Opened 7 days ago

Closed 7 days ago

#19423 closed defect (can't reproduce)

Black screen after loading session file

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

Description 

The following bug report has been submitted:
Platform:        macOS-13.3-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Black screen upon loading chimerax session with a cryo EM density map, cif model, and pdb models. 

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/mackenziepatterson/Library/CloudStorage/Box-
> Box/pyroptolysins/model building/MB001/PyLys2_map_modelangelo_fitting.cxs"

Opened cryosparc_P34_J896_map_sharp.mrc as #1, grid size 1000,1000,1000, pixel
0.941, shown at level 0.05, step 1, values float32  
Log from Thu Nov 20 08:47:40 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/mackenziepatterson/Library/CloudStorage/Box-
> Box/pyroptolysins/model building/MB001/cryosparc_P34_J896_map_sharp.mrc"

Opened cryosparc_P34_J896_map_sharp.mrc as #1, grid size 1000,1000,1000, pixel
0.941, shown at step 1, values float32  

> volume #1 level 0.05,0 level 0.03957,0.8 level 0.3117,1

> volume #1 region 0,0,0,999,999,999 step 4

[Repeated 1 time(s)]

> set bgColor white

> lighting full

> volume #1

> lighting shadows flase

Invalid "shadows" argument: Expected true or false (or 1 or 0)  

> lighting shadows false

> volume #1 step 1

> volume #1 level 0.05

> transparency #1 70

> open "/Users/mackenziepatterson/Library/CloudStorage/Box-
> Box/pyroptolysins/model building/MB001/J891_model_raw.cif"

Summary of feedback from opening
/Users/mackenziepatterson/Library/CloudStorage/Box-Box/pyroptolysins/model
building/MB001/J891_model_raw.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Missing or incorrect sequence information. Inferred polymer connectivity.  
  
  
Chain information for J891_model_raw.cif #2  
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Nz | No description available  
O | No description available  
O0 Of Ro SO Th | No description available  
O1 | No description available  
O2 Od Pv SD SG SH | No description available  
O3 | No description available  
O4 PY RF Sp TK TW | No description available  
O5 Ou PZ | No description available  
O6 Oj Oz PL Pq | No description available  
O7 | No description available  
O8 | No description available  
O9 P7 PN Pa Pi Pn Rc Re Sx TI TM | No description available  
OA | No description available  
OB | No description available  
OC | No description available  
OD | No description available  
OE | No description available  
OF | No description available  
OG | No description available  
OH | No description available  
OI | No description available  
OJ | No description available  
OK | No description available  
OL | No description available  
OM | No description available  
ON PA | No description available  
OO Pm RY Ri So | No description available  
OP OT PX | No description available  
OQ Pp | No description available  
OR Qg SE | No description available  
OS | No description available  
OU Qp Sr | No description available  
OV T3 | No description available  
OW QL Rk UG | No description available  
OX | No description available  
OY Qb | No description available  
OZ QV | No description available  
Oa Oy QX Sf T5 | No description available  
Ob Oi PI Su | No description available  
Oc Qn R3 | No description available  
Oe Ov PS TN UA | No description available  
Og On Pk Qf Sg Si | No description available  
Oh | No description available  
Ok R7 UC | No description available  
Ol | No description available  
Om | No description available  
Oo | No description available  
Op QU Rd TV | No description available  
Oq R1 Rn TU | No description available  
Or Q7 Q9 Qj RC SM TR | No description available  
Os RL SQ Sd | No description available  
Ot Qz | No description available  
Ow TT | No description available  
Ox | No description available  
P | No description available  
P0 | No description available  
P1 | No description available  
P2 | No description available  
P3 TO | No description available  
P4 PQ QI TJ Tk | No description available  
P5 Pu QR Tt | No description available  
P6 | No description available  
P8 TY | No description available  
P9 | No description available  
PB RI SI | No description available  
PC PO QN RJ | No description available  
PD Te | No description available  
PE QQ RR | No description available  
PF | No description available  
PG | No description available  
PH | No description available  
PJ | No description available  
PK Ts | No description available  
PM | No description available  
PP | No description available  
PR Rj | No description available  
PT | No description available  
PU | No description available  
PV Ty | No description available  
PW SF TA TG | No description available  
Pb Rv S1 Sw | No description available  
Pc QT T0 | No description available  
Pd | No description available  
Pe QO RT Ru S8 Sv | No description available  
Pf QE Qi Ql SA SB SW | No description available  
Pg | No description available  
Ph Ra | No description available  
Pj Qa RV Tn Tv UD | No description available  
Pl | No description available  
Po RB Tf | No description available  
Pr QY Qm | No description available  
Ps QC RP | No description available  
Pt RW Tg | No description available  
Pw RX SY | No description available  
Px | No description available  
Py Tj | No description available  
Pz R2 RS S3 SL SZ TZ | No description available  
Q | No description available  
Q0 R0 RO | No description available  
Q1 UB | No description available  
Q2 | No description available  
Q3 | No description available  
Q4 | No description available  
Q5 | No description available  
Q6 | No description available  
Q8 SX TX | No description available  
QA | No description available  
QB | No description available  
QD | No description available  
QF QH Qq Sb Sc | No description available  
QG | No description available  
QJ | No description available  
QK Rs | No description available  
QM Qd S0 SR TH Ti | No description available  
QP S6 Sj | No description available  
QS | No description available  
QW | No description available  
QZ RE SN | No description available  
Qc Tr | No description available  
Qe Qr Rp Sa Se Sl TC | No description available  
Qh T8 | No description available  
Qk Tu | No description available  
Qo | No description available  
Qs S4 Tx | No description available  
Qt SS ST | No description available  
Qu RU | No description available  
Qv R6 Td | No description available  
Qw RZ TQ | No description available  
Qx | No description available  
Qy | No description available  
R | No description available  
R4 Tw | No description available  
R5 | No description available  
R8 | No description available  
R9 | No description available  
RA | No description available  
RD | No description available  
RG St | No description available  
RH | No description available  
RK TE | No description available  
RM | No description available  
RN | No description available  
RQ | No description available  
Rb S9 SV T7 | No description available  
Rf Rt Sk | No description available  
Rg S2 | No description available  
Rh | No description available  
Rl Sz | No description available  
Rm | No description available  
Rq SP | No description available  
Rr | No description available  
Rw SC | No description available  
Rx T1 | No description available  
Ry | No description available  
Rz | No description available  
S T | No description available  
S5 | No description available  
S7 | No description available  
SJ TB Tl | No description available  
SK | No description available  
SU | No description available  
Sh | No description available  
Sm | No description available  
Sn | No description available  
Sq Ta UF | No description available  
Ss | No description available  
Sy UI | No description available  
T2 | No description available  
T4 | No description available  
T6 | No description available  
T9 | No description available  
TD | No description available  
TF | No description available  
TL | No description available  
TP | No description available  
TS | No description available  
Tb | No description available  
Tc | No description available  
Tm | No description available  
To | No description available  
Tp | No description available  
Tq | No description available  
Tz | No description available  
U | No description available  
UE | No description available  
UH | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s u | No description available  
t | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

