 1 model selected  

> save chainsTMP/FH_uu.pdb format pdb models #1/FH selectedOnly true

> open chainsTMP/FH_uu_Mod.pdb

Chain information for FH_uu_Mod.pdb #88  
---  
Chain | Description  
FH | No description available  
  

> select #1/FL

1998 atoms, 2068 bonds, 233 residues, 1 model selected  

> save chainsTMP/FL_uu.pdb format pdb models #1/FL selectedOnly true

> open chainsTMP/FL_uu_Mod.pdb

Chain information for FL_uu_Mod.pdb #89  
---  
Chain | Description  
FL | No description available  
  

> select #1/FO

1174 atoms, 1201 bonds, 148 residues, 1 model selected  

> save chainsTMP/FO_uu.pdb format pdb models #1/FO selectedOnly true

> open chainsTMP/FO_uu_Mod.pdb

Chain information for FO_uu_Mod.pdb #90  
---  
Chain | Description  
FO | No description available  
  

> select #1/Fy

480 atoms, 491 bonds, 58 residues, 1 model selected  

> save chainsTMP/Fy_ul.pdb format pdb models #1/Fy selectedOnly true

> open chainsTMP/Fy_ul_Mod.pdb

Chain information for Fy_ul_Mod.pdb #91  
---  
Chain | Description  
Fy | No description available  
  

> select #1/Fz

402 atoms, 412 bonds, 48 residues, 1 model selected  

> save chainsTMP/Fz_ul.pdb format pdb models #1/Fz selectedOnly true

> open chainsTMP/Fz_ul_Mod.pdb

Chain information for Fz_ul_Mod.pdb #92  
---  
Chain | Description  
Fz | No description available  
  

> select #1/GT

1489 atoms, 2104 bonds, 92 residues, 1 model selected  

> save chainsTMP/GT_uu.pdb format pdb models #1/GT selectedOnly true

> open chainsTMP/GT_uu_Mod.pdb

Chain information for GT_uu_Mod.pdb #93  
---  
Chain | Description  
GT | No description available  
  

> select #1/IE

1375 atoms, 1402 bonds, 1 pseudobond, 175 residues, 2 models selected  

> save chainsTMP/IE_uu.pdb format pdb models #1/IE selectedOnly true

> open chainsTMP/IE_uu_Mod.pdb

Chain information for IE_uu_Mod.pdb #94  
---  
Chain | Description  
IE | No description available  
  

> select #1/IY

2336 atoms, 2377 bonds, 294 residues, 1 model selected  

> save chainsTMP/IY_uu.pdb format pdb models #1/IY selectedOnly true

> open chainsTMP/IY_uu_Mod.pdb

Chain information for IY_uu_Mod.pdb #95  
---  
Chain | Description  
IY | No description available  
  

> select #1/JC

1254 atoms, 1276 bonds, 162 residues, 1 model selected  

> save chainsTMP/JC_uu.pdb format pdb models #1/JC selectedOnly true

> open chainsTMP/JC_uu_Mod.pdb

Chain information for JC_uu_Mod.pdb #96  
---  
Chain | Description  
JC | No description available  
  

> select #1/a

799 atoms, 822 bonds, 94 residues, 1 model selected  

> save chainsTMP/a_l.pdb format pdb models #1/a selectedOnly true

> open chainsTMP/a_l_Mod.pdb

Chain information for a_l_Mod.pdb #97  
---  
Chain | Description  
a | No description available  
  

> combine #2-97 close true modelId #2 name fixedModel

Computing secondary structure  
[Repeated 95 time(s)]

> hide #!1 models

> save "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J450_008_volume_map_sharp_NOSEQ/superComplexConsolidation/superComplexConsolidatedV1.cif"
> models #2

Not saving entity_poly_seq for non-authoritative sequences  

> addh #2 hbond false

Summary of feedback from adding hydrogens to fixedModel #2  
---  
warnings | C-terminal fixedModel #2/GT SER 97 O does not look like carboxylate oxygen; cannot complete teminus  
Unknown hybridization for atoms (S4, S1, S3, S2) of residue type SF4; not
adding hydrogens to them  
Unknown hybridization for atoms (S4, S1, S3, S2) of residue type F3S; not
adding hydrogens to them  
notes | No usable SEQRES records for fixedModel (#2) chain AG; guessing termini instead  
No usable SEQRES records for fixedModel (#2) chain Ar; guessing termini
instead  
No usable SEQRES records for fixedModel (#2) chain I0; guessing termini
instead  
No usable SEQRES records for fixedModel (#2) chain Il; guessing termini
instead  
No usable SEQRES records for fixedModel (#2) chain Ix; guessing termini
instead  
86 messages similar to the above omitted  
Chain-initial residues that are actual N termini: fixedModel #2/AG PHE 18,
fixedModel #2/Ar LEU 23, fixedModel #2/I0 SER 160, fixedModel #2/Il TYR 26,
fixedModel #2/Ix ASP 152, fixedModel #2/Iy THR 22, fixedModel #2/J6 THR 2,
fixedModel #2/JI PRO 11, fixedModel #2/JJ MET 1, fixedModel #2/JN ALA 2,
fixedModel #2/Jw VAL 21, fixedModel #2/Jx LYS 11, fixedModel #2/K5 ALA 14,
fixedModel #2/KI THR 26, fixedModel #2/Ke ALA 44, fixedModel #2/Kp PRO 53,
fixedModel #2/Ks GLU 4, fixedModel #2/L3 VAL 52, fixedModel #2/LG TRP 20,
fixedModel #2/LO TYR 37, fixedModel #2/LR SER 78, fixedModel #2/LY PRO 182,
fixedModel #2/M PRO 2, fixedModel #2/Mg ILE 36, fixedModel #2/Mq SER 34,
fixedModel #2/Mr THR 38, fixedModel #2/NF LYS 30, fixedModel #2/NM TYR 82,
fixedModel #2/Np MET 1, fixedModel #2/TB MET 18, fixedModel #2/Y MET 1,
fixedModel #2/t0 THR 38, fixedModel #2/t1 THR 2, fixedModel #2/t2 TYR 37,
fixedModel #2/t3 PHE 18, fixedModel #2/t4 LEU 23, fixedModel #2/t5 THR 26,
fixedModel #2/t6 MET 1, fixedModel #2/t7 MET 1, fixedModel #2/t8 VAL 21,
fixedModel #2/t9 ASP 152, fixedModel #2/ta MET 1, fixedModel #2/tb SER 160,
fixedModel #2/tc THR 22, fixedModel #2/td TYR 26, fixedModel #2/te GLU 4,
fixedModel #2/tf ALA 2, fixedModel #2/tg PRO 182, fixedModel #2/R MET 1,
fixedModel #2/A ALA 34, fixedModel #2/A0 PRO 204, fixedModel #2/AU LYS 35,
fixedModel #2/Ab GLU 206, fixedModel #2/Aj LYS 208, fixedModel #2/Aq LYS 25,
fixedModel #2/B ALA 23, fixedModel #2/BI ALA 23, fixedModel #2/BK THR 37,
fixedModel #2/BP GLY 22, fixedModel #2/C SER 85, fixedModel #2/C0 ILE 33,
fixedModel #2/C1 ILE 33, fixedModel #2/C2 ILE 33, fixedModel #2/C3 ILE 33,
fixedModel #2/C4 SER 34, fixedModel #2/C5 ILE 33, fixedModel #2/C6 ILE 33,
fixedModel #2/C7 ILE 33, fixedModel #2/C8 ILE 33, fixedModel #2/C9 ILE 33,
fixedModel #2/D TYR 18, fixedModel #2/D6 VAL 7, fixedModel #2/E PHE 33,
fixedModel #2/E1 LEU 51, fixedModel #2/E4 GLN 35, fixedModel #2/Ek ASN 26,
fixedModel #2/Eq ASN 62, fixedModel #2/Es VAL 2, fixedModel #2/Ev GLY 3,
fixedModel #2/F9 HIS 37, fixedModel #2/FF HIS 98, fixedModel #2/FH VAL 18,
fixedModel #2/FL MET 1, fixedModel #2/FO PHE 12, fixedModel #2/Fy PRO 60,
fixedModel #2/Fz VAL 58, fixedModel #2/GT ALA 6, fixedModel #2/IE LYS 26,
fixedModel #2/IY SER 2, fixedModel #2/JC GLU 22, fixedModel #2/a TYR 3  
Chain-initial residues that are not actual N termini: fixedModel #2/JI GLU
259, fixedModel #2/K5 LYS 143, fixedModel #2/K5 ARG 299, fixedModel #2/K5 LYS
338, fixedModel #2/K5 ILE 361, fixedModel #2/K5 GLU 490, fixedModel #2/K5 MET
567, fixedModel #2/L3 TYR 94, fixedModel #2/L3 VAL 198, fixedModel #2/L3 VAL
312, fixedModel #2/NF ARG 189, fixedModel #2/AU GLN 151, fixedModel #2/AU GLN
436, fixedModel #2/Ab THR 521, fixedModel #2/BK GLN 151, fixedModel #2/BK VAL
437, fixedModel #2/D ILE 234, fixedModel #2/D6 VAL 63, fixedModel #2/E GLN
151, fixedModel #2/E GLN 438, fixedModel #2/E1 ASP 217, fixedModel #2/FF MET
124, fixedModel #2/IE VAL 199  
Chain-final residues that are actual C termini: fixedModel #2/R HIS 62,
fixedModel #2/A PRO 357, fixedModel #2/A0 LYS 685, fixedModel #2/AU VAL 574,
fixedModel #2/Ab ARG 690, fixedModel #2/Aj HIS 690, fixedModel #2/Aq GLN 187,
fixedModel #2/B LYS 160, fixedModel #2/BI GLN 187, fixedModel #2/BK VAL 574,
fixedModel #2/BP GLN 187, fixedModel #2/C MET 349, fixedModel #2/C0 SER 106,
fixedModel #2/C1 SER 106, fixedModel #2/C2 SER 106, fixedModel #2/C3 SER 106,
fixedModel #2/C4 SER 106, fixedModel #2/C5 SER 106, fixedModel #2/C6 SER 106,
fixedModel #2/C7 SER 106, fixedModel #2/C8 SER 106, fixedModel #2/C9 SER 106,
fixedModel #2/D VAL 258, fixedModel #2/D6 THR 70, fixedModel #2/E GLY 575,
fixedModel #2/E1 GLY 239, fixedModel #2/E4 GLY 203, fixedModel #2/Ek SER 103,
fixedModel #2/Eq TYR 145, fixedModel #2/Es HIS 136, fixedModel #2/Ev ALA 386,
fixedModel #2/F9 GLN 103, fixedModel #2/FF PRO 174, fixedModel #2/FH VAL 157,
fixedModel #2/FL GLY 233, fixedModel #2/FO ALA 159, fixedModel #2/Fy ALA 117,
fixedModel #2/Fz VAL 105, fixedModel #2/GT SER 97, fixedModel #2/IE GLY 204,
fixedModel #2/IY ASN 295, fixedModel #2/JC GLU 183, fixedModel #2/a GLN 96  
Chain-final residues that are not actual C termini: fixedModel #2/AG SER 196,
fixedModel #2/Ar TRP 118, fixedModel #2/I0 LYS 383, fixedModel #2/Il GLU 104,
fixedModel #2/Ix ILE 279, fixedModel #2/Iy GLN 115, fixedModel #2/J6 PHE 199,
fixedModel #2/JI LYS 491, fixedModel #2/JI PHE 252, fixedModel #2/JJ ILE 549,
fixedModel #2/JN VAL 108, fixedModel #2/Jw PHE 144, fixedModel #2/Jx ASP 124,
fixedModel #2/K5 PRO 602, fixedModel #2/K5 ILE 138, fixedModel #2/K5 GLU 268,
fixedModel #2/K5 LEU 311, fixedModel #2/K5 VAL 354, fixedModel #2/K5 ALA 484,
fixedModel #2/K5 ARG 546, fixedModel #2/KI GLU 225, fixedModel #2/Ke LEU 138,
fixedModel #2/Kp GLU 224, fixedModel #2/Ks ALA 156, fixedModel #2/L3 ARG 325,
fixedModel #2/L3 LEU 84, fixedModel #2/L3 GLY 117, fixedModel #2/L3 HIS 283,
fixedModel #2/LG SER 123, fixedModel #2/LO LYS 342, fixedModel #2/LR GLY 148,
fixedModel #2/LY ALA 345, fixedModel #2/M PHE 103, fixedModel #2/Mg ALA 250,
fixedModel #2/Mq LYS 90, fixedModel #2/Mr LEU 147, fixedModel #2/NF SER 246,
fixedModel #2/NF LEU 183, fixedModel #2/NM MET 144, fixedModel #2/Np VAL 283,
fixedModel #2/TB THR 81, fixedModel #2/Y ILE 210, fixedModel #2/t0 LEU 147,
fixedModel #2/t1 PHE 199, fixedModel #2/t2 LYS 342, fixedModel #2/t3 SER 196,
fixedModel #2/t4 TRP 118, fixedModel #2/t5 GLU 225, fixedModel #2/t6 ILE 549,
fixedModel #2/t7 VAL 283, fixedModel #2/t8 PHE 144, fixedModel #2/t9 ILE 279,
fixedModel #2/ta ILE 210, fixedModel #2/tb LYS 383, fixedModel #2/tc GLN 115,
fixedModel #2/td GLU 104, fixedModel #2/te ALA 156, fixedModel #2/tf VAL 108,
fixedModel #2/tg ALA 345, fixedModel #2/AU LEU 139, fixedModel #2/AU ASP 430,
fixedModel #2/Ab VAL 515, fixedModel #2/BK GLY 138, fixedModel #2/BK ASP 430,
fixedModel #2/D LYS 206, fixedModel #2/D6 LEU 52, fixedModel #2/E LEU 139,
fixedModel #2/E ALA 429, fixedModel #2/E1 GLU 123, fixedModel #2/FF TYR 118,
fixedModel #2/IE VAL 194  
Adding 'H' to fixedModel #2/JI GLU 259  
Adding 'H' to fixedModel #2/K5 LYS 143  
Adding 'H' to fixedModel #2/K5 ARG 299  
Adding 'H' to fixedModel #2/K5 LYS 338  
Adding 'H' to fixedModel #2/K5 ILE 361  
18 messages similar to the above omitted  
fixedModel #2/AG SER 196 is not terminus, removing H atom from 'C'  
fixedModel #2/Ar TRP 118 is not terminus, removing H atom from 'C'  
fixedModel #2/I0 LYS 383 is not terminus, removing H atom from 'C'  
fixedModel #2/Il GLU 104 is not terminus, removing H atom from 'C'  
fixedModel #2/Ix ILE 279 is not terminus, removing H atom from 'C'  
43 messages similar to the above omitted  
135317 hydrogens added  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Loading residue template for 3PE from internal database  
Loading residue template for ATP from internal database  
Loading residue template for FAD from internal database  
Loading residue template for LPP from internal database  
Loading residue template for PC1 from internal database  

Chain HM, residue 1 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> delete #2/GT:27@H*

> select clear

> select up

33 atoms, 38 bonds, 1 residue, 1 model selected  

> select up

33 atoms, 38 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected atoms"

