Crash restoring a session in msgpack_deserialize()

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-4.15.0-166-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00007fc4f570e680 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core/serialize.py", line 70 in msgpack_deserialize
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core/session.py", line 687 in restore
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core/session.py", line 982 in open
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core_formats/__init__.py", line 26 in open
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/open_command/cmd.py", line 422 in collated_open
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/open_command/cmd.py", line 179 in provider_open
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/open_command/cmd.py", line 118 in cmd_open
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core/commands/run.py", line 36 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/widgets/htmlview.py", line 462 in cxcmd
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/widgets/htmlview.py", line 444 in defer
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py", line 366 in thread_safe
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/widgets/htmlview.py", line 453 in chimerax_intercept
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/widgets/htmlview.py", line 357 in intercept
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/widgets/htmlview.py", line 85 in _intercept
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/widgets/htmlview.py", line 324 in interceptRequest
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py", line 293 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/ChimeraX_main.py", line 866 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.8/runpy.py", line 87 in _run_code
  File "/usr/lib/ucsf-chimerax/lib/python3.8/runpy.py", line 194 in _run_module_as_main


Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/home/prabirk/Downloads/Ross Heme binder with LH2 BChls.cxs"

Log from Tue Feb 1 10:38:31 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/drornoy/Documents/Protein Designs/Heme binding 4HB/Ross Heme
> binder with LH2 BChls.cxs" format session

Log from Wed Jan 19 19:30:16 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/drornoy/Documents/Presentations/Technion Food Eng. 2021/Chl
> proteins/LHCII trimer.cxs" format session

Log from Mon Jan 18 13:01:26 2021UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "/Users/drornoy/Documents/Presentations/Technion Food Eng. 2021/PSI PC
> FD complex.cxs" format session

Log from Tue Jan 12 09:08:15 2021UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "/Users/drornoy/Documents/David B/Fdx PsaCDE interactions.cxs" format
> session

Log from Mon Nov 30 18:38:32 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.  
drorn@migal.org.il is subscribed to the ChimeraX announcements list  

> open "/Users/drornoy/Documents/David B/Homology models PetF1
> PetF3/Ferodoxin.py" format python

ChimeraX cannot open a regular Chimera session.  
An exporter from Chimera to ChimeraX is being worked on but is not ready at
this time.  

> open /Users/drornoy/Downloads/6yez.pdb format pdb

6yez.pdb title:  
Plant ψ-ferredoxin-plastocyanin supercomplex [more info...]  
  
Chain information for 6yez.pdb  
---  
Chain | Description  
1.1/1 | No description available  
1.1/2 | No description available  
1.1/3 | No description available  
1.1/4 | No description available  
1.1/A | No description available  
1.1/B | No description available  
1.1/C | No description available  
1.1/D | No description available  
1.1/E | No description available  
1.1/F | No description available  
1.1/G | No description available  
1.1/H | No description available  
1.1/I | No description available  
1.1/J | No description available  
1.1/K | No description available  
1.1/L | No description available  
1.1/N | No description available  
1.1/P | No description available  
  

> select /N,/C-E

Expected an objects specifier or a keyword  

> select /N/C-E

3016 atoms, 3068 bonds, 48 pseudobonds, 389 residues, 2 models selected  

> select /N/C-E &protein

2996 atoms, 3064 bonds, 386 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select /1-4

12301 atoms, 11130 bonds, 199 pseudobonds, 2535 residues, 3 models selected  

> hide (#1.2#!1.1 & sel) target a

> hide sel cartoons

> select :FeS,SF4

28 atoms, 4 bonds, 55 pseudobonds, 4 residues, 2 models selected  

> style sel sphere

Changed 28 atom styles  

> color sel byhetero

> ui tool show Contacts

> contacts sel select true makePseudobonds false reveal true

104 contacts  

> style sel stick

Changed 109 atom styles  

> style sel sphere

Changed 109 atom styles  

> style sel stick

Changed 109 atom styles  

> style sel sphere

Changed 109 atom styles  

> show sel atoms

> style sel stick

Changed 109 atom styles  

> select :FeS,SF4

28 atoms, 4 bonds, 55 pseudobonds, 4 residues, 2 models selected  

> style sel sphere

Changed 28 atom styles  

> contacts sel select true makePseudobonds false reveal true

104 contacts  

> hide sel atoms

> show sel atoms

> show sel atoms

> hide sel atoms

> show sel atoms

> hide sel atoms

> show sel atoms

> select :FeS,SF4

28 atoms, 4 bonds, 55 pseudobonds, 4 residues, 2 models selected  

> contacts sel restrict /C-E select true makePseudobonds false reveal true

61 contacts  

> style sel stick

Changed 62 atom styles  

> style sel sphere

Changed 62 atom styles  

> select :FeS,SF4

28 atoms, 4 bonds, 55 pseudobonds, 4 residues, 2 models selected  

> contacts sel restrict /C-E distanceOnly 4.0 select true makePseudobonds
> false reveal true