Cannot find consistent set of bond orders for ring system containing atom CD2
in residue TRP /Am:9  

Cannot find consistent set of bond orders for ring system containing atom CD2
in residue TRP /An:9  

Cannot find consistent set of bond orders for ring system containing atom CD2
in residue TRP /BF:9  

Cannot find consistent set of bond orders for ring system containing atom CD2
in residue TRP /NB:10  

Cannot find consistent set of bond orders for ring system containing atom CD2
in residue TRP /Mc:5  

Cannot find consistent set of bond orders for ring system containing atom CD2
in residue TRP /MJ:3  

Cannot find consistent set of bond orders for ring system containing atom CD2
in residue TRP /Cb:8  

> hide cartoons

> show cartoons

Computing secondary structure  

> hide atoms

> hide #!1 models

> open "/Users/mackenziepatterson/Library/CloudStorage/Box-
> Box/pyroptolysins/model
> building/MB001/phyre_models/Phyre_PyLys2NTD_1t1t_8sl0.pdb"

Chain information for Phyre_PyLys2NTD_1t1t_8sl0.pdb #3  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> select #3

1026 atoms, 1047 bonds, 140 residues, 1 model selected  

> color #3 #1732e1ff

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,60.979,0,1,0,-242.67,0,0,1,32.358

> view matrix models #3,1,0,0,105.82,0,1,0,-265.28,0,0,1,40.902

> view matrix models #3,1,0,0,54.306,0,1,0,-133.89,0,0,1,34.161

> view matrix models #3,1,0,0,216.31,0,1,0,-122.32,0,0,1,40.225

> view matrix models #3,1,0,0,144.1,0,1,0,-118.42,0,0,1,42.67

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.50316,0.75147,0.42676,198.22,0.35873,0.63089,-0.68796,240.64,-0.78622,-0.19306,-0.58701,1219.9

> view matrix models
> #3,-0.42241,0.85312,0.3062,156.51,0.44116,0.48861,-0.75275,314.83,-0.7918,-0.18289,-0.58276,1214.6

> view matrix models
> #3,-0.47589,0.84133,0.25633,209.86,0.59771,0.52317,-0.60749,158.96,-0.6452,-0.13589,-0.75184,1196.4

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.47589,0.84133,0.25633,208.25,0.59771,0.52317,-0.60749,163.62,-0.6452,-0.13589,-0.75184,1176

> hide #3 models

> show #!1 models

> hide #!1 models

> ui tool show "Show Sequence Viewer"

> sequence chain #3/?

Alignment identifier is 3/  

> show #3 models

> view matrix models
> #3,-0.47589,0.84133,0.25633,206.02,0.59771,0.52317,-0.60749,167.83,-0.6452,-0.13589,-0.75184,1178.6

> view matrix models
> #3,-0.47589,0.84133,0.25633,205.18,0.59771,0.52317,-0.60749,169.68,-0.6452,-0.13589,-0.75184,1178

> view matrix models
> #3,-0.47589,0.84133,0.25633,204.46,0.59771,0.52317,-0.60749,171.29,-0.6452,-0.13589,-0.75184,1177.7

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.045937,0.9465,-0.31941,205.88,0.65884,-0.21164,-0.7219,621.15,-0.75088,-0.2436,-0.61387,1226.4

> view matrix models
> #3,-0.040362,0.93832,-0.34339,218.81,0.68791,-0.22316,-0.69063,600.7,-0.72467,-0.2641,-0.63648,1236.6

> view matrix models
> #3,0.055379,0.9555,-0.28974,141.51,0.70283,-0.24342,-0.66841,595.78,-0.7092,-0.16663,-0.68504,1194.7

> view matrix models
> #3,0.05784,0.95787,-0.28133,135.26,0.76206,-0.22441,-0.60737,530.64,-0.64491,-0.17926,-0.74293,1198.8

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.05784,0.95787,-0.28133,151.16,0.76206,-0.22441,-0.60737,527.27,-0.64491,-0.17926,-0.74293,1199.7

> view matrix models
> #3,0.05784,0.95787,-0.28133,155.31,0.76206,-0.22441,-0.60737,524.15,-0.64491,-0.17926,-0.74293,1200