Deleted the following atoms from residue LEU GT28: HN2, HC8, HC9, HC13, CB,
HC2, CG, CD1, CD2, C, HC10, HC5, HC4, HC14, HC11, HC6, N, HC7, HC3, HN1, HC,
HC1, CA, O, HC12  

> delete #3@H*

> delete #2@H*

> select up

8 atoms, 7 bonds, 1 residue, 1 model selected  

> bond #2/GT:27@C #2/GT:28@N

Created 3 bonds  

> bond #2/GT:28@C #2/GT:29@N

Created 2 bonds  

> bond #2/GT:26@C #2/GT:27@N

Created 5 bonds  

> addh #2 hbond false

Summary of feedback from adding hydrogens to fixedModel #2.2  
---  
warnings | C-terminal fixedModel #2.2/GT SER 97 O does not look like carboxylate oxygen; cannot complete teminus  
Unknown hybridization for atoms (S4, S1, S3, S2) of residue type SF4; not
adding hydrogens to them  
Unknown hybridization for atoms (S4, S1, S3, S2) of residue type F3S; not
adding hydrogens to them  
notes | No usable SEQRES records for fixedModel (#2.2) chain AG; guessing termini instead  
No usable SEQRES records for fixedModel (#2.2) chain Ar; guessing termini
instead  
No usable SEQRES records for fixedModel (#2.2) chain I0; guessing termini
instead  
No usable SEQRES records for fixedModel (#2.2) chain Il; guessing termini
instead  
No usable SEQRES records for fixedModel (#2.2) chain Ix; guessing termini
instead  
86 messages similar to the above omitted  
Chain-initial residues that are actual N termini: fixedModel #2.2/AG PHE 18,
fixedModel #2.2/Ar LEU 23, fixedModel #2.2/I0 SER 160, fixedModel #2.2/Il TYR
26, fixedModel #2.2/Ix ASP 152, fixedModel #2.2/Iy THR 22, fixedModel #2.2/J6
THR 2, fixedModel #2.2/JI PRO 11, fixedModel #2.2/JJ MET 1, fixedModel #2.2/JN
ALA 2, fixedModel #2.2/Jw VAL 21, fixedModel #2.2/Jx LYS 11, fixedModel
#2.2/K5 ALA 14, fixedModel #2.2/KI THR 26, fixedModel #2.2/Ke ALA 44,
fixedModel #2.2/Kp PRO 53, fixedModel #2.2/Ks GLU 4, fixedModel #2.2/L3 VAL
52, fixedModel #2.2/LG TRP 20, fixedModel #2.2/LO TYR 37, fixedModel #2.2/LR
SER 78, fixedModel #2.2/LY PRO 182, fixedModel #2.2/M PRO 2, fixedModel
#2.2/Mg ILE 36, fixedModel #2.2/Mq SER 34, fixedModel #2.2/Mr THR 38,
fixedModel #2.2/NF LYS 30, fixedModel #2.2/NM TYR 82, fixedModel #2.2/Np MET
1, fixedModel #2.2/TB MET 18, fixedModel #2.2/Y MET 1, fixedModel #2.2/t0 THR
38, fixedModel #2.2/t1 THR 2, fixedModel #2.2/t2 TYR 37, fixedModel #2.2/t3
PHE 18, fixedModel #2.2/t4 LEU 23, fixedModel #2.2/t5 THR 26, fixedModel
#2.2/t6 MET 1, fixedModel #2.2/t7 MET 1, fixedModel #2.2/t8 VAL 21, fixedModel
#2.2/t9 ASP 152, fixedModel #2.2/ta MET 1, fixedModel #2.2/tb SER 160,
fixedModel #2.2/tc THR 22, fixedModel #2.2/td TYR 26, fixedModel #2.2/te GLU
4, fixedModel #2.2/tf ALA 2, fixedModel #2.2/tg PRO 182, fixedModel #2.2/R MET
1, fixedModel #2.2/A ALA 34, fixedModel #2.2/A0 PRO 204, fixedModel #2.2/AU
LYS 35, fixedModel #2.2/Ab GLU 206, fixedModel #2.2/Aj LYS 208, fixedModel
#2.2/Aq LYS 25, fixedModel #2.2/B ALA 23, fixedModel #2.2/BI ALA 23,
fixedModel #2.2/BK THR 37, fixedModel #2.2/BP GLY 22, fixedModel #2.2/C SER
85, fixedModel #2.2/C0 ILE 33, fixedModel #2.2/C1 ILE 33, fixedModel #2.2/C2
ILE 33, fixedModel #2.2/C3 ILE 33, fixedModel #2.2/C4 SER 34, fixedModel
#2.2/C5 ILE 33, fixedModel #2.2/C6 ILE 33, fixedModel #2.2/C7 ILE 33,
fixedModel #2.2/C8 ILE 33, fixedModel #2.2/C9 ILE 33, fixedModel #2.2/D TYR
18, fixedModel #2.2/D6 VAL 7, fixedModel #2.2/E PHE 33, fixedModel #2.2/E1 LEU
51, fixedModel #2.2/E4 GLN 35, fixedModel #2.2/Ek ASN 26, fixedModel #2.2/Eq
ASN 62, fixedModel #2.2/Es VAL 2, fixedModel #2.2/Ev GLY 3, fixedModel #2.2/F9
HIS 37, fixedModel #2.2/FF HIS 98, fixedModel #2.2/FH VAL 18, fixedModel
#2.2/FL MET 1, fixedModel #2.2/FO PHE 12, fixedModel #2.2/Fy PRO 60,
fixedModel #2.2/Fz VAL 58, fixedModel #2.2/GT ALA 6, fixedModel #2.2/IE LYS
26, fixedModel #2.2/IY SER 2, fixedModel #2.2/JC GLU 22, fixedModel #2.2/a TYR
3  
Chain-initial residues that are not actual N termini: fixedModel #2.2/JI GLU
259, fixedModel #2.2/K5 LYS 143, fixedModel #2.2/K5 ARG 299, fixedModel
#2.2/K5 LYS 338, fixedModel #2.2/K5 ILE 361, fixedModel #2.2/K5 GLU 490,
fixedModel #2.2/K5 MET 567, fixedModel #2.2/L3 TYR 94, fixedModel #2.2/L3 VAL
198, fixedModel #2.2/L3 VAL 312, fixedModel #2.2/NF ARG 189, fixedModel
#2.2/AU GLN 151, fixedModel #2.2/AU GLN 436, fixedModel #2.2/Ab THR 521,
fixedModel #2.2/BK GLN 151, fixedModel #2.2/BK VAL 437, fixedModel #2.2/D ILE
234, fixedModel #2.2/D6 VAL 63, fixedModel #2.2/E GLN 151, fixedModel #2.2/E
GLN 438, fixedModel #2.2/E1 ASP 217, fixedModel #2.2/FF MET 124, fixedModel
#2.2/IE VAL 199  
Chain-final residues that are actual C termini: fixedModel #2.2/R HIS 62,
fixedModel #2.2/A PRO 357, fixedModel #2.2/A0 LYS 685, fixedModel #2.2/AU VAL
574, fixedModel #2.2/Ab ARG 690, fixedModel #2.2/Aj HIS 690, fixedModel
#2.2/Aq GLN 187, fixedModel #2.2/B LYS 160, fixedModel #2.2/BI GLN 187,
fixedModel #2.2/BK VAL 574, fixedModel #2.2/BP GLN 187, fixedModel #2.2/C MET
349, fixedModel #2.2/C0 SER 106, fixedModel #2.2/C1 SER 106, fixedModel
#2.2/C2 SER 106, fixedModel #2.2/C3 SER 106, fixedModel #2.2/C4 SER 106,
fixedModel #2.2/C5 SER 106, fixedModel #2.2/C6 SER 106, fixedModel #2.2/C7 SER
106, fixedModel #2.2/C8 SER 106, fixedModel #2.2/C9 SER 106, fixedModel #2.2/D
VAL 258, fixedModel #2.2/D6 THR 70, fixedModel #2.2/E GLY 575, fixedModel
#2.2/E1 GLY 239, fixedModel #2.2/E4 GLY 203, fixedModel #2.2/Ek SER 103,
fixedModel #2.2/Eq TYR 145, fixedModel #2.2/Es HIS 136, fixedModel #2.2/Ev ALA
386, fixedModel #2.2/F9 GLN 103, fixedModel #2.2/FF PRO 174, fixedModel
#2.2/FH VAL 157, fixedModel #2.2/FL GLY 233, fixedModel #2.2/FO ALA 159,
fixedModel #2.2/Fy ALA 117, fixedModel #2.2/Fz VAL 105, fixedModel #2.2/GT SER
97, fixedModel #2.2/IE GLY 204, fixedModel #2.2/IY ASN 295, fixedModel #2.2/JC
GLU 183, fixedModel #2.2/a GLN 96  
Chain-final residues that are not actual C termini: fixedModel #2.2/AG SER
196, fixedModel #2.2/Ar TRP 118, fixedModel #2.2/I0 LYS 383, fixedModel
#2.2/Il GLU 104, fixedModel #2.2/Ix ILE 279, fixedModel #2.2/Iy GLN 115,
fixedModel #2.2/J6 PHE 199, fixedModel #2.2/JI LYS 491, fixedModel #2.2/JI PHE
252, fixedModel #2.2/JJ ILE 549, fixedModel #2.2/JN VAL 108, fixedModel
#2.2/Jw PHE 144, fixedModel #2.2/Jx ASP 124, fixedModel #2.2/K5 PRO 602,
fixedModel #2.2/K5 ILE 138, fixedModel #2.2/K5 GLU 268, fixedModel #2.2/K5 LEU
311, fixedModel #2.2/K5 VAL 354, fixedModel #2.2/K5 ALA 484, fixedModel
#2.2/K5 ARG 546, fixedModel #2.2/KI GLU 225, fixedModel #2.2/Ke LEU 138,
fixedModel #2.2/Kp GLU 224, fixedModel #2.2/Ks ALA 156, fixedModel #2.2/L3 ARG
325, fixedModel #2.2/L3 LEU 84, fixedModel #2.2/L3 GLY 117, fixedModel #2.2/L3
HIS 283, fixedModel #2.2/LG SER 123, fixedModel #2.2/LO LYS 342, fixedModel
#2.2/LR GLY 148, fixedModel #2.2/LY ALA 345, fixedModel #2.2/M PHE 103,
fixedModel #2.2/Mg ALA 250, fixedModel #2.2/Mq LYS 90, fixedModel #2.2/Mr LEU
147, fixedModel #2.2/NF SER 246, fixedModel #2.2/NF LEU 183, fixedModel
#2.2/NM MET 144, fixedModel #2.2/Np VAL 283, fixedModel #2.2/TB THR 81,
fixedModel #2.2/Y ILE 210, fixedModel #2.2/t0 LEU 147, fixedModel #2.2/t1 PHE
199, fixedModel #2.2/t2 LYS 342, fixedModel #2.2/t3 SER 196, fixedModel
#2.2/t4 TRP 118, fixedModel #2.2/t5 GLU 225, fixedModel #2.2/t6 ILE 549,
fixedModel #2.2/t7 VAL 283, fixedModel #2.2/t8 PHE 144, fixedModel #2.2/t9 ILE
279, fixedModel #2.2/ta ILE 210, fixedModel #2.2/tb LYS 383, fixedModel
#2.2/tc GLN 115, fixedModel #2.2/td GLU 104, fixedModel #2.2/te ALA 156,
fixedModel #2.2/tf VAL 108, fixedModel #2.2/tg ALA 345, fixedModel #2.2/AU LEU
139, fixedModel #2.2/AU ASP 430, fixedModel #2.2/Ab VAL 515, fixedModel
#2.2/BK GLY 138, fixedModel #2.2/BK ASP 430, fixedModel #2.2/D LYS 206,
fixedModel #2.2/D6 LEU 52, fixedModel #2.2/E LEU 139, fixedModel #2.2/E ALA
429, fixedModel #2.2/E1 GLU 123, fixedModel #2.2/FF TYR 118, fixedModel
#2.2/IE VAL 194  
Adding 'H' to fixedModel #2.2/JI GLU 259  
Adding 'H' to fixedModel #2.2/K5 LYS 143  
Adding 'H' to fixedModel #2.2/K5 ARG 299  
Adding 'H' to fixedModel #2.2/K5 LYS 338  
Adding 'H' to fixedModel #2.2/K5 ILE 361  
18 messages similar to the above omitted  
fixedModel #2.2/AG SER 196 is not terminus, removing H atom from 'C'  
fixedModel #2.2/Ar TRP 118 is not terminus, removing H atom from 'C'  
fixedModel #2.2/I0 LYS 383 is not terminus, removing H atom from 'C'  
fixedModel #2.2/Il GLU 104 is not terminus, removing H atom from 'C'  
fixedModel #2.2/Ix ILE 279 is not terminus, removing H atom from 'C'  
43 messages similar to the above omitted  
135304 hydrogens added  
  

Chain HM, residue 1 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Fetching CCD LEU_LEO2 from http://ligand-
expo.rcsb.org/reports/L/LEU_LEO2/LEU_LEO2.cif  
Fetching CCD LEU_LFZW from http://ligand-
expo.rcsb.org/reports/L/LEU_LFZW/LEU_LFZW.cif  
Deleted the following atoms from residue LEU GT55: HC3, HN1, HN2, N, HC2, HC1,
HC11, HC10, HC4, HC7, HC, HC9, CA, CG, C, O, HC6, HC12, HC13, HC14, CB, CD1,
CD2, HC8, HC5  
Deleted the following atoms from residue LEU GT43: HC7, HC4, HN1, N, HC3, HN2,
HC, HC12, HC10, HC8, CD2, CA, CG, HC2, HC5, HC1, C, HC14, HC13, HC6, HC9,
HC11, O, CB, CD1  
Deleted the following atoms from residue LEU GT33: HC8, HC4, N, C, CB, HC3,
HC6, HC13, HC14, HC12, CD2, HC2, HC1, HC, O, CA, HC10, HN1, HC5, HC11, HC9,
HN2, HC7, CG, CD1  
Deleted the following atoms from residue LEU GT24: HC7, HC11, HC12, HC, HC3,
C, O, CD2, CB, HC2, CG, CD1, HC6, HN2, N, HC14, HC10, HC4, HC13, HC1, HC8,
HC9, HC5, CA, HN1  