94 distances  

> style sel stick

Changed 75 atom styles  

> color sel byhetero

> select :FeS,SF4

28 atoms, 4 bonds, 55 pseudobonds, 4 residues, 2 models selected  

> style sel sphere

Changed 28 atom styles  

> select /N/C-E &protein

2996 atoms, 3064 bonds, 386 residues, 1 model selected  

> hide sel atoms

> select :FeS,SF4

28 atoms, 4 bonds, 55 pseudobonds, 4 residues, 2 models selected  

> contacts sel restrict /C-E distanceOnly 4.0 select true makePseudobonds
> false reveal true

94 distances  

> color sel byhetero

> style sel stick

Changed 75 atom styles  

> select /N/C-E &protein

2996 atoms, 3064 bonds, 386 residues, 1 model selected  

> style sel stick

Changed 2996 atom styles  

> select :FeS,SF4

28 atoms, 4 bonds, 55 pseudobonds, 4 residues, 2 models selected  

> style sel sphere

Changed 28 atom styles  

> select /N

728 atoms, 740 bonds, 5 pseudobonds, 98 residues, 2 models selected  

> contacts sel restrict /C-E distanceOnly 4.0 select true makePseudobonds
> false reveal true

21 distances  

> interfaces sel & ~solvent

0 buried areas:  

> interfaces sel & ~solvent

0 buried areas:  

> style sel sphere

Changed 29 atom styles  

> color sel byhetero

> style sel stick

Changed 29 atom styles  

> save "/Users/drornoy/Documents/David B/Fdx PsaCDE interactions.cxs"

opened ChimeraX session  

> select ::name="CU"

1 atom, 1 residue, 1 model selected  

> close session

> open 6yez format mmcif fromDatabase pdb

6yez title:  
Plant PSI-ferredoxin-plastocyanin supercomplex [more info...]  
  
Chain information for 6yez #1  
---  
Chain | Description  
1 | Lhca1  
2 | Chlorophyll a-b binding protein, chloroplastic  
3 | Chlorophyll a-b binding protein 3, chloroplastic  
4 | Chlorophyll a-b binding protein P4, chloroplastic  
A | Photosystem I P700 chlorophyll a apoprotein A1  
B | Photosystem I P700 chlorophyll a apoprotein A2  
C | Photosystem I iron-sulfur center  
D | PsaD  
E | PsaE  
F | PsaF  
G | PsaG  
H | PsaH  
I | Photosystem I reaction center subunit VIII  
J | PsaJ  
K | Photosystem I reaction center subunit X psaK  
L | PsaL  
N | Ferredoxin-1, chloroplastic  
P | Plastocyanin  
  
Non-standard residues in 6yez #1  
---  
3PH — 1,2-diacyl-glycerol-3-Sn-phosphate (phosphatidic acid)  
BCR — β-carotene  
C7Z —
(1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-
cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol  
CA — calcium ion  
CHL — chlorophyll B  
CL0 — chlorophyll A isomer  
CLA — chlorophyll A  
CU — copper (II) ion  
DGD — digalactosyl diacyl glycerol (DGDG)  
FES — FE2/S2 (inorganic) cluster  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMG — 1,2-distearoyl-monogalactosyl-diglyceride  
LMT — dodecyl-β-D-maltoside  
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
((3R,3'R)-β,β-carotene-3,3'-diol; lutein)  
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)  
SF4 — iron/sulfur cluster  
XAT — (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-
tetrahydro-β,β-carotene-3,3'-diol (violaxanthin)  
  

> select protein

26860 atoms, 27694 bonds, 3438 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> lighting simple

> cartoon style sel modeHelix tube sides 20

> select :FES,SF4

28 atoms, 40 bonds, 4 residues, 1 model selected  

> style sel sphere

Changed 28 atom styles  

> select :FES,SF4,CU

29 atoms, 40 bonds, 5 residues, 1 model selected  

> style sel sphere

Changed 29 atom styles  

> style sel sphere

Changed 29 atom styles  

> select :3PH

33 atoms, 32 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select :DGD

366 atoms, 373 bonds, 7 residues, 1 model selected  

> hide sel atoms

> select :LHG

295 atoms, 287 bonds, 8 residues, 1 model selected  

> hide sel atoms

> select :C7Z

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

> hide sel atoms

> select :LMG

646 atoms, 646 bonds, 19 residues, 1 model selected  

> hide sel atoms

> select :LMT

199 atoms, 205 bonds, 6 residues, 1 model selected  

> hide sel atoms

> select :XAT,BCR,LUT

1462 atoms, 1502 bonds, 36 residues, 1 model selected  

> color sel orange

> color sel byhetero

> select :CHL,CL0,CLA

9224 atoms, 9852 bonds, 628 pseudobonds, 157 residues, 2 models selected  

> color (#!1 & sel) forest green

> color sel bychain

> color (#!1 & sel) forest green

> color sel byhetero

> select :PQN

66 atoms, 68 bonds, 2 residues, 1 model selected  

> color sel hot pink

> color sel purple

> color sel byhetero

> color sel cornflower blue

> ui tool show "Side View"