> view matrix models
> #3,0.05784,0.95787,-0.28133,155.23,0.76206,-0.22441,-0.60737,525.08,-0.64491,-0.17926,-0.74293,1200

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.13805,0.96219,-0.23482,95.609,0.72206,-0.26005,-0.6411,578.96,-0.67792,-0.081054,-0.73065,1152.5

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.13805,0.96219,-0.23482,98.023,0.72206,-0.26005,-0.6411,577.39,-0.67792,-0.081054,-0.73065,1152.6

> view matrix models
> #3,0.13805,0.96219,-0.23482,97.874,0.72206,-0.26005,-0.6411,579.1,-0.67792,-0.081054,-0.73065,1152.4

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.12718,0.96095,-0.24576,108.4,0.73486,-0.2577,-0.62735,565.79,-0.66619,-0.10081,-0.73894,1162.3

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.12718,0.96095,-0.24576,108.8,0.73486,-0.2577,-0.62735,565.32,-0.66619,-0.10081,-0.73894,1161.9

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.084544,0.98101,-0.17453,84.648,0.75626,-0.17723,-0.62981,510.02,-0.64879,-0.078746,-0.75689,1149.2

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.084544,0.98101,-0.17453,83.808,0.75626,-0.17723,-0.62981,511.03,-0.64879,-0.078746,-0.75689,1149.7

> view matrix models
> #3,0.084544,0.98101,-0.17453,83.686,0.75626,-0.17723,-0.62981,511.21,-0.64879,-0.078746,-0.75689,1148.6

> view matrix models
> #3,0.084544,0.98101,-0.17453,83.651,0.75626,-0.17723,-0.62981,511.69,-0.64879,-0.078746,-0.75689,1148.5

> view matrix models
> #3,0.084544,0.98101,-0.17453,83.339,0.75626,-0.17723,-0.62981,510.31,-0.64879,-0.078746,-0.75689,1151.5

> view matrix models
> #3,0.084544,0.98101,-0.17453,83.311,0.75626,-0.17723,-0.62981,510,-0.64879,-0.078746,-0.75689,1151

> view matrix models
> #3,0.084544,0.98101,-0.17453,83.607,0.75626,-0.17723,-0.62981,511.1,-0.64879,-0.078746,-0.75689,1151.4

> open "/Users/mackenziepatterson/Library/CloudStorage/Box-
> Box/pyroptolysins/model
> building/MB001/phyre_models/Phyre_PyLys2CTDext_1t1t_5ly6.pdb"

Chain information for Phyre_PyLys2CTDext_1t1t_5ly6.pdb #4  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> color #4 #8810ecff

> color #4 #6108ecff

> color #4 #0081ecff

> select #4

768 atoms, 786 bonds, 97 residues, 1 model selected  

> view matrix models #4,1,0,0,26.598,0,1,0,-21.502,0,0,1,243.25

> view matrix models #4,1,0,0,97.735,0,1,0,-106.51,0,0,1,206.16

> view matrix models #4,1,0,0,191.1,0,1,0,-131.84,0,0,1,203.92

> view matrix models #4,1,0,0,117.62,0,1,0,-56.942,0,0,1,219.57

> view matrix models #4,1,0,0,242.08,0,1,0,-15.392,0,0,1,212.07

> view matrix models #4,1,0,0,190.96,0,1,0,150.5,0,0,1,214.19

> view matrix models #4,1,0,0,204.97,0,1,0,142.88,0,0,1,197.38

> select #2/Ag:3

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

> select #2/Ag:4

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/Ag:5

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

> select #2/Ag:6

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

> select #2/Ag:7

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select add #2/Ag:3

20 atoms, 18 bonds, 2 residues, 1 model selected  

> select add #2/Ag:4

27 atoms, 24 bonds, 3 residues, 1 model selected  

> select add #2/Ag:5

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select add #2/Ag:6

41 atoms, 36 bonds, 5 residues, 1 model selected  

> show sel atoms

> style sel sticks

Expected a keyword  

> select #4

768 atoms, 786 bonds, 97 residues, 1 model selected  

> view matrix models #4,1,0,0,198.82,0,1,0,180.16,0,0,1,211.55

> view matrix models #4,1,0,0,208.24,0,1,0,130.56,0,0,1,220.79

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.98555,0.03984,-0.16465,245.55,0.11049,0.58559,0.80304,-0.28636,0.12841,-0.80963,0.57273,529.75

> view matrix models
> #4,0.87767,-0.47694,0.04721,392.39,0.23404,0.51247,0.82619,-34.719,-0.41824,-0.71407,0.56141,727.94