> info residues #2/GT

residue id #2.2/GT:6 name ALA index 0  
residue id #2.2/GT:7 name PHE index 1  
residue id #2.2/GT:8 name HIS index 2  
residue id #2.2/GT:9 name ASP index 3  
residue id #2.2/GT:10 name VAL index 4  
residue id #2.2/GT:11 name SER index 5  
residue id #2.2/GT:12 name THR index 6  
residue id #2.2/GT:13 name ASP index 7  
residue id #2.2/GT:14 name ALA index 8  
residue id #2.2/GT:15 name ILE index 9  
residue id #2.2/GT:16 name ARG index 10  
residue id #2.2/GT:17 name GLN index 11  
residue id #2.2/GT:18 name MET index 12  
residue id #2.2/GT:19 name GLN index 13  
residue id #2.2/GT:20 name ALA index 14  
residue id #2.2/GT:21 name SER index 15  
residue id #2.2/GT:22 name GLU index 16  
residue id #2.2/GT:23 name ALA index 17  
residue id #2.2/GT:24 name LEU index 18  
residue id #2.2/GT:25 name GLN index 19  
residue id #2.2/GT:26 name LYS index 20  
residue id #2.2/GT:27 name HIS index 21  
residue id #2.2/GT:28 name LEU index 22  
residue id #2.2/GT:29 name GLU index 23  
residue id #2.2/GT:30 name ASN index 24  
residue id #2.2/GT:31 name ALA index 25  
residue id #2.2/GT:32 name GLN index 26  
residue id #2.2/GT:33 name LEU index 27  
residue id #2.2/GT:34 name ALA index 28  
residue id #2.2/GT:35 name HIS index 29  
residue id #2.2/GT:36 name ARG index 30  
residue id #2.2/GT:37 name VAL index 31  
residue id #2.2/GT:38 name CYS index 32  
residue id #2.2/GT:39 name VAL index 33  
residue id #2.2/GT:40 name ALA index 34  
residue id #2.2/GT:41 name LYS index 35  
residue id #2.2/GT:42 name ALA index 36  
residue id #2.2/GT:43 name LEU index 37  
residue id #2.2/GT:44 name LYS index 38  
residue id #2.2/GT:45 name ALA index 39  
residue id #2.2/GT:46 name ASP index 40  
residue id #2.2/GT:47 name GLU index 41  
residue id #2.2/GT:48 name PRO index 42  
residue id #2.2/GT:49 name PRO index 43  
residue id #2.2/GT:50 name VAL index 44  
residue id #2.2/GT:51 name GLU index 45  
residue id #2.2/GT:52 name LYS index 46  
residue id #2.2/GT:53 name CYS index 47  
residue id #2.2/GT:54 name ALA index 48  
residue id #2.2/GT:55 name LEU index 49  
residue id #2.2/GT:56 name THR index 50  
residue id #2.2/GT:57 name TRP index 51  
residue id #2.2/GT:58 name GLY index 52  
residue id #2.2/GT:59 name GLU index 53  
residue id #2.2/GT:60 name VAL index 54  
residue id #2.2/GT:61 name VAL index 55  
residue id #2.2/GT:62 name MET index 56  
residue id #2.2/GT:63 name ARG index 57  
residue id #2.2/GT:64 name TYR index 58  
residue id #2.2/GT:65 name ASN index 59  
residue id #2.2/GT:66 name GLN index 60  
residue id #2.2/GT:67 name TRP index 61  
residue id #2.2/GT:68 name SER index 62  
residue id #2.2/GT:69 name GLU index 63  
residue id #2.2/GT:70 name TYR index 64  
residue id #2.2/GT:71 name ARG index 65  
residue id #2.2/GT:72 name PRO index 66  
residue id #2.2/GT:73 name ALA index 67  
residue id #2.2/GT:74 name PHE index 68  
residue id #2.2/GT:75 name HIS index 69  
residue id #2.2/GT:76 name ASP index 70  
residue id #2.2/GT:77 name SER index 71  
residue id #2.2/GT:78 name ASP index 72  
residue id #2.2/GT:79 name ALA index 73  
residue id #2.2/GT:80 name GLN index 74  
residue id #2.2/GT:81 name LYS index 75  
residue id #2.2/GT:82 name ARG index 76  
residue id #2.2/GT:83 name TYR index 77  
residue id #2.2/GT:84 name SER index 78  
residue id #2.2/GT:85 name LYS index 79  
residue id #2.2/GT:86 name TYR index 80  
residue id #2.2/GT:87 name TRP index 81  
residue id #2.2/GT:88 name THR index 82  
residue id #2.2/GT:89 name LYS index 83  
residue id #2.2/GT:90 name LYS index 84  
residue id #2.2/GT:91 name ARG index 85  
residue id #2.2/GT:92 name GLN index 86  
residue id #2.2/GT:93 name ALA index 87  
residue id #2.2/GT:94 name ALA index 88  
residue id #2.2/GT:95 name ASP index 89  
residue id #2.2/GT:96 name ASP index 90  
residue id #2.2/GT:97 name SER index 91  