> select #2/Ag:3@CA

1 atom, 1 residue, 1 model selected  

> select add #2/Ag:4

8 atoms, 6 bonds, 2 residues, 1 model selected  

> select add #2/Ag:6@CB

9 atoms, 6 bonds, 3 residues, 1 model selected  

> select add #2/Ag:7@NH2

10 atoms, 6 bonds, 4 residues, 1 model selected  

> select add #2/Ag:7@NH1

11 atoms, 6 bonds, 4 residues, 1 model selected  

> hide sel atoms

> select add #2/Ag:2

19 atoms, 13 bonds, 5 residues, 1 model selected  

> select add #2/Mv:1

23 atoms, 16 bonds, 6 residues, 1 model selected  

> hide sel atoms

> select add #2/Ag:5@NZ

24 atoms, 16 bonds, 7 residues, 1 model selected  

> select add #2/Ag:3@NZ

25 atoms, 16 bonds, 7 residues, 1 model selected  

> select add #2/Ag:3@CD

26 atoms, 16 bonds, 7 residues, 1 model selected  

> select add #2/Ag:3@CB

27 atoms, 16 bonds, 7 residues, 1 model selected  

> select add #2/Ag:3@CG

28 atoms, 16 bonds, 7 residues, 1 model selected  

> select add #2/Ag:3@CE

29 atoms, 16 bonds, 7 residues, 1 model selected  

> select add #2/Ag:5@CE

30 atoms, 16 bonds, 7 residues, 1 model selected  

> select subtract #2/Ag:5@CE

29 atoms, 16 bonds, 7 residues, 1 model selected  

> select add #2/Ag:5@CD

30 atoms, 16 bonds, 7 residues, 1 model selected  

> select add #2/Ag:5@CB

31 atoms, 16 bonds, 7 residues, 1 model selected  

> select add #2/Ag:5@CA

32 atoms, 16 bonds, 7 residues, 1 model selected  

> select add #2/Ag:7@CD

33 atoms, 16 bonds, 7 residues, 1 model selected  

> select subtract #2/Ag:7@CD

32 atoms, 16 bonds, 7 residues, 1 model selected  

> select add #2/Ag:7@CD

33 atoms, 16 bonds, 7 residues, 1 model selected  

> select add #2/Ag:7@CZ

34 atoms, 16 bonds, 7 residues, 1 model selected  

> hide sel atoms

> select add #2/Ag:5@CE

35 atoms, 16 bonds, 7 residues, 1 model selected  

> select add #2/Ag:5@CG

36 atoms, 16 bonds, 7 residues, 1 model selected  

> select add #2/Ag:7@CB

37 atoms, 16 bonds, 7 residues, 1 model selected  

> select add #2/Ag:7@CG

38 atoms, 16 bonds, 7 residues, 1 model selected  

> hide sel atoms

> select add #2/Ag:7@NE

39 atoms, 16 bonds, 7 residues, 1 model selected  

> hide sel atoms

> select #4

768 atoms, 786 bonds, 97 residues, 1 model selected  

> view matrix models
> #4,0.89065,-0.45175,0.051637,378.15,0.12078,0.34455,0.93097,35.6,-0.43835,-0.82293,0.36144,822.58

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.89065,-0.45175,0.051637,375.48,0.12078,0.34455,0.93097,75.933,-0.43835,-0.82293,0.36144,803.73

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.85764,-0.514,-0.015664,425.97,0.19935,0.30424,0.9315,55.896,-0.47403,-0.80202,0.3634,811.45

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.85764,-0.514,-0.015664,430.29,0.19935,0.30424,0.9315,59.727,-0.47403,-0.80202,0.3634,810.81

> view matrix models
> #4,0.85764,-0.514,-0.015664,434.89,0.19935,0.30424,0.9315,62.955,-0.47403,-0.80202,0.3634,811.89

> view matrix models
> #4,0.85764,-0.514,-0.015664,435.43,0.19935,0.30424,0.9315,57.713,-0.47403,-0.80202,0.3634,814.25

> view matrix models
> #4,0.85764,-0.514,-0.015664,435.54,0.19935,0.30424,0.9315,57.348,-0.47403,-0.80202,0.3634,814.03

> view matrix models
> #4,0.85764,-0.514,-0.015664,436.74,0.19935,0.30424,0.9315,58.092,-0.47403,-0.80202,0.3634,813.79

> view matrix models
> #4,0.85764,-0.514,-0.015664,436.99,0.19935,0.30424,0.9315,56.818,-0.47403,-0.80202,0.3634,813.93

> view matrix models
> #4,0.85764,-0.514,-0.015664,437.94,0.19935,0.30424,0.9315,56.184,-0.47403,-0.80202,0.3634,812.49

> view matrix models
> #4,0.85764,-0.514,-0.015664,438.12,0.19935,0.30424,0.9315,55.862,-0.47403,-0.80202,0.3634,812.19

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.8402,-0.54198,-0.018126,454.53,0.23897,0.34005,0.90954,34.414,-0.48679,-0.76852,0.41522,793.42

> view matrix models
> #4,0.80742,-0.58822,-0.045598,489.46,0.26472,0.29213,0.91901,36.039,-0.52726,-0.7541,0.39158,811.87

> hide #2 models

> show #!1 models

> save
> /Users/mackenziepatterson/Documents/temp_csx_sessions/PyLys2_map_modelangelo_fitting.cxs

> show #2 models

> select #4

768 atoms, 786 bonds, 97 residues, 1 model selected  

> view matrix models
> #4,0.89426,-0.40557,-0.18924,435.76,0.33128,0.31554,0.88921,9.408,-0.30092,-0.85787,0.41653,744.16

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.89426,-0.40557,-0.18924,436.4,0.33128,0.31554,0.88921,8.551,-0.30092,-0.85787,0.41653,743.18

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.89022,-0.41418,-0.18962,440.81,0.33374,0.3097,0.89034,9.0358,-0.31004,-0.85589,0.41393,747.01

> view matrix models
> #4,0.88343,-0.33156,-0.33109,455.7,0.43223,0.3038,0.84905,-18.671,-0.18092,-0.89318,0.4117,706.02

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.88343,-0.33156,-0.33109,456.27,0.43223,0.3038,0.84905,-19.371,-0.18092,-0.89318,0.4117,705.48

> view matrix models
> #4,0.88343,-0.33156,-0.33109,455.03,0.43223,0.3038,0.84905,-19.227,-0.18092,-0.89318,0.4117,706.1

> hide #2 models

> open "/Users/mackenziepatterson/Library/CloudStorage/Box-
> Box/pyroptolysins/model building/MB001/fold_2025_08_13_15_56_model_0.cif"