> delete #2@H*

> bond #2.2/GT:6@C #2.2/GT:7@N

Created 5 bonds  

> bond #2.2/GT:7@C #2.2/GT:8@N

Created 5 bonds  

> bond #2.2/GT:8@C #2.2/GT:9@N

Created 5 bonds  

> bond #2.2/GT:9@C #2.2/GT:10@N

Created 5 bonds  

> bond #2.2/GT:10@C #2.2/GT:11@N

Created 5 bonds  

> bond #2.2/GT:11@C #2.2/GT:12@N

Created 5 bonds  

> bond #2.2/GT:12@C #2.2/GT:13@N

Created 5 bonds  

> bond #2.2/GT:13@C #2.2/GT:14@N

Created 5 bonds  

> bond #2.2/GT:14@C #2.2/GT:15@N

Created 5 bonds  

> bond #2.2/GT:15@C #2.2/GT:16@N

Created 5 bonds  

> bond #2.2/GT:16@C #2.2/GT:17@N

Created 5 bonds  

> bond #2.2/GT:17@C #2.2/GT:18@N

Created 5 bonds  

> bond #2.2/GT:18@C #2.2/GT:19@N

Created 5 bonds  

> bond #2.2/GT:19@C #2.2/GT:20@N

Created 5 bonds  

> bond #2.2/GT:20@C #2.2/GT:21@N

Created 5 bonds  

> bond #2.2/GT:21@C #2.2/GT:22@N

Created 5 bonds  

> bond #2.2/GT:22@C #2.2/GT:23@N

Created 5 bonds  

> bond #2.2/GT:23@C #2.2/GT:24@N

Created 3 bonds  

> bond #2.2/GT:24@C #2.2/GT:25@N

Created 2 bonds  

> bond #2.2/GT:25@C #2.2/GT:26@N

Created 5 bonds  

> bond #2.2/GT:26@C #2.2/GT:27@N

Created 0 bonds  

> bond #2.2/GT:27@C #2.2/GT:28@N

Created 0 bonds  

> bond #2.2/GT:28@C #2.2/GT:29@N

Created 0 bonds  

> bond #2.2/GT:29@C #2.2/GT:30@N

Created 5 bonds  

> bond #2.2/GT:30@C #2.2/GT:31@N

Created 5 bonds  

> bond #2.2/GT:31@C #2.2/GT:32@N

Created 5 bonds  

> bond #2.2/GT:32@C #2.2/GT:33@N

Created 3 bonds  

> bond #2.2/GT:33@C #2.2/GT:34@N

Created 2 bonds  

> bond #2.2/GT:34@C #2.2/GT:35@N

Created 5 bonds  

> bond #2.2/GT:35@C #2.2/GT:36@N

Created 5 bonds  

> bond #2.2/GT:36@C #2.2/GT:37@N

Created 5 bonds  

> bond #2.2/GT:37@C #2.2/GT:38@N

Created 5 bonds  

> bond #2.2/GT:38@C #2.2/GT:39@N

Created 5 bonds  

> bond #2.2/GT:39@C #2.2/GT:40@N

Created 5 bonds  

> bond #2.2/GT:40@C #2.2/GT:41@N

Created 5 bonds  

> bond #2.2/GT:41@C #2.2/GT:42@N

Created 5 bonds  

> bond #2.2/GT:42@C #2.2/GT:43@N

Created 3 bonds  

> bond #2.2/GT:43@C #2.2/GT:44@N

Created 2 bonds  

> bond #2.2/GT:44@C #2.2/GT:45@N

Created 5 bonds  

> bond #2.2/GT:45@C #2.2/GT:46@N

Created 5 bonds  

> bond #2.2/GT:46@C #2.2/GT:47@N

Created 5 bonds  

> bond #2.2/GT:47@C #2.2/GT:48@N

Created 5 bonds  

> bond #2.2/GT:48@C #2.2/GT:49@N

Created 5 bonds  

> bond #2.2/GT:49@C #2.2/GT:50@N

Created 5 bonds  

> bond #2.2/GT:50@C #2.2/GT:51@N

Created 5 bonds  

> bond #2.2/GT:51@C #2.2/GT:52@N

Created 5 bonds  

> bond #2.2/GT:52@C #2.2/GT:53@N

Created 5 bonds  

> bond #2.2/GT:53@C #2.2/GT:54@N

Created 5 bonds  

> bond #2.2/GT:54@C #2.2/GT:55@N

Created 3 bonds  

> bond #2.2/GT:55@C #2.2/GT:56@N

Created 2 bonds  

> bond #2.2/GT:56@C #2.2/GT:57@N

Created 5 bonds  

> bond #2.2/GT:57@C #2.2/GT:58@N

Created 5 bonds  

> bond #2.2/GT:58@C #2.2/GT:59@N

Created 5 bonds  

> bond #2.2/GT:59@C #2.2/GT:60@N

Created 5 bonds  

> bond #2.2/GT:60@C #2.2/GT:61@N

Created 5 bonds  

> bond #2.2/GT:61@C #2.2/GT:62@N

Created 5 bonds  

> bond #2.2/GT:62@C #2.2/GT:63@N

Created 5 bonds  

> bond #2.2/GT:63@C #2.2/GT:64@N

Created 5 bonds  

> bond #2.2/GT:64@C #2.2/GT:65@N

Created 5 bonds  

> bond #2.2/GT:65@C #2.2/GT:66@N

Created 5 bonds  

> bond #2.2/GT:66@C #2.2/GT:67@N

Created 5 bonds  

> bond #2.2/GT:67@C #2.2/GT:68@N

Created 5 bonds  

> bond #2.2/GT:68@C #2.2/GT:69@N

Created 5 bonds  

> bond #2.2/GT:69@C #2.2/GT:70@N

Created 5 bonds  

> bond #2.2/GT:70@C #2.2/GT:71@N

Created 5 bonds  

> bond #2.2/GT:71@C #2.2/GT:72@N

Created 5 bonds  

> bond #2.2/GT:72@C #2.2/GT:73@N

Created 5 bonds  

> bond #2.2/GT:73@C #2.2/GT:74@N

Created 2 bonds  

> bond #2.2/GT:74@C #2.2/GT:75@N

Created 2 bonds  

> bond #2.2/GT:75@C #2.2/GT:76@N

Created 5 bonds  

> bond #2.2/GT:76@C #2.2/GT:77@N

Created 5 bonds  

> bond #2.2/GT:77@C #2.2/GT:78@N

Created 5 bonds  

> bond #2.2/GT:78@C #2.2/GT:79@N

Created 5 bonds  

> bond #2.2/GT:79@C #2.2/GT:80@N

Created 5 bonds  

> bond #2.2/GT:80@C #2.2/GT:81@N

Created 5 bonds  

> bond #2.2/GT:81@C #2.2/GT:82@N

Created 5 bonds  

> bond #2.2/GT:82@C #2.2/GT:83@N

Created 5 bonds  

> bond #2.2/GT:83@C #2.2/GT:84@N

Created 5 bonds  

> bond #2.2/GT:84@C #2.2/GT:85@N

Created 5 bonds  

> bond #2.2/GT:85@C #2.2/GT:86@N

Created 5 bonds  

> bond #2.2/GT:86@C #2.2/GT:87@N

Created 5 bonds  

> bond #2.2/GT:87@C #2.2/GT:88@N

Created 5 bonds  

> bond #2.2/GT:88@C #2.2/GT:89@N

Created 5 bonds  

> bond #2.2/GT:89@C #2.2/GT:90@N

Created 5 bonds  

> bond #2.2/GT:90@C #2.2/GT:91@N

Created 5 bonds  

> bond #2.2/GT:91@C #2.2/GT:92@N

Created 5 bonds  

> bond #2.2/GT:92@C #2.2/GT:93@N

Created 5 bonds  

> bond #2.2/GT:93@C #2.2/GT:94@N

Created 5 bonds  

> bond #2.2/GT:94@C #2.2/GT:95@N

Created 5 bonds  

> bond #2.2/GT:95@C #2.2/GT:96@N

Created 5 bonds  

> bond #2.2/GT:96@C #2.2/GT:97@N

Created 5 bonds  

> addh #2 hbond false

Summary of feedback from adding hydrogens to fixedModel #2.2  
---  
warnings | C-terminal fixedModel #2.2/GT SER 97 O does not look like carboxylate oxygen; cannot complete teminus  
Unknown hybridization for atoms (S4, S1, S3, S2) of residue type SF4; not
adding hydrogens to them  
Unknown hybridization for atoms (S4, S1, S3, S2) of residue type F3S; not
adding hydrogens to them  
notes | No usable SEQRES records for fixedModel (#2.2) chain AG; guessing termini instead  
No usable SEQRES records for fixedModel (#2.2) chain Ar; guessing termini
instead  
No usable SEQRES records for fixedModel (#2.2) chain I0; guessing termini
instead  
No usable SEQRES records for fixedModel (#2.2) chain Il; guessing termini
instead  
No usable SEQRES records for fixedModel (#2.2) chain Ix; guessing termini
instead  
86 messages similar to the above omitted  
Chain-initial residues that are actual N termini: fixedModel #2.2/AG PHE 18,
fixedModel #2.2/Ar LEU 23, fixedModel #2.2/I0 SER 160, fixedModel #2.2/Il TYR
26, fixedModel #2.2/Ix ASP 152, fixedModel #2.2/Iy THR 22, fixedModel #2.2/J6
THR 2, fixedModel #2.2/JI PRO 11, fixedModel #2.2/JJ MET 1, fixedModel #2.2/JN
ALA 2, fixedModel #2.2/Jw VAL 21, fixedModel #2.2/Jx LYS 11, fixedModel
#2.2/K5 ALA 14, fixedModel #2.2/KI THR 26, fixedModel #2.2/Ke ALA 44,
fixedModel #2.2/Kp PRO 53, fixedModel #2.2/Ks GLU 4, fixedModel #2.2/L3 VAL
52, fixedModel #2.2/LG TRP 20, fixedModel #2.2/LO TYR 37, fixedModel #2.2/LR
SER 78, fixedModel #2.2/LY PRO 182, fixedModel #2.2/M PRO 2, fixedModel
#2.2/Mg ILE 36, fixedModel #2.2/Mq SER 34, fixedModel #2.2/Mr THR 38,
fixedModel #2.2/NF LYS 30, fixedModel #2.2/NM TYR 82, fixedModel #2.2/Np MET
1, fixedModel #2.2/TB MET 18, fixedModel #2.2/Y MET 1, fixedModel #2.2/t0 THR
38, fixedModel #2.2/t1 THR 2, fixedModel #2.2/t2 TYR 37, fixedModel #2.2/t3
PHE 18, fixedModel #2.2/t4 LEU 23, fixedModel #2.2/t5 THR 26, fixedModel
#2.2/t6 MET 1, fixedModel #2.2/t7 MET 1, fixedModel #2.2/t8 VAL 21, fixedModel
#2.2/t9 ASP 152, fixedModel #2.2/ta MET 1, fixedModel #2.2/tb SER 160,
fixedModel #2.2/tc THR 22, fixedModel #2.2/td TYR 26, fixedModel #2.2/te GLU
4, fixedModel #2.2/tf ALA 2, fixedModel #2.2/tg PRO 182, fixedModel #2.2/R MET
1, fixedModel #2.2/A ALA 34, fixedModel #2.2/A0 PRO 204, fixedModel #2.2/AU
LYS 35, fixedModel #2.2/Ab GLU 206, fixedModel #2.2/Aj LYS 208, fixedModel
#2.2/Aq LYS 25, fixedModel #2.2/B ALA 23, fixedModel #2.2/BI ALA 23,
fixedModel #2.2/BK THR 37, fixedModel #2.2/BP GLY 22, fixedModel #2.2/C SER
85, fixedModel #2.2/C0 ILE 33, fixedModel #2.2/C1 ILE 33, fixedModel #2.2/C2
ILE 33, fixedModel #2.2/C3 ILE 33, fixedModel #2.2/C4 SER 34, fixedModel
#2.2/C5 ILE 33, fixedModel #2.2/C6 ILE 33, fixedModel #2.2/C7 ILE 33,
fixedModel #2.2/C8 ILE 33, fixedModel #2.2/C9 ILE 33, fixedModel #2.2/D TYR
18, fixedModel #2.2/D6 VAL 7, fixedModel #2.2/E PHE 33, fixedModel #2.2/E1 LEU
51, fixedModel #2.2/E4 GLN 35, fixedModel #2.2/Ek ASN 26, fixedModel #2.2/Eq
ASN 62, fixedModel #2.2/Es VAL 2, fixedModel #2.2/Ev GLY 3, fixedModel #2.2/F9
HIS 37, fixedModel #2.2/FF HIS 98, fixedModel #2.2/FH VAL 18, fixedModel
#2.2/FL MET 1, fixedModel #2.2/FO PHE 12, fixedModel #2.2/Fy PRO 60,
fixedModel #2.2/Fz VAL 58, fixedModel #2.2/GT ALA 6, fixedModel #2.2/IE LYS
26, fixedModel #2.2/IY SER 2, fixedModel #2.2/JC GLU 22, fixedModel #2.2/a TYR
3  
Chain-initial residues that are not actual N termini: fixedModel #2.2/JI GLU
259, fixedModel #2.2/K5 LYS 143, fixedModel #2.2/K5 ARG 299, fixedModel
#2.2/K5 LYS 338, fixedModel #2.2/K5 ILE 361, fixedModel #2.2/K5 GLU 490,
fixedModel #2.2/K5 MET 567, fixedModel #2.2/L3 TYR 94, fixedModel #2.2/L3 VAL
198, fixedModel #2.2/L3 VAL 312, fixedModel #2.2/NF ARG 189, fixedModel
#2.2/AU GLN 151, fixedModel #2.2/AU GLN 436, fixedModel #2.2/Ab THR 521,
fixedModel #2.2/BK GLN 151, fixedModel #2.2/BK VAL 437, fixedModel #2.2/D ILE
234, fixedModel #2.2/D6 VAL 63, fixedModel #2.2/E GLN 151, fixedModel #2.2/E
GLN 438, fixedModel #2.2/E1 ASP 217, fixedModel #2.2/FF MET 124, fixedModel
#2.2/IE VAL 199  
Chain-final residues that are actual C termini: fixedModel #2.2/R HIS 62,
fixedModel #2.2/A PRO 357, fixedModel #2.2/A0 LYS 685, fixedModel #2.2/AU VAL
574, fixedModel #2.2/Ab ARG 690, fixedModel #2.2/Aj HIS 690, fixedModel
#2.2/Aq GLN 187, fixedModel #2.2/B LYS 160, fixedModel #2.2/BI GLN 187,
fixedModel #2.2/BK VAL 574, fixedModel #2.2/BP GLN 187, fixedModel #2.2/C MET
349, fixedModel #2.2/C0 SER 106, fixedModel #2.2/C1 SER 106, fixedModel
#2.2/C2 SER 106, fixedModel #2.2/C3 SER 106, fixedModel #2.2/C4 SER 106,
fixedModel #2.2/C5 SER 106, fixedModel #2.2/C6 SER 106, fixedModel #2.2/C7 SER
106, fixedModel #2.2/C8 SER 106, fixedModel #2.2/C9 SER 106, fixedModel #2.2/D
VAL 258, fixedModel #2.2/D6 THR 70, fixedModel #2.2/E GLY 575, fixedModel
#2.2/E1 GLY 239, fixedModel #2.2/E4 GLY 203, fixedModel #2.2/Ek SER 103,
fixedModel #2.2/Eq TYR 145, fixedModel #2.2/Es HIS 136, fixedModel #2.2/Ev ALA
386, fixedModel #2.2/F9 GLN 103, fixedModel #2.2/FF PRO 174, fixedModel
#2.2/FH VAL 157, fixedModel #2.2/FL GLY 233, fixedModel #2.2/FO ALA 159,
fixedModel #2.2/Fy ALA 117, fixedModel #2.2/Fz VAL 105, fixedModel #2.2/GT SER
97, fixedModel #2.2/IE GLY 204, fixedModel #2.2/IY ASN 295, fixedModel #2.2/JC
GLU 183, fixedModel #2.2/a GLN 96  
Chain-final residues that are not actual C termini: fixedModel #2.2/AG SER
196, fixedModel #2.2/Ar TRP 118, fixedModel #2.2/I0 LYS 383, fixedModel
#2.2/Il GLU 104, fixedModel #2.2/Ix ILE 279, fixedModel #2.2/Iy GLN 115,
fixedModel #2.2/J6 PHE 199, fixedModel #2.2/JI LYS 491, fixedModel #2.2/JI PHE
252, fixedModel #2.2/JJ ILE 549, fixedModel #2.2/JN VAL 108, fixedModel
#2.2/Jw PHE 144, fixedModel #2.2/Jx ASP 124, fixedModel #2.2/K5 PRO 602,
fixedModel #2.2/K5 ILE 138, fixedModel #2.2/K5 GLU 268, fixedModel #2.2/K5 LEU
311, fixedModel #2.2/K5 VAL 354, fixedModel #2.2/K5 ALA 484, fixedModel
#2.2/K5 ARG 546, fixedModel #2.2/KI GLU 225, fixedModel #2.2/Ke LEU 138,
fixedModel #2.2/Kp GLU 224, fixedModel #2.2/Ks ALA 156, fixedModel #2.2/L3 ARG
325, fixedModel #2.2/L3 LEU 84, fixedModel #2.2/L3 GLY 117, fixedModel #2.2/L3
HIS 283, fixedModel #2.2/LG SER 123, fixedModel #2.2/LO LYS 342, fixedModel
#2.2/LR GLY 148, fixedModel #2.2/LY ALA 345, fixedModel #2.2/M PHE 103,
fixedModel #2.2/Mg ALA 250, fixedModel #2.2/Mq LYS 90, fixedModel #2.2/Mr LEU
147, fixedModel #2.2/NF SER 246, fixedModel #2.2/NF LEU 183, fixedModel
#2.2/NM MET 144, fixedModel #2.2/Np VAL 283, fixedModel #2.2/TB THR 81,
fixedModel #2.2/Y ILE 210, fixedModel #2.2/t0 LEU 147, fixedModel #2.2/t1 PHE
199, fixedModel #2.2/t2 LYS 342, fixedModel #2.2/t3 SER 196, fixedModel
#2.2/t4 TRP 118, fixedModel #2.2/t5 GLU 225, fixedModel #2.2/t6 ILE 549,
fixedModel #2.2/t7 VAL 283, fixedModel #2.2/t8 PHE 144, fixedModel #2.2/t9 ILE
279, fixedModel #2.2/ta ILE 210, fixedModel #2.2/tb LYS 383, fixedModel
#2.2/tc GLN 115, fixedModel #2.2/td GLU 104, fixedModel #2.2/te ALA 156,
fixedModel #2.2/tf VAL 108, fixedModel #2.2/tg ALA 345, fixedModel #2.2/AU LEU
139, fixedModel #2.2/AU ASP 430, fixedModel #2.2/Ab VAL 515, fixedModel
#2.2/BK GLY 138, fixedModel #2.2/BK ASP 430, fixedModel #2.2/D LYS 206,
fixedModel #2.2/D6 LEU 52, fixedModel #2.2/E LEU 139, fixedModel #2.2/E ALA
429, fixedModel #2.2/E1 GLU 123, fixedModel #2.2/FF TYR 118, fixedModel
#2.2/IE VAL 194  
Adding 'H' to fixedModel #2.2/JI GLU 259  
Adding 'H' to fixedModel #2.2/K5 LYS 143  
Adding 'H' to fixedModel #2.2/K5 ARG 299  
Adding 'H' to fixedModel #2.2/K5 LYS 338  
Adding 'H' to fixedModel #2.2/K5 ILE 361  
18 messages similar to the above omitted  
fixedModel #2.2/AG SER 196 is not terminus, removing H atom from 'C'  
fixedModel #2.2/Ar TRP 118 is not terminus, removing H atom from 'C'  
fixedModel #2.2/I0 LYS 383 is not terminus, removing H atom from 'C'  
fixedModel #2.2/Il GLU 104 is not terminus, removing H atom from 'C'  
fixedModel #2.2/Ix ILE 279 is not terminus, removing H atom from 'C'  
43 messages similar to the above omitted  
135029 hydrogens added  
  

Chain HM, residue 1 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Deleted the following atoms from residue ALA GT6: O, HC2, CA, HC1, HN3, HN4,
CB, HN2, HC4, HC5, HN5, HC, N, C, HN1, HC3  
Deleted the following atoms from residue PHE GT7: CE2, CE1, CA, O, C, CB, CZ,
CD1, CD2, HA, HE2, HE1, CG, N  

> delete ~#2/GT&#2

> delete ~#2/GT@C,N,CA&#2

Fetching CCD SER_LL_DHG from http://ligand-
expo.rcsb.org/reports/S/SER_LL_DHG/SER_LL_DHG.cif  
Fetching CCD CYS_LL_DHG from http://ligand-
expo.rcsb.org/reports/C/CYS_LL_DHG/CYS_LL_DHG.cif  

> close #1

> close #2

[deleted to fit within ticket limits]


> volume #2 level 0.192

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J436_002_volume_map_sharp_WITHSEQ/"

'/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
Computer/supercomplex/supercomplexV-
IV2-II/cryosparc_P43_J436_002_volume_map_sharp_WITHSEQ/' has no suffix  

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J436_002_volume_map_sharp.mrc"

Opened cryosparc_P43_J436_002_volume_map_sharp.mrc as #10, grid size
500,500,500, pixel 1.21, shown at level 0.109, step 2, values float32  

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J450_008_volume_map_sharp.mrc"

Opened cryosparc_P43_J450_008_volume_map_sharp.mrc as #11, grid size
500,500,500, pixel 1.21, shown at level 0.118, step 2, values float32  

> hide #!7 models

> hide #8 models

> hide #!9 models

> hide #3 models

> hide #!2 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> volume #10 level 0.1306

> volume #10 step 1

> volume #11 step 1

> volume #11 level 0.145

> volume #11 level 0.1676

> ui tool show "Hide Dust"

> surface dust #11 size 7.25

> volume #11 level 0.1766

> volume #11 level 0.1585

> color
> #1/Av,lx,Mr,LY,LO,Np,AG,KI,Ar,Jw,JN,J6,Y,JJ,Il,Iy,I0,Ks,AV,t9,t0,tg,t2,t7,t3,t5,t4,t8,tf,t1,ta,t6,td,tc,tb,te,Ix
> mediumvioletred

> color
> #1/A0,Ab,Aj,AU,E,BK,Aq,BI,BP,IE,IY,C0,C1,C2,C3,C4,C5,C6,C7,C8,C9,B,C,D,F9,FF,A,Es,Eq,Ek,Fy,Fz,FH,a,GT,FL,FO,E1,F9,E4,Ev,R,JC,D6,v0,v1,v2,v3,v4,v5,v6,v7,v8,v9,vA,vB,vC,vD,vE,vF,vG,vH,vI,vJ,vK,vL,vM,vN,vO,vP,vQ,vR,vS,vT,vU,vV,vW,vX,vY,vZ,va,vb,vc,vd,ve,vf,vg,vh
> limegreen

> color
> #1/Kp,K5,JI,NF,NM,L3,M,LR,Jx,Ke,Mq,LG,TB,Mg,r0,r1,r2,r3,r4,r5,r6,r7,r8,r9,rA,rB,rC,rD
> goldenrod

> hide #!11 models

> show #!11 models

> color zone #4 near #1

> color zone #11 near #1

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J436_002_volume_map_sharp_NOSEQ/lipidLayer/lipidLayer.mrc"

Opened lipidLayer.mrc as #12, grid size 500,500,500, pixel 1.21, shown at
level 9e-05, step 2, values float32  

> volume #12 level 0.0614 step 1

> surface dust #12 size 12.1

> color zone #11 near #1 distance 6

> color zone #11 near #1 distance 30

> hide #!1 models

> volume #12 level 0.06961

> volume #11 level 0.1766

> volume #11 level 0.1314

> save
> /Users/rafaelrocha/supercomplex/Manuscript/figures/figureA/supercomplexMapcolored.cxs

Taking snapshot of stepper: combination  

> set bgColor white

> camera ortho

> lighting soft

> lighting flat

[Repeated 1 time(s)]

> lighting soft

> lighting full

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> save
> /Users/rafaelrocha/supercomplex/Manuscript/figures/figureA/supercomplexMapcolored.cxs

Taking snapshot of stepper: combination  

> save /Users/rafaelrocha/Desktop/image1.png supersample 3

> lighting flat

> lighting soft

> save
> /Users/rafaelrocha/supercomplex/Manuscript/figures/figureA/supercomplexMapcoloredView1.cxs

Taking snapshot of stepper: combination  

——— End of log from Thu Mar 6 18:11:35 2025 ———

opened ChimeraX session  

> hide #!11 models

> show #!11 models

> hide #!12 models

> hide #11.1 models

> show #11.1 models

> show #!12 models

> hide #11.1 models

> hide #!11 models

> show #!11 models

> show #11.1 models

> ui tool show "Volume Viewer"

> volume #11 level 0.2041

> volume #11 level 0.2854

> volume #12 color #ffb2b2a5

> volume #12 color #ffb2b27f

> volume #12 color #ffb2b261

> volume #12 color #ffb2b253

> volume #12 color #fffb00

> volume #12 color #fffb004b

> volume #12 color #fffb001c

> volume #12 color #ff9300

> volume #12 color #ff930025

> close session

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J436_002_volume_map_sharp_NOSEQ/lipidLayer/lipidLayer.mrc"

Opened lipidLayer.mrc as #1, grid size 500,500,500, pixel 1.21, shown at level
9e-05, step 2, values float32  

> volume #1 level 0.0614 step 1

> surface dust #1 size 12.1

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J447_004_volume_map_sharp.mrc"

Opened cryosparc_P43_J447_004_volume_map_sharp.mrc as #2, grid size
500,500,500, pixel 1.21, shown at level 0.141, step 2, values float32  

> ui tool show "Volume Viewer"

> volume #2 level 0.2411

> volume #2 step 1

> volume #2 level 0.386

> volume #2 level 0.4222

> combine #2

No structures specified  

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J447_004_volume_map_sharp.mrc"

Opened cryosparc_P43_J447_004_volume_map_sharp.mrc as #3, grid size
500,500,500, pixel 1.21, shown at level 0.141, step 2, values float32  

> volume #3 step 1

> volume #3 level 0.422

> hide #!1 models

> show #!1 models

> select #3

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,25.967,0,1,0,-74.508,0,0,1,54.481

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.96347,0.21584,-0.15855,17.961,0.11114,-0.86087,-0.49654,586.03,-0.24367,0.46078,-0.85341,518.26

> undo

> view matrix models
> #3,0.79666,0.53908,-0.27336,3.7392,0.30967,0.024356,0.95053,-147.33,0.51907,-0.8419,-0.14754,479.71

> view matrix models
> #3,0.41525,0.8748,0.24958,-133.48,0.82548,-0.47763,0.30074,36.066,0.38229,0.081143,-0.92047,466.87

> view matrix models
> #3,0.92112,0.382,-0.074955,-42.746,0.3655,-0.91493,-0.17121,434.82,-0.13398,0.13031,-0.98238,620.91

> view matrix models
> #3,0.77637,0.50102,-0.38241,52.076,0.39703,-0.85997,-0.32065,451.97,-0.48951,0.097114,-0.86657,701.63

> ui mousemode right "move picked models"

> view matrix models
> #3,0.77637,0.50102,-0.38241,25.472,0.39703,-0.85997,-0.32065,553.28,-0.48951,0.097114,-0.86657,791.74

> view matrix models
> #3,0.77637,0.50102,-0.38241,48.552,0.39703,-0.85997,-0.32065,561.62,-0.48951,0.097114,-0.86657,784.76

> view matrix models
> #3,0.77637,0.50102,-0.38241,47.648,0.39703,-0.85997,-0.32065,558.97,-0.48951,0.097114,-0.86657,777.13

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.77258,0.48635,-0.40815,60.448,0.42424,-0.8737,-0.23805,531.51,-0.47237,0.01076,-0.88133,801.91

> ui mousemode right "translate selected atoms"

> ui mousemode right "translate selected models"

> undo

> redo

> view matrix models
> #3,0.77258,0.48635,-0.40815,60.729,0.42424,-0.8737,-0.23805,519.64,-0.47237,0.01076,-0.88133,788.01

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.7692,0.46542,-0.43784,76.393,0.45541,-0.87994,-0.1353,483.05,-0.44825,-0.095323,-0.88881,814.52

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.7692,0.46542,-0.43784,78.867,0.45541,-0.87994,-0.1353,475.67,-0.44825,-0.095323,-0.88881,816.66

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.76763,0.44829,-0.45801,90.16,0.47641,-0.87717,-0.060079,447.23,-0.42869,-0.17208,-0.88691,833.14

> view matrix models
> #3,0.72786,0.50151,-0.46766,88.772,0.53068,-0.84388,-0.079009,426.91,-0.43427,-0.19067,-0.88037,838.41

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.72786,0.50151,-0.46766,91.256,0.53068,-0.84388,-0.079009,427.89,-0.43427,-0.19067,-0.88037,834.48

> view matrix models
> #3,0.72786,0.50151,-0.46766,91.452,0.53068,-0.84388,-0.079009,427.05,-0.43427,-0.19067,-0.88037,836.48

> fitmap #3 inMap #2

Fit map cryosparc_P43_J447_004_volume_map_sharp.mrc in map
cryosparc_P43_J447_004_volume_map_sharp.mrc using 105968 points  
correlation = 0.4206, correlation about mean = 0.08093, overlap = 5552  
steps = 192, shift = 2.67, angle = 3.86 degrees  
  
Position of cryosparc_P43_J447_004_volume_map_sharp.mrc (#3) relative to
cryosparc_P43_J447_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.70495300 0.54639925 -0.45220476 78.64226718  
0.58474847 -0.80857250 -0.06541996 397.75796400  
-0.40138574 -0.21830804 -0.88951173 840.41486088  
Axis -0.92315911 -0.30685216 0.23155781  
Axis point 0.00000000 204.68777447 421.13573001  
Rotation angle (degrees) 175.25006938  
Shift along axis -0.04758910  
  

> select clear

> hide #!1 models

> select #3

2 models selected  

> view matrix models
> #3,0.70495,0.5464,-0.4522,94.095,0.58475,-0.80857,-0.06542,382.42,-0.40139,-0.21831,-0.88951,915.39

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.73095,0.52721,-0.43331,86.787,0.60816,-0.7913,0.063135,333.76,-0.30959,-0.30967,-0.89903,918.34

> view matrix models
> #3,0.74706,0.51616,-0.41891,81.241,0.61655,-0.7736,0.14634,302.31,-0.24854,-0.3676,-0.89616,916.83

> view matrix models
> #3,0.84605,0.51148,-0.15029,-22.991,0.53261,-0.82307,0.19717,327,-0.022852,-0.24687,-0.96878,835.81

> view matrix models
> #3,0.86191,0.50238,-0.068814,-48.189,0.50238,-0.82764,0.25023,322.04,0.068758,-0.25025,-0.96574,809.16

> ui mousemode right "translate selected atoms"

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.86191,0.50238,-0.068814,-70.521,0.50238,-0.82764,0.25023,319.92,0.068758,-0.25025,-0.96574,760.67

> view matrix models
> #3,0.86191,0.50238,-0.068814,-73.911,0.50238,-0.82764,0.25023,318.11,0.068758,-0.25025,-0.96574,779.72

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.82213,0.56703,0.050903,-115.61,0.54654,-0.81112,0.20827,312.28,0.15938,-0.1434,-0.97675,724.71

> view matrix models
> #3,0.71078,0.70337,0.0081739,-111.25,0.69421,-0.7033,0.15307,252.92,0.11342,-0.10313,-0.98818,729.48

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.71078,0.70337,0.0081739,-129.07,0.69421,-0.7033,0.15307,261.92,0.11342,-0.10313,-0.98818,702.76

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.77057,0.63617,0.038746,-135.37,0.63611,-0.77144,0.015606,338.34,0.039819,0.012621,-0.99913,693.12

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.77057,0.63617,0.038746,-132.87,0.63611,-0.77144,0.015606,340.39,0.039819,0.012621,-0.99913,714.15

> view matrix models
> #3,0.77057,0.63617,0.038746,-134.68,0.63611,-0.77144,0.015606,340.23,0.039819,0.012621,-0.99913,711.19

> view matrix models
> #3,0.77057,0.63617,0.038746,-134.98,0.63611,-0.77144,0.015606,340.2,0.039819,0.012621,-0.99913,710.77

> fitmap #3 inMap #2

Fit map cryosparc_P43_J447_004_volume_map_sharp.mrc in map
cryosparc_P43_J447_004_volume_map_sharp.mrc using 105968 points  
correlation = 0.8071, correlation about mean = 0.2903, overlap = 2.137e+04  
steps = 216, shift = 14.3, angle = 12.5 degrees  
  
Position of cryosparc_P43_J447_004_volume_map_sharp.mrc (#3) relative to
cryosparc_P43_J447_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.75695655 0.63234719 -0.16478417 -60.47340925  
0.63240914 -0.77238923 -0.05893719 369.54862535  
-0.16454628 -0.05959813 -0.98456722 774.04954826  
Axis -0.93727259 -0.33734815 0.08784255  
Axis point 0.00000000 195.73006534 384.15619129  
Rotation angle (degrees) 179.97979811  
Shift along axis 0.00800704  
  

> show #!1 models

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J450_008_volume_map_sharp.mrc"

Opened cryosparc_P43_J450_008_volume_map_sharp.mrc as #4, grid size
500,500,500, pixel 1.21, shown at level 0.118, step 2, values float32  

> volume #4 step 1

> volume #4 level 0.1273

> volume #4 level 0.2123

> volume #4 level 0.3541

> volume #4 level 0.3966

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/F1ATPsynthase/cryosparc_P43_J497_map_sharp_Zflipped.mrc"

Opened cryosparc_P43_J497_map_sharp_Zflipped.mrc as #5, grid size 270,270,270,
pixel 1.38, shown at level 0.00314, step 2, values float32  

> volume #5 step 1

> volume #5 level 0.3502

> select clear

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/CV-Full/cryosparc_P31_J281_004_volume_map_sharp--VC-
> Conf1.mrc"

Opened cryosparc_P31_J281_004_volume_map_sharp--VC-Conf1.mrc as #6, grid size
500,500,500, pixel 1.16, shown at level 0.0804, step 2, values float32  

> volume #6 step 1

> volume #6 level 0.4589

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> volume #6 level 0.3021

> close #6

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/F1ATPsynthase/cryosparc_P31_J253_004_volume_map_sharp_Zflipped.mrc"

Opened cryosparc_P31_J253_004_volume_map_sharp_Zflipped.mrc as #6, grid size
290,290,290, pixel 1.16, shown at level 0.174, step 2, values float32  

> volume #6 level 0.4743

> volume #6 step 1

> close #6

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/ATPsynthasedimer/cryosparc_P43_J459_005_volume_map_sharp_Zflipped.mrc"

Opened cryosparc_P43_J459_005_volume_map_sharp_Zflipped.mrc as #6, grid size
500,500,500, pixel 1.21, shown at level 0.163, step 2, values float32  

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/ATPsynthasedimer/cryosparc_P43_J460_map_sharp-
> EMHanced_Zflipped.mrc"

Opened cryosparc_P43_J460_map_sharp-EMHanced_Zflipped.mrc as #7, grid size
500,500,500, pixel 1.21, shown at level 0.000886, step 2, values float32  

> volume #6 step 1

> volume #7 step 1

> volume #7 level 0.171

> volume #6 level 0.2657

> volume #7 level 0.1876

> volume #7 level 0.337

> volume #6 level 0.7439

> close #6

> close #7

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/CV-Full/cryosparc_P31_J281_004_volume_map_sharp--VC-
> Conf1.mrc"

Opened cryosparc_P31_J281_004_volume_map_sharp--VC-Conf1.mrc as #6, grid size
500,500,500, pixel 1.16, shown at level 0.0804, step 2, values float32  

> volume #6 step 1

> volume #6 level 0.2534

> volume #6 level 0.2264

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/CV-Full/cryosparc_P31_J282_005_volume_map_sharp--CV-
> Conf2.mrc"

Opened cryosparc_P31_J282_005_volume_map_sharp--CV-Conf2.mrc as #7, grid size
500,500,500, pixel 1.16, shown at level 0.0834, step 2, values float32  

> volume #7 step 1

> volume #7 level 0.227

> volume #7 level 0.2114

> show #!5 models

> hide #!5 models

> show #!5 models

> close #5

> hide #!7 models

> show #!3 models

> show #!2 models

> volume #4 level 0.1685

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!3 models

> hide #!2 models

> hide #!4 models

> show #!4 models

> select #7

2 models selected  

> view matrix models #7,1,0,0,12.131,0,1,0,-91.07,0,0,1,-140.96

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.82248,-0.34893,-0.44918,315.63,0.55681,0.65514,0.51064,-320.52,0.1161,-0.6701,0.73313,111.48

> ui mousemode right "move picked models"

> view matrix models
> #7,0.82248,-0.34893,-0.44918,334.69,0.55681,0.65514,0.51064,-280.49,0.1161,-0.6701,0.73313,141.94

> view matrix models #4,1,0,0,0.56364,0,1,0,0.75168,0,0,1,-1.0537

> fitmap #7 inMap #4

Fit map cryosparc_P31_J282_005_volume_map_sharp--CV-Conf2.mrc in map
cryosparc_P43_J450_008_volume_map_sharp.mrc using 192946 points  
correlation = 0.6694, correlation about mean = 0.0529, overlap = 5747  
steps = 448, shift = 21.3, angle = 14.3 degrees  
  
Position of cryosparc_P31_J282_005_volume_map_sharp--CV-Conf2.mrc (#7)
relative to cryosparc_P43_J450_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.74949281 -0.45315914 -0.48260471 396.43284842  
0.62339907 0.72844591 0.28414809 -236.07059316  
0.22278713 -0.51382228 0.82846397 43.83383750  
Axis -0.52693276 -0.46579934 0.71089581  
Axis point 625.45642796 450.26334447 0.00000000  
Rotation angle (degrees) 49.21659294  
Shift along axis -67.77063796  
  

> hide #!4 models

> show #!4 models

> hide #!4 models

> volume #7 level 0.2301

> show #!4 models

> volume #4 level 0.4013

> volume #7 level 0.1708

> volume #4 level 0.3314

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.73981,-0.48272,-0.46868,404.55,0.63927,0.72154,0.26592,-232.91,0.20981,-0.49634,0.84239,37.649

> view matrix models
> #7,0.34084,-0.49781,-0.7975,620.54,0.93965,0.2072,0.27226,-174.83,0.029704,-0.84217,0.53839,277.48

> view matrix models
> #7,0.13127,-0.40136,-0.90646,685.71,0.91816,-0.29558,0.26384,-19.973,-0.37383,-0.86692,0.32972,463.79

> ui mousemode right "translate selected models"

> view matrix models
> #7,0.13127,-0.40136,-0.90646,687.33,0.91816,-0.29558,0.26384,9.6358,-0.37383,-0.86692,0.32972,484.21

> fitmap #7 inMap #4

Fit map cryosparc_P31_J282_005_volume_map_sharp--CV-Conf2.mrc in map
cryosparc_P43_J450_008_volume_map_sharp.mrc using 281244 points  
correlation = 0.6359, correlation about mean = -0.08187, overlap = 1.055e+04  
steps = 340, shift = 34.5, angle = 18.1 degrees  
  
Position of cryosparc_P31_J282_005_volume_map_sharp--CV-Conf2.mrc (#7)
relative to cryosparc_P43_J450_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.20417158 -0.63912338 -0.74150877 678.04765959  
0.84071522 -0.27357227 0.46728590 -57.13486252  
-0.50150959 -0.71880422 0.48146507 407.83172779  
Axis -0.62045988 -0.12554684 0.77412371  
Axis point 535.58044638 299.04488771 0.00000000  
Rotation angle (degrees) 107.09565300  
Shift along axis -97.81605804  
  

> show #!1 models

> show #!2 models

> show #!3 models

> show #!6 models

> hide #!6 models

> volume #7 level 0.2114

> ui mousemode right zoom

> ui mousemode right translate

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/CV-Full/cryosparc_P31_J281_004_volume_map_sharp--VC-
> Conf1.mrc"

Opened cryosparc_P31_J281_004_volume_map_sharp--VC-Conf1.mrc as #5, grid size
500,500,500, pixel 1.16, shown at level 0.0804, step 2, values float32  

> volume #5 level 0.1683

> volume #5 step 1

> select #4

2 models selected  

> show #!6 models

> hide #!6 models

> show #!6 models

> select #5

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #5,1,0,0,70.923,0,1,0,96.436,0,0,1,276.93

> volume #5 level 0.2711

> volume #5 level 0.3603

> close #5

> close #6

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/CV-Full/cryosparc_P31_J282_005_volume_map_sharp--CV-
> Conf2.mrc"

Opened cryosparc_P31_J282_005_volume_map_sharp--CV-Conf2.mrc as #5, grid size
500,500,500, pixel 1.16, shown at level 0.0834, step 2, values float32  