Chain information for fold_2025_08_13_15_56_model_0.cif #5  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> select #5

2744 atoms, 2809 bonds, 358 residues, 1 model selected  

> view matrix models #5,1,0,0,-57.719,0,1,0,136.3,0,0,1,251.39

> view matrix models #5,1,0,0,369.89,0,1,0,-189.77,0,0,1,349

> view matrix models #5,1,0,0,423.88,0,1,0,-223.66,0,0,1,445.19

> view matrix models #5,1,0,0,573.79,0,1,0,-263.33,0,0,1,492.14

> view matrix models #5,1,0,0,817.04,0,1,0,-210.35,0,0,1,562.18

> view matrix models #5,1,0,0,511.28,0,1,0,-107.87,0,0,1,498.02

> view matrix models #5,1,0,0,858.72,0,1,0,-3.1473,0,0,1,568.11

> view matrix models #5,1,0,0,876.12,0,1,0,168.59,0,0,1,285.4

> view matrix models #5,1,0,0,788.22,0,1,0,184.84,0,0,1,515.07

> view matrix models #5,1,0,0,601.5,0,1,0,229.75,0,0,1,497.84

> view matrix models #5,1,0,0,506.8,0,1,0,352.04,0,0,1,471.9

> view matrix models #5,1,0,0,569.19,0,1,0,490.93,0,0,1,463.55

> view matrix models #5,1,0,0,588.58,0,1,0,456.35,0,0,1,470.48

> view matrix models #5,1,0,0,638.27,0,1,0,448.32,0,0,1,474.69

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.88766,-0.18,0.42387,640.81,-0.28599,0.9369,-0.20106,449.1,-0.36093,-0.2997,-0.88313,478.11

> view matrix models
> #5,-0.84177,-0.044472,0.53799,640.67,-0.45904,0.58342,-0.67,449.83,-0.28408,-0.81095,-0.51152,476.87

> view matrix models
> #5,0.8894,-0.13012,-0.43822,639.05,0.046038,0.97926,-0.19733,448.54,0.4548,0.15533,0.87694,474.22

> view matrix models
> #5,0.85647,-0.098409,-0.50673,639.25,0.19205,0.97194,0.13584,447.73,0.47915,-0.21366,0.85133,473.86

> hide #5:1-247 cartoons

> view matrix models
> #5,0.89076,-0.1063,-0.44187,637.97,0.19145,0.96955,0.1527,447.33,0.41218,-0.22061,0.88399,472.69

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.89076,-0.1063,-0.44187,634.97,0.19145,0.96955,0.1527,470.6,0.41218,-0.22061,0.88399,449.12

> view matrix models
> #5,0.89076,-0.1063,-0.44187,642.53,0.19145,0.96955,0.1527,478.56,0.41218,-0.22061,0.88399,450.87

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.58633,-0.13677,-0.79845,649.14,0.20263,0.97907,-0.018919,482.64,0.78432,-0.15069,0.60177,459.6

> view matrix models
> #5,0.68298,-0.22158,-0.69602,647.67,0.27857,0.95987,-0.03223,483.51,0.67523,-0.17188,0.7173,456.27

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.68298,-0.22158,-0.69602,648.93,0.27857,0.95987,-0.03223,480.58,0.67523,-0.17188,0.7173,452.54

> view matrix models
> #5,0.68298,-0.22158,-0.69602,648.66,0.27857,0.95987,-0.03223,479.18,0.67523,-0.17188,0.7173,452.65

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.66994,-0.26803,-0.69235,648.67,0.14179,0.96158,-0.23506,483.1,0.72875,0.059307,0.68221,452.92

> view matrix models
> #5,0.6673,-0.24421,-0.70361,648.83,0.12132,0.96774,-0.22083,482.61,0.73484,0.061995,0.6754,453.11

> view matrix models
> #5,0.66985,-0.13495,-0.73013,649.04,0.029629,0.98742,-0.15532,480.41,0.7419,0.082412,0.66542,453.31

> hide #4 models

> show #2 models

> hide #!1 models

> color #5 #010000ff

> view matrix models
> #5,0.73975,-0.37094,-0.56141,646.42,0.29672,0.92866,-0.22261,483.91,0.60393,-0.0019046,0.79704,449.66

> view matrix models
> #5,0.73544,-0.26153,-0.62509,647.47,0.18276,0.96489,-0.18867,482.25,0.65248,0.024514,0.75741,450.8

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.73544,-0.26153,-0.62509,647.7,0.18276,0.96489,-0.18867,481.66,0.65248,0.024514,0.75741,451.59

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.85254,-0.11233,0.51044,610.32,0.43597,-0.6915,0.57598,471.67,0.28827,0.71359,0.63851,449.41

> view matrix models
> #5,-0.75066,0.64982,-0.11931,622.85,-0.2969,-0.17045,0.93957,456.44,0.59022,0.74073,0.32089,458.7

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.75066,0.64982,-0.11931,623.72,-0.2969,-0.17045,0.93957,452.95,0.59022,0.74073,0.32089,462.21

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.79995,0.56289,-0.20792,625.84,-0.40849,-0.25701,0.87583,454.09,0.43956,0.78556,0.43553,458.38

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.79995,0.56289,-0.20792,627.26,-0.40849,-0.25701,0.87583,455.77,0.43956,0.78556,0.43553,457.72

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.81213,0.56416,-0.14888,625.78,-0.32878,-0.23169,0.91555,455.23,0.48202,0.79249,0.37365,459.42

> hide #2 models

> show #!1 models

> show #4 models

> save
> /Users/mackenziepatterson/Documents/temp_csx_sessions/PyLys2_map_modelangelo_fitting.cxs