> volume #5 step 1

> volume #5 level 0.1975

> select #5

2 models selected  

> view matrix models #5,1,0,0,64.833,0,1,0,4.8039,0,0,1,369.26

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J450_008_volume_map_sharp.mrc"

Opened cryosparc_P43_J450_008_volume_map_sharp.mrc as #6, grid size
500,500,500, pixel 1.21, shown at level 0.118, step 2, values float32  

> select #6

2 models selected  

> volume #6 step 1

> volume #6 level 0.2123

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.86316,0.45836,-0.2118,-30.342,0.47569,-0.87885,0.036716,412.65,-0.16931,-0.13244,-0.97662,715.28

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.86316,0.45836,-0.2118,-24.375,0.47569,-0.87885,0.036716,423.76,-0.16931,-0.13244,-0.97662,800.74

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.86496,0.45863,-0.2037,-27.555,0.45628,-0.88773,-0.061243,463.19,-0.20892,-0.039971,-0.97712,784.83

> hide #!6 models

> show #!6 models

> hide #!4 models

> show #!4 models

> hide #!5 models

> show #!5 models

> hide #!3 models

> show #!3 models

> fitmap #6 inMap #3

Fit map cryosparc_P43_J450_008_volume_map_sharp.mrc in map
cryosparc_P43_J447_004_volume_map_sharp.mrc using 221510 points  
correlation = 0.714, correlation about mean = 0.05245, overlap = 1.496e+04  
steps = 248, shift = 10.1, angle = 12.2 degrees  
  
Position of cryosparc_P43_J450_008_volume_map_sharp.mrc (#6) relative to
cryosparc_P43_J447_004_volume_map_sharp.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99999418 -0.00128579 0.00313164 -0.29910969  
0.00127502 0.99999317 0.00344053 -1.58796252  
-0.00313605 -0.00343652 0.99998907 2.03625929  
Axis -0.71259782 0.64945647 0.26535003  
Axis point 0.00000000 612.69668537 410.29613482  
Rotation angle (degrees) 0.27647278  
Shift along axis -0.27784615  
  

> hide #!7 models

> hide #!6 models

> show #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> hide #!1 models

> view matrix models
> #6,0.74923,0.61838,-0.23718,-30.94,0.60241,-0.7851,-0.14397,409.47,-0.27524,-0.035008,-0.96074,791.9

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.74923,0.61838,-0.23718,-32.626,0.60241,-0.7851,-0.14397,410.01,-0.27524,-0.035008,-0.96074,784.28

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.75339,0.62751,-0.19656,-49.454,0.61874,-0.77769,-0.11119,392.56,-0.22263,-0.037853,-0.97417,773.75

> fitmap #6 inMap #3

Fit map cryosparc_P43_J450_008_volume_map_sharp.mrc in map
cryosparc_P43_J447_004_volume_map_sharp.mrc using 221510 points  
correlation = 0.7141, correlation about mean = 0.05247, overlap = 1.496e+04  
steps = 128, shift = 8.08, angle = 3.71 degrees  
  
Position of cryosparc_P43_J450_008_volume_map_sharp.mrc (#6) relative to
cryosparc_P43_J447_004_volume_map_sharp.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99999418 -0.00127223 0.00313848 -0.30333720  
0.00126145 0.99999319 0.00344021 -1.58259177  
-0.00314285 -0.00343624 0.99998905 2.03895294  
Axis -0.71244109 0.65078339 0.26250460  
Axis point 0.00000000 613.36055411 408.52504306  
Rotation angle (degrees) 0.27650932  
Shift along axis -0.27858001  
  

> show #!7 models

> select #7

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #7,0.20417,-0.63912,-0.74151,602.47,0.84072,-0.27357,0.46729,134.32,-0.50151,-0.7188,0.48147,843.12

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.96834,0.10523,-0.22638,-16.543,0.091003,-0.99321,-0.072431,749.6,-0.23247,0.049536,-0.97134,1004.4

> view matrix models
> #7,0.93499,-0.065573,-0.34856,84.248,-0.042069,-0.99633,0.074586,742.65,-0.35217,-0.055074,-0.93432,1059.6

> view matrix models
> #7,0.65701,-0.29226,-0.69493,347.87,-0.51928,-0.84369,-0.13612,908.37,-0.54652,0.4503,-0.70608,892.4

> view matrix models
> #7,0.69516,-0.52849,-0.48729,339.7,-0.63963,-0.14541,-0.7548,936.37,0.32805,0.83639,-0.43912,428.13

> ui mousemode right "translate selected models"

> view matrix models
> #7,0.69516,-0.52849,-0.48729,311.8,-0.63963,-0.14541,-0.7548,801.93,0.32805,0.83639,-0.43912,368.2

> view matrix models
> #7,0.69516,-0.52849,-0.48729,409.44,-0.63963,-0.14541,-0.7548,780.45,0.32805,0.83639,-0.43912,326

> view matrix models
> #7,0.69516,-0.52849,-0.48729,387.59,-0.63963,-0.14541,-0.7548,816.92,0.32805,0.83639,-0.43912,309

> view matrix models
> #7,0.69516,-0.52849,-0.48729,393.89,-0.63963,-0.14541,-0.7548,811.8,0.32805,0.83639,-0.43912,311.95

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.52227,-0.69327,-0.49659,498.03,-0.59514,0.12076,-0.7945,731.7,0.61077,0.71049,-0.34952,235.83

> view matrix models
> #7,0.59283,-0.71182,-0.37666,443.49,-0.46012,0.084473,-0.88383,731.12,0.66094,0.69727,-0.27745,201.35

> ui mousemode right "translate selected models"

> view matrix models
> #7,0.59283,-0.71182,-0.37666,452.99,-0.46012,0.084473,-0.88383,746.94,0.66094,0.69727,-0.27745,198.5

> view matrix models
> #7,0.59283,-0.71182,-0.37666,448,-0.46012,0.084473,-0.88383,745.59,0.66094,0.69727,-0.27745,198.11

> view matrix models
> #7,0.59283,-0.71182,-0.37666,449.18,-0.46012,0.084473,-0.88383,746.59,0.66094,0.69727,-0.27745,193.46

> hide #!6 models

> show #!6 models

> fitmap #7 inMap #6

Fit map cryosparc_P31_J282_005_volume_map_sharp--CV-Conf2.mrc in map
cryosparc_P43_J450_008_volume_map_sharp.mrc using 192946 points  
correlation = 0.6696, correlation about mean = -0.1143, overlap = 8244  
steps = 240, shift = 12.7, angle = 18.4 degrees  
  
Position of cryosparc_P31_J282_005_volume_map_sharp--CV-Conf2.mrc (#7)
relative to cryosparc_P43_J450_008_volume_map_sharp.mrc (#6) coordinates:  
Matrix rotation and translation  
0.20312660 -0.64110921 -0.74008022 678.37340089  
0.84039152 -0.27372523 0.46777853 -57.22143882  
-0.50247571 -0.71697535 0.48318182 406.92766566  
Axis -0.61970912 -0.12428377 0.77492848  
Axis point 534.97941779 298.49297001 0.00000000  
Rotation angle (degrees) 107.08010281  
Shift along axis -97.94265212  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.80615,-0.51629,-0.28909,312.98,-0.47941,-0.28351,-0.83054,846.23,0.34684,0.80813,-0.47606,320.82

> ui mousemode right "translate selected models"

> view matrix models
> #7,0.80615,-0.51629,-0.28909,314,-0.47941,-0.28351,-0.83054,842.31,0.34684,0.80813,-0.47606,318.18

> fitmap #7 inMap #6

Fit map cryosparc_P31_J282_005_volume_map_sharp--CV-Conf2.mrc in map
cryosparc_P43_J450_008_volume_map_sharp.mrc using 192946 points  
correlation = 0.6695, correlation about mean = -0.1143, overlap = 8244  
steps = 136, shift = 4.52, angle = 7.86 degrees  
  
Position of cryosparc_P31_J282_005_volume_map_sharp--CV-Conf2.mrc (#7)
relative to cryosparc_P43_J450_008_volume_map_sharp.mrc (#6) coordinates:  
Matrix rotation and translation  
0.20319129 -0.64113789 -0.74003761 678.34926801  
0.84034988 -0.27370815 0.46786332 -57.23537821  
-0.50251919 -0.71695621 0.48316499 406.94002707  
Axis -0.61973700 -0.12423744 0.77491362  
Axis point 534.98910619 298.47836436 0.00000000  
Rotation angle (degrees) 107.07815610  
Shift along axis -97.94399324  
  

> volume #6 level 0.3116

> volume #6 level 0.3399

> volume #7 level 0.2178

> volume #3 level 0.4595

> show #!5 models

> show #!4 models

> show #!2 models

> show #!1 models

> hide #!5 models

> show #!5 models

> undo

[Repeated 9 time(s)]

> redo

[Repeated 9 time(s)]

> select #7

3 models selected  

> select #5

2 models selected  

> view matrix models #5,1,0,0,37.731,0,1,0,22.534,0,0,1,-287.61

> hide #!4 models

> show #!4 models

> volume #6 level 0.331

> hide #!5 models

> show #!5 models

> hide #!6 models

> hide #!4 models

> show #!4 models

> hide #!5 models

> show #!5 models

> hide #!7 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> view matrix models #5,1,0,0,-6.9004,0,1,0,0.27774,0,0,1,-157.75

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.81449,-0.095544,-0.57226,232.73,-0.092415,0.95239,-0.29055,121.22,0.57277,0.28953,0.76688,-325.96

> view matrix models
> #5,0.74591,-0.34675,-0.56867,313.53,0.17663,0.92621,-0.33308,63.341,0.6422,0.148,0.75212,-306.38

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.74591,-0.34675,-0.56867,371.86,0.17663,0.92621,-0.33308,93.059,0.6422,0.148,0.75212,-244.44

> view matrix models
> #5,0.74591,-0.34675,-0.56867,420.05,0.17663,0.92621,-0.33308,-16.769,0.6422,0.148,0.75212,-307.58

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.21468,-0.5565,-0.80263,689.85,0.97618,0.14858,0.15808,-191.22,0.031279,-0.81745,0.57515,156.12

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.21468,-0.5565,-0.80263,698.48,0.97618,0.14858,0.15808,-97.393,0.031279,-0.81745,0.57515,251.95

> view matrix models
> #5,0.21468,-0.5565,-0.80263,678.12,0.97618,0.14858,0.15808,-91.44,0.031279,-0.81745,0.57515,265.51

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.087295,-0.063242,-0.99417,696.22,0.93149,-0.35895,-0.058958,109.08,-0.35313,-0.93121,0.090244,541.3

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.087295,-0.063242,-0.99417,670.32,0.93149,-0.35895,-0.058958,157.63,-0.35313,-0.93121,0.090244,577.07

> volume #5 level 0.2197

> view matrix models
> #5,-0.087295,-0.063242,-0.99417,593.99,0.93149,-0.35895,-0.058958,296.36,-0.35313,-0.93121,0.090244,517.77

> view matrix models
> #5,-0.087295,-0.063242,-0.99417,625.31,0.93149,-0.35895,-0.058958,194.28,-0.35313,-0.93121,0.090244,564.23

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.20527,-0.55257,-0.80779,623.56,0.68046,-0.51265,0.5236,126.33,-0.70344,-0.65715,0.27077,528.56

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.20527,-0.55257,-0.80779,630.67,0.68046,-0.51265,0.5236,41.913,-0.70344,-0.65715,0.27077,543.15

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.1695,-0.60205,-0.78026,647.25,0.89148,-0.24386,0.38183,-55.728,-0.42016,-0.76031,0.49538,416.19

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.1695,-0.60205,-0.78026,683.96,0.89148,-0.24386,0.38183,-45.575,-0.42016,-0.76031,0.49538,398.38

> view matrix models
> #5,0.1695,-0.60205,-0.78026,686.98,0.89148,-0.24386,0.38183,-43.945,-0.42016,-0.76031,0.49538,391.52

> fitmap #5 inMap #4

Fit map cryosparc_P31_J282_005_volume_map_sharp--CV-Conf2.mrc in map
cryosparc_P43_J450_008_volume_map_sharp.mrc using 179766 points  
correlation = 0.678, correlation about mean = -0.1153, overlap = 7826  
steps = 168, shift = 11.7, angle = 6.31 degrees  
  
Position of cryosparc_P31_J282_005_volume_map_sharp--CV-Conf2.mrc (#5)
relative to cryosparc_P43_J450_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.20298555 -0.64196204 -0.73937920 678.42792536  
0.84023995 -0.27352886 0.46816534 -57.38104789  
-0.50278593 -0.71628674 0.48387974 406.55778158  
Axis -0.61947637 -0.12373987 0.77520157  
Axis point 534.79686498 298.26528894 0.00000000  
Rotation angle (degrees) 107.05753086  
Shift along axis -98.00551600  
  

> show #!3 models

> show #!2 models

> show #!1 models

> show #!6 models

> show #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> hide #!7 models

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J436_002_volume_map_sharp_NOSEQ/lipidLayer/lipidLayer.mrc"

Opened lipidLayer.mrc as #8, grid size 500,500,500, pixel 1.21, shown at level
9e-05, step 2, values float32  

> volume #8 level 0.0614 step 1

> surface dust #8 size 12.1

> saelect #8

Unknown command: saelect #8  

> select #8

2 models selected  

> view matrix models #8,1,0,0,8.9036,0,1,0,123.29,0,0,1,230.69

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.51648,0.74645,-0.4196,47.247,0.71151,-0.64674,-0.27474,501.2,-0.47645,-0.15665,-0.86513,975.18

> ui mousemode right "translate selected models"

> view matrix models
> #8,0.51648,0.74645,-0.4196,66.848,0.71151,-0.64674,-0.27474,382.75,-0.47645,-0.15665,-0.86513,848.69

> show #!2 models

> hide #!2 models

> show #!2 models

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.8511,0.41466,-0.32202,43.997,0.39896,-0.90951,-0.11672,498.6,-0.34128,-0.029127,-0.93951,796.29

> view matrix models
> #8,0.7599,0.59375,-0.26459,-1.6871,0.59539,-0.79911,-0.083268,401.69,-0.26088,-0.09426,-0.96076,800.05

> ui mousemode right "translate selected models"

> view matrix models
> #8,0.7599,0.59375,-0.26459,-16.725,0.59539,-0.79911,-0.083268,396.61,-0.26088,-0.09426,-0.96076,799.17

> fitmap #8 inMap #1

Fit map lipidLayer.mrc in map lipidLayer.mrc using 472796 points  
correlation = 0.6805, correlation about mean = 0.5513, overlap = 8188  
steps = 276, shift = 4.17, angle = 6 degrees  
  
Position of lipidLayer.mrc (#8) relative to lipidLayer.mrc (#1) coordinates:  
Matrix rotation and translation  
0.75849569 0.62889167 -0.17081965 -57.74503051  
0.62888068 -0.77509304 -0.06115366 372.28139318  
-0.17086017 -0.06104040 -0.98340265 775.82372383  
Axis 0.93765443 0.33544803 -0.09098785  
Axis point 0.00000000 196.45741231 385.11613292  
Rotation angle (degrees) 179.99653959  
Shift along axis 0.14564814  
  