> hide #4 models

> show #4 models

> view matrix models
> #5,-0.82514,0.49252,-0.27669,629,-0.42773,-0.22473,0.87553,455.53,0.36904,0.84079,0.3961,457.99

> select #4

768 atoms, 786 bonds, 97 residues, 1 model selected  

> view matrix models
> #4,0.86654,-0.26563,-0.42256,465.95,0.49313,0.32495,0.80699,-39.594,-0.077045,-0.90766,0.41257,667.65

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.86654,-0.26563,-0.42256,466.48,0.49313,0.32495,0.80699,-39.227,-0.077045,-0.90766,0.41257,667.78

> hide #5 models

> view matrix models
> #4,0.86654,-0.26563,-0.42256,467.89,0.49313,0.32495,0.80699,-38.383,-0.077045,-0.90766,0.41257,668.7

> view matrix models
> #4,0.86654,-0.26563,-0.42256,468.05,0.49313,0.32495,0.80699,-38.374,-0.077045,-0.90766,0.41257,668.63

> view matrix models
> #4,0.86654,-0.26563,-0.42256,468.33,0.49313,0.32495,0.80699,-39.194,-0.077045,-0.90766,0.41257,668.68

> save
> /Users/mackenziepatterson/Documents/temp_csx_sessions/PyLys2_map_modelangelo_fitting.cxs

> fitmap #4 inMap #1

Fit molecule Phyre_PyLys2CTDext_1t1t_5ly6.pdb (#4) to map
cryosparc_P34_J896_map_sharp.mrc (#1) using 768 atoms  
average map value = 0.04642, steps = 68  
shifted from previous position = 3.02  
rotated from previous position = 4.45 degrees  
atoms outside contour = 493, contour level = 0.05  
  
Position of Phyre_PyLys2CTDext_1t1t_5ly6.pdb (#4) relative to
cryosparc_P34_J896_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.89903402 -0.23694917 -0.36822944 431.32869861  
0.43420500 0.37370800 0.81963915 -36.34102221  
-0.05660253 -0.89677055 0.43886072 649.75607308  
Axis -0.91829672 -0.16672358 0.35907434  
Axis point 0.00000000 500.37058747 458.55266550  
Rotation angle (degrees) 69.15743337  
Shift along axis -156.71809271  
  

> fitmap #3 inMap #1

Fit molecule Phyre_PyLys2NTD_1t1t_8sl0.pdb (#3) to map
cryosparc_P34_J896_map_sharp.mrc (#1) using 1026 atoms  
average map value = 0.05765, steps = 316  
shifted from previous position = 2.38  
rotated from previous position = 10.5 degrees  
atoms outside contour = 575, contour level = 0.05  
  
Position of Phyre_PyLys2NTD_1t1t_8sl0.pdb (#3) relative to
cryosparc_P34_J896_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.00065441 0.99987371 -0.01587868 41.81418606  
0.74985361 -0.01001475 -0.66152798 433.97575254  
-0.66160346 -0.01233959 -0.74975236 1116.04658567  
Axis 0.68395664 0.68030753 -0.26341030  
Axis point 0.00000000 -11.19355083 642.40495578  
Rotation angle (degrees) 151.66779727  
Shift along axis 29.85789630  
  

> view matrix models
> #4,0.89903,-0.23695,-0.36823,429.58,0.43421,0.37371,0.81964,-36.116,-0.056603,-0.89677,0.43886,647.51

> view matrix models
> #4,0.89903,-0.23695,-0.36823,430.25,0.43421,0.37371,0.81964,-35.754,-0.056603,-0.89677,0.43886,647.51

> fitmap #4 inMap #1

Fit molecule Phyre_PyLys2CTDext_1t1t_5ly6.pdb (#4) to map
cryosparc_P34_J896_map_sharp.mrc (#1) using 768 atoms  
average map value = 0.04632, steps = 60  
shifted from previous position = 2.58  
rotated from previous position = 0.0599 degrees  
atoms outside contour = 496, contour level = 0.05  
  
Position of Phyre_PyLys2CTDext_1t1t_5ly6.pdb (#4) relative to
cryosparc_P34_J896_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.89885735 -0.23668099 -0.36883272 431.48708050  
0.43458380 0.37288676 0.81981241 -36.31387743  
-0.05650118 -0.89718313 0.43802973 650.08063580  
Axis -0.91826858 -0.16703843 0.35899998  
Axis point 0.00000000 499.99170074 458.70610570  
Rotation angle (degrees) 69.21348603  
Shift along axis -156.77628118  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.81672,-0.29489,-0.49599,516.77,0.57068,0.2856,0.7699,-52.201,-0.085381,-0.91185,0.40155,676.11

> view matrix models
> #4,0.79516,-0.34994,-0.49524,542.33,0.59138,0.26687,0.76095,-52.581,-0.13413,-0.89795,0.41915,687.2

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.79516,-0.34994,-0.49524,542.85,0.59138,0.26687,0.76095,-52.537,-0.13413,-0.89795,0.41915,687.33

> view matrix models
> #4,0.79516,-0.34994,-0.49524,542.91,0.59138,0.26687,0.76095,-52.565,-0.13413,-0.89795,0.41915,687.03

> view matrix models
> #4,0.79516,-0.34994,-0.49524,542.94,0.59138,0.26687,0.76095,-52.084,-0.13413,-0.89795,0.41915,686.64

> view matrix models
> #4,0.79516,-0.34994,-0.49524,542.74,0.59138,0.26687,0.76095,-51.839,-0.13413,-0.89795,0.41915,687.14

> fitmap #4 inMap #1

Fit molecule Phyre_PyLys2CTDext_1t1t_5ly6.pdb (#4) to map
cryosparc_P34_J896_map_sharp.mrc (#1) using 768 atoms  
average map value = 0.04634, steps = 64  
shifted from previous position = 0.597  
rotated from previous position = 11.9 degrees  
atoms outside contour = 494, contour level = 0.05  
  
Position of Phyre_PyLys2CTDext_1t1t_5ly6.pdb (#4) relative to
cryosparc_P34_J896_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.89899016 -0.23676442 -0.36845530 431.35534560  
0.43430240 0.37329342 0.81977646 -36.31088760  
-0.05655196 -0.89699199 0.43841446 649.93607229  
Axis -0.91831955 -0.16684075 0.35896150  
Axis point 0.00000000 500.19467210 458.58897937  
Rotation angle (degrees) 69.18516359  
Shift along axis -156.76188490  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.65521,-0.48641,-0.57802,663.62,0.68994,0.073639,0.72011,-22.925,-0.3077,-0.87062,0.38384,759.45

> view matrix models
> #4,0.61301,-0.51779,-0.59675,695.55,0.71291,0.036922,0.70029,-15.837,-0.34057,-0.85471,0.39177,765.96

> show #2 models

> hide #!1 models

> hide #3 models

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.61301,-0.51779,-0.59675,695.34,0.71291,0.036922,0.70029,-15.154,-0.34057,-0.85471,0.39177,765.37

> show #!1 models

> hide #2 models

> show #5 models

> maker #5 to #4

Unknown command: maker #5 to #4  

> mmaker #5 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Phyre_PyLys2CTDext_1t1t_5ly6.pdb, chain (blank) (#4) with
fold_2025_08_13_15_56_model_0.cif, chain A (#5), sequence alignment score =
372.8  
RMSD between 46 pruned atom pairs is 1.204 angstroms; (across all 97 pairs:
8.684)  
  

> hide #!1 models

> show #5:200-247 cartoons

> hide #5:200-247 cartoons

> combine #5

> color #6 #ff1107ff

> color #6 #ff0098ff

> show #3 models

> save
> /Users/mackenziepatterson/Documents/temp_csx_sessions/PyLys2_map_modelangelo_fitting.cxs

> select #6

2744 atoms, 2809 bonds, 358 residues, 1 model selected  

> show #6:220-247 cartoons

> hide #6:247-500 cartoons

> show #6:200-247 cartoons

> show #6:180-247 cartoons

> view matrix models
> #6,-0.70909,0.60988,-0.35388,577.88,-0.46949,-0.033922,0.88228,495.12,0.52608,0.79177,0.31039,457.31

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.46377,-0.80376,0.37268,585.61,0.28115,0.53243,0.79842,491.3,-0.84016,-0.2655,0.4729,464.43

> view matrix models
> #6,0.74789,-0.59634,0.29162,583.51,0.10172,0.53706,0.83739,492.33,-0.65598,-0.59661,0.46232,464.08

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.74789,-0.59634,0.29162,608.18,0.10172,0.53706,0.83739,480.94,-0.65598,-0.59661,0.46232,465.7

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.059996,0.56518,-0.82278,594.11,-0.5204,-0.68568,-0.50895,465.91,-0.85181,0.45872,0.25298,462.43

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.059996,0.56518,-0.82278,594.64,-0.5204,-0.68568,-0.50895,469.52,-0.85181,0.45872,0.25298,469.79

> view matrix models
> #6,0.059996,0.56518,-0.82278,591.55,-0.5204,-0.68568,-0.50895,471.8,-0.85181,0.45872,0.25298,461.65

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.17398,-0.84926,0.49848,610.28,0.36498,0.52576,0.76835,485.16,-0.91461,0.048262,0.40144,464.22

> view matrix models
> #6,0.33641,-0.61882,0.70985,612.41,0.46918,0.76371,0.44342,480.29,-0.81651,0.18388,0.54726,465.76

> view matrix models
> #6,0.87621,-0.4773,-0.066688,600.34,0.44263,0.74226,0.50312,481.18,-0.19064,-0.47035,0.86164,468.8

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.87621,-0.4773,-0.066688,611.65,0.44263,0.74226,0.50312,480.47,-0.19064,-0.47035,0.86164,473.28

> view matrix models
> #6,0.87621,-0.4773,-0.066688,611.12,0.44263,0.74226,0.50312,479.46,-0.19064,-0.47035,0.86164,473.79

> view matrix models
> #6,0.87621,-0.4773,-0.066688,598.39,0.44263,0.74226,0.50312,486.81,-0.19064,-0.47035,0.86164,472.51

> view matrix models
> #6,0.87621,-0.4773,-0.066688,597.91,0.44263,0.74226,0.50312,488.19,-0.19064,-0.47035,0.86164,470.49

> hide #6:180-247 cartoons

> show #6:150-170 cartoons

> view matrix models
> #6,0.87621,-0.4773,-0.066688,587.83,0.44263,0.74226,0.50312,499.63,-0.19064,-0.47035,0.86164,462.8

> ui mousemode right "rotate selected models"

> view matrix models
> #6,-0.0095949,-0.99502,0.099202,585.12,-0.4855,-0.082093,-0.87037,480.7,0.87418,-0.056513,-0.48229,454.14

> view matrix models
> #6,0.14943,-0.9688,0.19772,586.56,-0.14322,-0.21906,-0.96514,480.02,0.97834,0.1159,-0.17149,458.11

> view matrix models
> #6,0.014186,-0.98443,0.17521,585.96,-0.088202,-0.17578,-0.98047,480.19,0.996,-0.0015446,-0.089322,458.45