> hide #!1 models

> show #!1 models

> hide #!2 models

> vop add #8 to #1

> volume add #8 to #1

Expected a keyword  

> vop add #8,1 onGrid #1

Opened volume sum as #9, grid size 500,500,500, pixel 1.21, shown at step 1,
values float32  

> volume #9 level 0.08976

> surface dust #9 size 12.1

> show #!6 models

> show #!7 models

> show #!5 models

> show #!4 models

> show #!3 models

> show #!2 models

> show #!1 models

> hide #!1 models

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J246_007_volume_map_sharp_Zflip/superComplexConsolidatedV8.cif"

Summary of feedback from opening
/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
Computer/supercomplex/supercomplexV-
IV2-II/cryosparc_P43_J246_007_volume_map_sharp_Zflip/superComplexConsolidatedV8.cif  
---  
warnings | Unknown polymer entity '1' on line 2257  
Unknown polymer entity '2' on line 7589  
Unknown polymer entity '3' on line 14908  
Unknown polymer entity '4' on line 17767  
Unknown polymer entity '5' on line 26028  
59 messages similar to the above omitted  
Atom H5' is not in the residue template for ATP /AU:2000  
Atom H5' is not in the residue template for ATP /E:2000  
Atom H61 is not in the residue template for LPP /I0:1000  
Atom HO1 is not in the residue template for CDL /JJ:2000  
Atom HO1 is not in the residue template for CDL /Jw:1000  
Atom H3 is not in the residue template for 3PE /LG:1000  
Atom H3 is not in the residue template for 3PE /LO:1000  
Atom H61 is not in the residue template for LPP /LY:1000  
Atom H3 is not in the residue template for 3PE /Np:1001  
Too many hydrogens missing from residue template(s) to warn about  
Atom OMA is not in the residue template for HEM /HM:1  
Atom C13 is not in the residue template for HE9 /HM:1  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for superComplexConsolidatedV8.cif #10  
---  
Chain | Description  
A | No description available  
A0 | No description available  
AG t3 | No description available  
AU | No description available  
Ab | No description available  
Aj | No description available  
Aq | No description available  
Ar t4 | No description available  
B | No description available  
BI | No description available  
BK | No description available  
BP | No description available  
C | No description available  
C0 C1 C2 C3 C5 C6 C7 C8 C9 | No description available  
C4 | No description available  
D | No description available  
D6 | No description available  
E | No description available  
E1 | No description available  
E4 | No description available  
Ek | No description available  
Eq | No description available  
Es | No description available  
Ev | No description available  
F9 | No description available  
FF | No description available  
FH | No description available  
FL | No description available  
FO | No description available  
Fy | No description available  
Fz | No description available  
GT | No description available  
I0 tb | No description available  
IE | No description available  
IY | No description available  
Il td | No description available  
Ix t9 | No description available  
Iy tc | No description available  
J6 t1 | No description available  
JC | No description available  
JI | No description available  
JJ t6 | No description available  
JN tf | No description available  
Jw t8 | No description available  
Jx | No description available  
K5 | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial  
KI t5 | No description available  
Ke | No description available  
Kp | No description available  
Ks te | No description available  
L3 | Uncharacterized protein  
LG | No description available  
LO t2 | No description available  
LR | No description available  
LY tg | No description available  
M | No description available  
Mg | No description available  
Mq | No description available  
Mr t0 | No description available  
NF | No description available  
NM | No description available  
Np t7 | No description available  
R | No description available  
TB | No description available  
Y ta | No description available  
a | No description available  
  

> hide #!10 models

> show #!10 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> close #10

> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J246_007_volume_map_sharp_Zflip/supercomplexFullV1.cif"

Summary of feedback from opening
/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
Computer/supercomplex/supercomplexV-
IV2-II/cryosparc_P43_J246_007_volume_map_sharp_Zflip/supercomplexFullV1.cif  
---  
warnings | Unknown polymer entity '3' on line 16278  
Unknown polymer entity '4' on line 21610  
Unknown polymer entity '5' on line 28929  
Unknown polymer entity '6' on line 31788  
Unknown polymer entity '7' on line 40049  
59 messages similar to the above omitted  
Atom H5' is not in the residue template for ATP /AU:2000  
Atom H5' is not in the residue template for ATP /E:2000  
Atom H61 is not in the residue template for LPP /I0:1000  
Atom HO1 is not in the residue template for CDL /JJ:2000  
Atom HO1 is not in the residue template for CDL /Jw:1000  
Atom H3 is not in the residue template for 3PE /LG:1000  
Atom H3 is not in the residue template for 3PE /LO:1000  
Atom H61 is not in the residue template for LPP /LY:1000  
Atom H3 is not in the residue template for 3PE /Np:1001  
Too many hydrogens missing from residue template(s) to warn about  
Atom OMA is not in the residue template for HEM /HM:1  
Atom C13 is not in the residue template for HE9 /HP:1  
Atom C13 is not in the residue template for HE9 /HM:1  
Atom OMA is not in the residue template for HEM /HP:1  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for supercomplexFullV1.cif #10  
---  
Chain | Description  
A vQ | No description available  
A0 v0 | No description available  
AG t3 | No description available  
AU v3 | No description available  
Ab v1 | No description available  
Aj v2 | No description available  
Aq v6 | No description available  
Ar t4 | No description available  
B vL | No description available  
BI v7 | No description available  
BK v5 | No description available  
BP v8 | No description available  
C vM | No description available  
C0 C1 C2 C3 C5 C6 C7 C8 C9 vB vC vD vE vG vH vI vJ vK | No description available  
C4 vF | No description available  
D vN | No description available  
D6 vh | No description available  
E v4 | No description available  
E1 vb | No description available  
E4 vd | No description available  
Ek vT | No description available  
Eq vS | No description available  
Es vR | No description available  
Ev ve | No description available  
F9 vO | No description available  
FF vP | No description available  
FH vW | No description available  
FL vZ | No description available  
FO va | No description available  
Fy vU | No description available  
Fz vV | No description available  
GT vY | No description available  
I0 tb | No description available  
IE v9 | No description available  
IY vA | No description available  
Il td | No description available  
Ix t9 | No description available  
Iy tc | No description available  
J6 t1 | No description available  
JC vg | No description available  
JI r2 | No description available  
JJ t6 | No description available  
JN tf | No description available  
Jw t8 | No description available  
Jx r8 | No description available  
K5 r1 | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial  
KI t5 | No description available  
Ke r9 | No description available  
Kp r0 | No description available  
Ks te | No description available  
L3 r5 | Uncharacterized protein  
LG rB | No description available  
LO t2 | No description available  
LR r7 | No description available  
LY tg | No description available  
M r6 | No description available  
Mg rD | No description available  
Mq rA | No description available  
Mr t0 | No description available  
NF r3 | No description available  
NM r4 | No description available  
Np t7 | No description available  
R vf | No description available  
TB rC | No description available  
Y ta | No description available  
a vX | No description available  
  

> hide atoms

> show cartoons

> color #10/Kp,K5,JI,NF,NM,L3,M,LR,Jx,Ke,Mq,LG,TB,Mg lightgreen

> color #10/r0,r1,r2,r3,r4,r5,r6,r7,r8,r9,rA,rB,rC,rD springgreen

> color #10/Av,lx,Mr,LY,LO,Np,AG,KI,Ar,Jw,JN,J6,Y,JJ,Il,Iy,I0,Ks,Ix darkred

> color #10/AV,t9,t0,tg,t2,t7,t3,t5,t4,t8,tf,t1,ta,t6,td,tc,tb,te
> palevioletred

> color
> #10/A0,Ab,Aj,AU,E,BK,Aq,BI,BP,IE,IY,C0,C1,C2,C3,C4,C5,C6,C7,C8,C9,B,C,D,F9,FF,A,Es,Eq,Ek,Fy,Fz,FH,a,GT,FL,FO,E1,F9,E4,Ev,R,JC,D6
> darkcyan

> color
> #10/v0,v1,v2,v3,v4,v5,v6,v7,v8,v9,vA,vB,vC,vD,vE,vF,vG,vH,vI,vJ,vK,vL,vM,vN,vO,vP,vQ,vR,vS,vT,vU,vV,vW,vX,vY,vZ,va,vb,vc,vd,ve,vf,vg,vh
> cyan

> hide #!9 models

> color #10/r0,r1,r2,r3,r4,r5,r6,r7,r8,r9,rA,rB,rC,rD sea green

> color #10/r0,r1,r2,r3,r4,r5,r6,r7,r8,r9,rA,rB,rC,rD forestgreen

> color
> #10/v0,v1,v2,v3,v4,v5,v6,v7,v8,v9,vA,vB,vC,vD,vE,vF,vG,vH,vI,vJ,vK,vL,vM,vN,vO,vP,vQ,vR,vS,vT,vU,vV,vW,vX,vY,vZ,va,vb,vc,vd,ve,vf,vg,vh
> darkcyan

> color
> #10/A0,Ab,Aj,AU,E,BK,Aq,BI,BP,IE,IY,C0,C1,C2,C3,C4,C5,C6,C7,C8,C9,B,C,D,F9,FF,A,Es,Eq,Ek,Fy,Fz,FH,a,GT,FL,FO,E1,F9,E4,Ev,R,JC,D6
> cyan

> color #10/AV,t9,t0,tg,t2,t7,t3,t5,t4,t8,tf,t1,ta,t6,td,tc,tb,te darkred

> color #10/Av,lx,Mr,LY,LO,Np,AG,KI,Ar,Jw,JN,J6,Y,JJ,Il,Iy,I0,Ks,Ix pale
> violet red

> show #!9 models

> color #9 goldenrod

> transparency #9.1 50

> camera ortho

> cofr showPivot false

> lighting soft

> lighting depthCue false

> set bgColor white

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> show #!6 models

> show #!7 models

> show #!8 models

> hide #!8 models

> hide #!1 models

> color zone #2-7 near #10

> hide #!10 models

> color zone #2-7 near #10 distance 10

> color zone #2-7 near #10 distance 30

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> volume #2 level 0.5034

> color zone #2-7 near #10 distance 0

> volume #2 level 0.2723

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> volume #3 level 0.4282

> volume #3 level 0.272

> hide #!5 models

> show #!5 models

> volume #5 level 0.1785

> volume #5 level 0.1848

> hide #!6 models

> show #!6 models

> volume #6 level 0.185

> undo

> volume #7 level 185

> undo

[Repeated 1 time(s)]

> redo

[Repeated 2 time(s)]

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> volume #7 level 0.245

> volume #7 level 185

> volume #7 level 0.2228

> volume #7 level 0.1943

> volume #7 level 0.185

> hide #!4 models

> show #!4 models

> hide #!6 models

> show #!6 models

> volume #6 level 0.331

> surface dust #2-7 size 12.1

> hide #!4 models

> show #!4 models

> molmap

Missing or invalid "atoms" argument: empty atom specifier  

> molmap #10 resolution 5

Missing or invalid "resolution" argument: Expected a number  

> molmap #10 5

Opened supercomplexFullV1.cif map 5 as #11, grid size 164,207,299, pixel 1.67,
shown at level 0.111, step 1, values float32  

> close #11

> molmap #10/Av,lx,Mr,LY,LO,Np,AG,KI,Ar,Jw,JN,J6,Y,JJ,Il,Iy,I0,Ks,Ix 5

Opened supercomplexFullV1.cif map 5 as #11, grid size 119,103,83, pixel 1.67,
shown at level 0.116, step 1, values float32  

> vop

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!3 models

> show #!3 models

> hide #!4 models

> hide #!6 models

> hide #!7 models

> hide #!9 models

> hide #!3 models

> show #!3 models

> hide #!5 models

> vop subtract #3 #11

Opened volume difference as #12, grid size 500,500,500, pixel 1.21, shown at
step 1, values float32  

> volume #12 level 0.4582

> show #!2 models

> rename #11 fakeComplexIVA

> molmap #10/AV,t9,t0,tg,t2,t7,t3,t5,t4,t8,tf,t1,ta,t6,td,tc,tb,te 5

Opened supercomplexFullV1.cif map 5 as #13, grid size 129,98,83, pixel 1.67,
shown at level 0.112, step 1, values float32  

> rename #12 fakeComplexIVB

> hide #!2 models

> show #!2 models

> show #!3 models

> hide #!3 models

> vop subtract #2 #12

Opened volume difference as #14, grid size 500,500,500, pixel 1.21, shown at
step 1, values float32  

> volume #14 level 0.3924

> volume #14 level 0.401

> hide #!13 models

> show #!12 models

> volume #14 level 0.272

> volume #14 level 0.3749

> volume #14 level 0.3063

> volume #12 level 0.306

> show #!4 models

> hide #!4 models

> show #!4 models

> show #!5 models

> show #!10 models

> hide #!12 models

> hide #!14 models

> hide #!5 models

> hide #!4 models

> info chains sel

chain id /A chain_id A  
chain id /C3 chain_id C3  
chain id /C4 chain_id C4  
chain id /E1 chain_id E1  
chain id /E4 chain_id E4  
chain id /Ek chain_id Ek  
chain id /Eq chain_id Eq  
chain id /Es chain_id Es  
chain id /Ev chain_id Ev  
chain id /F9 chain_id F9  
chain id /FF chain_id FF  
chain id /FH chain_id FH  
chain id /FL chain_id FL  
chain id /FO chain_id FO  
chain id /Fy chain_id Fy  
chain id /Fz chain_id Fz  
chain id /GT chain_id GT  
chain id /LR chain_id LR  
chain id /R chain_id R  
chain id /a chain_id a  
chain id /t1 chain_id t1  
chain id /ta chain_id ta  
chain id /tb chain_id tb  
chain id /tc chain_id tc  
chain id /td chain_id td  
chain id /tg chain_id tg  

> select
> #10/A,C3,C4,E1,E4,Ek,Eq,Es,Ev,F9,FF,FH,FL,FO,Fy,Fz,GT,LR,R,a,t1,ta,tb,tc,td,tg

60515 atoms, 61309 bonds, 2 pseudobonds, 3469 residues, 2 models selected  

> show #!6 models

> show #!5 models

> show #!4 models

> show #!7 models

> hide #!6 models

> hide #!7 models

> hide #!10 models

> volume #4 level 0.2333

> hide #!4 models

> ui tool show "Map Eraser"

> select #15

1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #15,1,0,0,251.93,0,1,0,306.79,0,0,1,228.72

> view matrix models #15,1,0,0,224.86,0,1,0,291.43,0,0,1,244.07

> view matrix models #15,1,0,0,219.15,0,1,0,288.03,0,0,1,247.57

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> volume #4 level 0.331

> hide #!4 models

> view matrix models #15,1,0,0,214.01,0,1,0,278.94,0,0,1,249.69

> view matrix models #15,1,0,0,203.93,0,1,0,263.63,0,0,1,250.09

> view matrix models #15,1,0,0,205.46,0,1,0,264.04,0,0,1,243.7

> volume erase #5 center 205.46,264.04,243.7 radius 26.39

Opened cryosparc_P31_J282_005_volume_map_sharp--CV-Conf2.mrc copy as #16, grid
size 500,500,500, pixel 1.16, shown at step 1, values float32  