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.014186,-0.98443,0.17521,616.63,-0.088202,-0.17578,-0.98047,469.26,0.996,-0.0015446,-0.089322,449.46

> view matrix models
> #6,0.014186,-0.98443,0.17521,613.34,-0.088202,-0.17578,-0.98047,466.11,0.996,-0.0015446,-0.089322,448.89

> ui mousemode right "rotate selected models"

> view matrix models
> #6,-0.034638,-0.99665,0.074084,612.2,-0.27232,-0.061911,-0.96021,466.35,0.96158,-0.053434,-0.26926,446.86

> view matrix models
> #6,-0.71365,-0.69937,-0.039768,610.74,0.11885,-0.064936,-0.99079,466.98,0.69034,-0.7118,0.12946,447.27

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.71365,-0.69937,-0.039768,610.16,0.11885,-0.064936,-0.99079,465.91,0.69034,-0.7118,0.12946,453.48

> view matrix models
> #6,-0.71365,-0.69937,-0.039768,610.14,0.11885,-0.064936,-0.99079,462.74,0.69034,-0.7118,0.12946,453.2

> show #6:227-232cartoon

> show #6:227-232 cartoons

> show #6:227-247 cartoons

> show #6:112-130 cartoons

> show #6:112-160 cartoons

> show #6:112-170 cartoons

> hide #5 models

> show #!1 models

> view matrix models
> #6,-0.71365,-0.69937,-0.039768,609.58,0.11885,-0.064936,-0.99079,463.07,0.69034,-0.7118,0.12946,451.73

> view matrix models
> #6,-0.71365,-0.69937,-0.039768,609.7,0.11885,-0.064936,-0.99079,464.84,0.69034,-0.7118,0.12946,450.56

> hide #!1 models

> view matrix models
> #6,-0.71365,-0.69937,-0.039768,610.45,0.11885,-0.064936,-0.99079,460.07,0.69034,-0.7118,0.12946,449.07

> ui mousemode right "rotate selected models"

> view matrix models
> #6,-0.77289,-0.57824,0.2613,613.3,-0.086445,-0.31201,-0.94614,458.25,0.62863,-0.75385,0.19116,449.09

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.77289,-0.57824,0.2613,613.37,-0.086445,-0.31201,-0.94614,464.77,0.62863,-0.75385,0.19116,451.35

> show #!1 models

> hide #!1 models

> view matrix models
> #6,-0.77289,-0.57824,0.2613,611,-0.086445,-0.31201,-0.94614,463.4,0.62863,-0.75385,0.19116,451.85

> show #!1 models

> ui mousemode right "rotate selected models"

> view matrix models
> #6,-0.77445,-0.56023,0.29389,611.36,-0.062894,-0.39407,-0.91693,463.31,0.6295,-0.7286,0.26995,452.63

> hide #!1 models

> show #!1 models

> save
> /Users/mackenziepatterson/Documents/temp_csx_sessions/PyLys2_map_modelangelo_fitting.cxs

> fitmap #6 inMap #1

Fit molecule copy of fold_2025_08_13_15_56_model_0.cif (#6) to map
cryosparc_P34_J896_map_sharp.mrc (#1) using 2744 atoms  
average map value = 0.03286, steps = 44  
shifted from previous position = 0.802  
rotated from previous position = 1.11 degrees  
atoms outside contour = 1958, contour level = 0.05  
  
Position of copy of fold_2025_08_13_15_56_model_0.cif (#6) relative to
cryosparc_P34_J896_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.77880418 -0.55453742 0.29317622 611.74405413  
-0.07508492 -0.38161090 -0.92126835 463.44542578  
0.62275702 -0.73950075 0.25556277 451.92776778  
Axis 0.29820508 -0.54070511 0.78658230  
Axis point 158.80522003 439.25168450 0.00000000  
Rotation angle (degrees) 162.25570609  
Shift along axis 287.31625757  
  

> save
> /Users/mackenziepatterson/Documents/temp_csx_sessions/PyLys2_map_modelangelo_fitting.cxs

> select clear

> hide #!1 models

> show #6:207-227 cartoons

> hide #6:207-210 cartoons

> show #!1 models

> save
> /Users/mackenziepatterson/Documents/temp_csx_sessions/PyLys2_map_modelangelo_fitting.cxs

> hide #!1 models

> show #2 models

> hide #2 models

> show #!1 models

> save
> /Users/mackenziepatterson/Documents/temp_csx_sessions/PyLys2_map_modelangelo_fitting.cxs

——— End of log from Thu Nov 20 08:47:40 2025 ———

> view name session-start

opened ChimeraX session  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,5
      Model Number: Z17J00165LL/A
      Chip: Apple M2 Max
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 64 GB
      System Firmware Version: 8422.100.650
      OS Loader Version: 8422.100.650

Software:

    System Software Overview:

      System Version: macOS 13.3 (22E252)
      Kernel Version: Darwin 22.4.0
      Time since boot: 62 days, 12 hours

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 38
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        LG ULTRAGEAR:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 100.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        SB220Q:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 75.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    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-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    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-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

Change History (4)

comment:1 by Eric Pettersen, 7 days ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Black screen after loading session file

Reported by MacKenzie Patterson

comment:2 by Tom Goddard, 7 days ago

If you use the ChimeraX "view" command or in the Toolbar / Graphics tab use View All does it show any models in the graphics? Does the Models panel list the data sets you expect?

comment:3 by mpatterson@…, 7 days ago 

Hi, sorry this ended up being an issue with my system. I had to close some tabs.

comment:4 by Tom Goddard, 7 days ago

Resolution: → can't reproduce
Status: assigned → closed

Ok, not sure what "close some tabs" means.

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