> view matrix models #15,1,0,0,225.37,0,1,0,292.43,0,0,1,235.5

> volume erase #16 center 225.37,292.43,235.5 radius 26.39

> view matrix models #15,1,0,0,223.65,0,1,0,289.29,0,0,1,262.22

> view matrix models #15,1,0,0,219.65,0,1,0,282.04,0,0,1,273.28

> volume erase #16 center 219.65,282.04,273.28 radius 26.39

> view matrix models #15,1,0,0,259.73,0,1,0,297.14,0,0,1,261.24

> view matrix models #15,1,0,0,250.68,0,1,0,274.62,0,0,1,216.07

> view matrix models #15,1,0,0,248.31,0,1,0,275.61,0,0,1,218.05

> view matrix models #15,1,0,0,244.26,0,1,0,273.34,0,0,1,219.01

> volume erase #16 center 244.26,273.34,219.01 radius 26.39

> view matrix models #15,1,0,0,250.85,0,1,0,304.4,0,0,1,246.09

> view matrix models #15,1,0,0,250.95,0,1,0,286.74,0,0,1,249.52

> view matrix models #15,1,0,0,259.2,0,1,0,287.87,0,0,1,241.85

> view matrix models #15,1,0,0,259.23,0,1,0,287.42,0,0,1,241.84

> volume erase #16 center 259.23,287.42,241.84 radius 26.39

> view matrix models #15,1,0,0,266.27,0,1,0,296.97,0,0,1,280.79

> view matrix models #15,1,0,0,265.78,0,1,0,289.13,0,0,1,274.58

> view matrix models #15,1,0,0,271.73,0,1,0,284.05,0,0,1,275.03

> volume erase #16 center 271.73,284.05,275.03 radius 26.39

> view matrix models #15,1,0,0,274.79,0,1,0,283.17,0,0,1,263.88

> view matrix models #15,1,0,0,274.9,0,1,0,283.88,0,0,1,263.85

> view matrix models #15,1,0,0,274.88,0,1,0,285.72,0,0,1,263.92

> volume erase #16 center 274.88,285.72,263.92 radius 26.39

> view matrix models #15,1,0,0,246.41,0,1,0,285.25,0,0,1,282.45

> view matrix models #15,1,0,0,249.09,0,1,0,287.76,0,0,1,269.76

> volume erase #16 center 249.09,287.76,269.76 radius 26.39

> view matrix models #15,1,0,0,266.24,0,1,0,310.99,0,0,1,228.03

> view matrix models #15,1,0,0,255.69,0,1,0,311.64,0,0,1,231.63

> volume erase #16 center 255.69,311.64,231.63 radius 26.39

> show #!4 models

> view matrix models #15,1,0,0,304.6,0,1,0,295.09,0,0,1,220.32

> view matrix models #15,1,0,0,277.06,0,1,0,299.44,0,0,1,244.74

> view matrix models #15,1,0,0,292.27,0,1,0,298.59,0,0,1,236.39

> view matrix models #15,1,0,0,291.29,0,1,0,298.58,0,0,1,236.87

> hide #!4 models

> volume erase #16 center 291.29,298.58,236.87 radius 26.39

> view matrix models #15,1,0,0,289.43,0,1,0,293.37,0,0,1,260.33

> view matrix models #15,1,0,0,306.87,0,1,0,281.12,0,0,1,266.12

> volume erase #16 center 306.87,281.12,266.12 radius 26.39

> view matrix models #15,1,0,0,291.8,0,1,0,266.72,0,0,1,284.29

> view matrix models #15,1,0,0,285.06,0,1,0,269.74,0,0,1,287.74

> volume erase #16 center 285.06,269.74,287.74 radius 26.39

> view matrix models #15,1,0,0,282.2,0,1,0,297.97,0,0,1,232.7

> view matrix models #15,1,0,0,282.45,0,1,0,293.2,0,0,1,232.67

> view matrix models #15,1,0,0,284.09,0,1,0,290.61,0,0,1,230.55

> volume erase #16 center 284.09,290.61,230.55 radius 26.39

> view matrix models #15,1,0,0,260.13,0,1,0,308.58,0,0,1,211.48

> view matrix models #15,1,0,0,267.53,0,1,0,305.2,0,0,1,211.48

> view matrix models #15,1,0,0,269.8,0,1,0,304.44,0,0,1,205.53

> volume erase #16 center 269.8,304.44,205.53 radius 26.39

> view matrix models #15,1,0,0,243.33,0,1,0,297.59,0,0,1,201.82

> volume erase #16 center 243.33,297.59,201.82 radius 26.39

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!16 models

> show #!16 models

> show #!5 models

> hide #!5 models

> vop add #16

Opened cryosparc_P31_J282_005_volume_map_sharp--CV-Conf2.mrc copy resampled as
#17, grid size 500,500,500, pixel 1.16, shown at step 1, values float32  

> show #!16 models

> hide #15 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!16 models

> hide #!17 models

> show #!17 models

> show #!16 models

> hide #!17 models

> show #!17 models

> show #!7 models

> select #17

2 models selected  

> view matrix models
> #17,0.20299,-0.64196,-0.73938,720.88,0.84024,-0.27353,0.46817,-13.756,-0.50279,-0.71629,0.48388,617.69

> ui mousemode right "rotate selected models"

> view matrix models
> #17,0.13895,-0.65367,-0.74392,745.67,0.21861,0.75292,-0.62075,191,0.96587,-0.076371,0.24752,37.313

> view matrix models
> #17,0.35397,-0.7908,-0.49934,649.93,-0.45588,0.3203,-0.83041,580.75,0.81663,0.52158,-0.24713,51.654

> ui mousemode right "translate selected models"

> view matrix models
> #17,0.35397,-0.7908,-0.49934,636.57,-0.45588,0.3203,-0.83041,690.16,0.81663,0.52158,-0.24713,176.51

> view matrix models
> #17,0.35397,-0.7908,-0.49934,588.21,-0.45588,0.3203,-0.83041,641.57,0.81663,0.52158,-0.24713,205.62

> ui mousemode right "rotate selected models"

> view matrix models
> #17,0.78307,-0.49664,-0.37437,337.27,-0.55273,-0.27977,-0.785,825.9,0.28513,0.82163,-0.49358,357.47

> ui mousemode right "translate selected models"

> view matrix models
> #17,0.78307,-0.49664,-0.37437,331.11,-0.55273,-0.27977,-0.785,852.5,0.28513,0.82163,-0.49358,334.85

> ui mousemode right "rotate selected models"

> view matrix models
> #17,0.82938,-0.46514,-0.30946,290.37,-0.47995,-0.30969,-0.82082,847.18,0.28596,0.8293,-0.4801,328.87

> ui mousemode right "translate selected models"

> view matrix models
> #17,0.82938,-0.46514,-0.30946,293.43,-0.47995,-0.30969,-0.82082,843.84,0.28596,0.8293,-0.4801,329.17

> hide #!16 models

> show #!16 models

> fitmap #17 inMap #7

Fit map cryosparc_P31_J282_005_volume_map_sharp--CV-Conf2.mrc copy resampled
in map cryosparc_P31_J282_005_volume_map_sharp--CV-Conf2.mrc using 209698
points  
correlation = 1, correlation about mean = 1, overlap = 2.452e+04  
steps = 104, shift = 6.07, angle = 3.74 degrees  
  
Position of cryosparc_P31_J282_005_volume_map_sharp--CV-Conf2.mrc copy
resampled (#17) relative to cryosparc_P31_J282_005_volume_map_sharp--CV-
Conf2.mrc (#7) coordinates:  
Matrix rotation and translation  
0.99999999 0.00001502 -0.00001400 -0.00079880  
-0.00001502 0.99999999 -0.00001834 0.00851721  
0.00001401 0.00001833 1.00000000 -0.00699235  
Axis 0.66597422 -0.50879330 -0.54553434  
Axis point 0.00000000 412.65530310 435.38412340  
Rotation angle (degrees) 0.00157735  
Shift along axis -0.00105091  
  

> hide #!7 models

> hide #!4 models

> show #15 models

> hide #15 models

> show #15 models

> hide #!16 models

> show #!16 models

> show #!2 models

> show #!3 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!4 models

> hide #15 models

> show #!5 models

> hide #!5 models

> show #!6 models

> show #!7 models

> hide #!7 models

> show #!8 models

> hide #!8 models

> show #!9 models

> show #!10 models

> hide #!10 models

> show #!13 models

> hide #!13 models

> show #!14 models

> hide #!14 models

> show #!14 models

> show #!13 models

> hide #!13 models

> show #!11 models

> hide #!11 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!14 models

> show #!14 models

> show #!13 models

> hide #!13 models

> rename #13 fakeComplexIVB

> rename #12 volumeDifference

> surface dust #4,6,12,14,16,17 size 12.1

> hide #!17 models

> hide #!16 models

> hide #!14 models

> hide #!12 models

> hide #!9 models

> show #!9 models

> hide #!6 models

> hide #!4 models

> hide #!9 models

> show #!10 models

> select #10&ligand

11879 atoms, 11905 bonds, 78 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 11879 atom styles  

> select #10&±ligand

Expected an objects specifier or a keyword  

> select #10&~ligand

432885 atoms, 438033 bonds, 30 pseudobonds, 27212 residues, 2 models selected  

> hide sel cartoons

> select up

114 atoms, 117 bonds, 1 residue, 1 model selected  

> select up

228 atoms, 234 bonds, 3 residues, 1 model selected  

> select up

444764 atoms, 449938 bonds, 27280 residues, 1 model selected  

> select clear

> select up

114 atoms, 117 bonds, 1 residue, 1 model selected  

> color sel dark red

> select up

114 atoms, 117 bonds, 1 residue, 1 model selected  

> color sel dark red

> select up

114 atoms, 117 bonds, 1 residue, 1 model selected  

> color sel dark red

> select up

71 atoms, 74 bonds, 1 residue, 1 model selected  

> color sel dark red

> select up

43 atoms, 42 bonds, 1 residue, 1 model selected  

> color sel dark red

> select up

114 atoms, 117 bonds, 1 residue, 1 model selected  

> select up

114 atoms, 117 bonds, 1 residue, 1 model selected  

> color sel pale violet red

> select up

114 atoms, 117 bonds, 1 residue, 1 model selected  

> color sel pale violet red

> select up

114 atoms, 117 bonds, 1 residue, 1 model selected  

> color sel pale violet red

> select up

71 atoms, 74 bonds, 1 residue, 1 model selected  

> color sel pale violet red

> select #10&ligand

11879 atoms, 11905 bonds, 78 residues, 1 model selected  

> select #10&~ligand

432885 atoms, 438033 bonds, 30 pseudobonds, 27212 residues, 2 models selected  

> show sel cartoons

> hide sel cartoons

> select clear

> select up

77 atoms, 80 bonds, 1 residue, 1 model selected  

> color sel light green

> select up

7 atoms, 9 bonds, 1 residue, 1 model selected  

> color sel light green

> select up

8 atoms, 12 bonds, 1 residue, 1 model selected  

> color sel light green

> select #10&~ligand

432885 atoms, 438033 bonds, 30 pseudobonds, 27212 residues, 2 models selected  

> select clear

> select up

4 atoms, 4 bonds, 1 residue, 1 model selected  

> color sel light green

> select clear

> select up

84 atoms, 89 bonds, 1 residue, 1 model selected  

> color sel light green

> select clear

[Repeated 1 time(s)]

> select up

77 atoms, 80 bonds, 1 residue, 1 model selected  

> color sel forest green

> view matrix models #10,1,0,0,0.013167,0,1,0,-0.0035219,0,0,1,0.036517

> select up

444764 atoms, 449938 bonds, 27280 residues, 1 model selected  

> select clear

> select up

7 atoms, 9 bonds, 1 residue, 1 model selected  

> color sel forest green

[Repeated 1 time(s)]

> select up

8 atoms, 12 bonds, 1 residue, 1 model selected  

> color sel forest green

> select up

4 atoms, 4 bonds, 1 residue, 1 model selected  

> color sel forest green

> select up

84 atoms, 89 bonds, 1 residue, 1 model selected  

> color sel forest green

> select clear

> select #10&~ligand

432885 atoms, 438033 bonds, 30 pseudobonds, 27212 residues, 2 models selected  

> show sel cartoons

> show #!4 models

> show #!6 models

> hide #!10 models

> show #!12 models

> show #!14 models

> show #!16 models

> show #!17 models

> show #!9 models

> show #!10 models

> color zone #4,6,12,14,16,17 near #10 distance 30

> hide #!10 models

> show #!10 models

> hide #!10 models

> save
> /Users/rafaelrocha/supercomplex/Manuscript/figures/figureA/fullComplexMapVisualization.cxs

Taking snapshot of stepper: combination  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 322, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1424, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 365, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 329, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 2'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x327233990> ->
<chimerax.atomic.structure.AtomicStructure object at 0x328337b50>
'combination'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 1051, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 741, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'isolde residue stepper 2' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x327233990> ->
<chimerax.atomic.structure.AtomicStructure object at 0x328337b50>
'combination': Error while saving session data for 'isolde residue stepper 2'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x327233990> ->
<chimerax.atomic.structure.AtomicStructure object at 0x328337b50>
'combination'  
  
ValueError: error processing: 'isolde residue stepper 2' -> -> 'combination':
Error while saving session data for 'isolde residue stepper 2' -> ->
'combination'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 322, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1424, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 365, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 329, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 2'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x327233990> ->
<chimerax.atomic.structure.AtomicStructure object at 0x328337b50>
'combination'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 1051, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 741, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'isolde residue stepper 2' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x327233990> ->
<chimerax.atomic.structure.AtomicStructure object at 0x328337b50>
'combination': Error while saving session data for 'isolde residue stepper 2'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x327233990> ->
<chimerax.atomic.structure.AtomicStructure object at 0x328337b50>
'combination'  
  
ValueError: error processing: 'isolde residue stepper 2' -> -> 'combination':
Error while saving session data for 'isolde residue stepper 2' -> ->
'combination'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,6
      Model Number: Z1AX002ENFN/A
      Chip: Apple M3 Pro
      Total Number of Cores: 12 (6 performance and 6 efficiency)
      Memory: 36 GB
      System Firmware Version: 11881.1.1
      OS Loader Version: 11881.1.1

Software:

    System Software Overview:

      System Version: macOS 15.0.1 (24A348)
      Kernel Version: Darwin 24.0.0
      Time since boot: 68 days, 1 hour, 48 minutes

Graphics/Displays:

    Apple M3 Pro:

      Chipset Model: Apple M3 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 18
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL U3223QE:
          Resolution: 6720 x 3780
          UI Looks like: 3360 x 1890 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        ASUS VG278HE:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    biopython: 1.84
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.23.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.8.dev0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-maskChains: 1.4
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2

Change History (2)

comment:1 by Eric Pettersen, 7 months ago

Cc: Tom Goddard added
Component: Unassigned → Third Party
Description: modified (diff)
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: ResidueStepper's 'positions' attribute is None

comment:2 by Tom Goddard, 7 months ago

Tristan, model.positions = None means the model has been closed. But in this bug report session saving is still trying to save this model named "combination" apparently because ResidueStepper still holds a reference to it even though it has been closed.

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