> select :1011-1013,1021-1023

390 atoms, 414 bonds, 24 pseudobonds, 6 residues, 2 models selected  

> color (#!1 & sel) lime

> select :CU

1 atom, 1 residue, 1 model selected  

> color sel byelement

> color sel light sea green

> color sel cyan

> select /B:650-663

119 atoms, 125 bonds, 14 residues, 1 model selected  

> select /B:650-667

155 atoms, 163 bonds, 18 residues, 1 model selected  

> select /B:650-665

135 atoms, 141 bonds, 16 residues, 1 model selected  

> select /B:650-666

141 atoms, 147 bonds, 17 residues, 1 model selected  

> select /B:650-662

108 atoms, 113 bonds, 13 residues, 1 model selected  

> select /B:6450-662

Nothing selected  

> select /B:645-662

156 atoms, 165 bonds, 18 residues, 1 model selected  

> hide sel cartoons

> hide sel cartoons

> select /B:645-662

156 atoms, 165 bonds, 18 residues, 1 model selected  

> show sel cartoons

> select /B:647-662

135 atoms, 142 bonds, 16 residues, 1 model selected  

> hide sel cartoons

> select /B:701-718

138 atoms, 140 bonds, 18 residues, 1 model selected  

> hide sel cartoons

> hide sel cartoons

> save "/Users/drornoy/Documents/Presentations/Technion Food Eng. 2021/PSI PC
> FD complex.cxs"

> select :1011-1013,1021-1023

390 atoms, 414 bonds, 24 pseudobonds, 6 residues, 2 models selected  

> style (#!1 & sel) ringFill thick

Changed 6 residue ring styles  

> style (#!1 & sel) ringFill off

Changed 6 residue ring styles  

> style sel sphere

Changed 390 atom styles  

> color sel byhetero

> style (#!1 & sel) stick

Changed 390 atom styles  

> ui tool show "Color Actions"

> color sel green yellow

> color sel lime green

> color sel byhetero

> color sel byhetero

> color sel medium aquamarine

> color sel dark cyan

> color sel byhetero

> select :1011-1013,1021-1023@MG

6 atoms, 6 residues, 1 model selected  

> style sel ball

Changed 6 atom styles  

> style sel sphere

Changed 6 atom styles  

> select :CLA,CHL,CL0 &~:1011-1013,1021-1023

8834 atoms, 9438 bonds, 604 pseudobonds, 151 residues, 2 models selected  

> color sel lawn green

> color sel spring green

> color sel lime

> color sel byhetero

> select clear

> lighting flat

> select :1011-1013,1021-1023

390 atoms, 414 bonds, 24 pseudobonds, 6 residues, 2 models selected  

> color sel green yellow

> color sel byhetero

> select clear

> select :1011-1013,1021-1023

390 atoms, 414 bonds, 24 pseudobonds, 6 residues, 2 models selected  

> color sel pale green

> color sel byhetero

> select clear

> select :1011-1013,1021-1023

390 atoms, 414 bonds, 24 pseudobonds, 6 residues, 2 models selected  

> color sel light green

> color sel byhetero

> select clear

> help help:user

> size :1011-1013,1021-1023 stickRadius 0.3

Changed 414 bond radii  

> size :1011-1013,1021-1023 stickRadius 0.4

Changed 414 bond radii  

> size :1011-1013,1021-1023,2001,2002 stickRadius 0.4

Changed 482 bond radii  

> select :CU

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> select :2001,2002

66 atoms, 68 bonds, 2 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel pale goldenrod

> color sel khaki

> color sel moccasin

> color sel peach puff

> color sel antique white

> color sel burly wood

> color sel gold

> color sel goldenrod

> color sel dark goldenrod

> color sel peru

> color sel burly wood

> color sel tan

> color sel burly wood

> color sel wheat

> select clear

> select :2001,2002

66 atoms, 68 bonds, 2 residues, 1 model selected  

> color sel byhetero

> select clear

> save "/Users/drornoy/Documents/Presentations/Technion Food Eng. 2021/PSI PC
> FD ET chain.cxs"

> save "/Users/drornoy/Documents/Presentations/Technion Food Eng. 2021/PSI PC
> FD complex.cxs"

opened ChimeraX session  

> select ~/4

36620 atoms, 38022 bonds, 616 pseudobonds, 3466 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> select /4:CLA

631 atoms, 675 bonds, 44 pseudobonds, 11 residues, 2 models selected  

> select /4:CLA,CHL

833 atoms, 893 bonds, 60 pseudobonds, 15 residues, 2 models selected  

> select /4:CHL

202 atoms, 218 bonds, 16 pseudobonds, 4 residues, 2 models selected  

> color (#!1 & sel) forest green

> ui tool show "Color Actions"

> color sel spring green

> color sel spring green

> color sel byhetero

> select clear

> cd "/Users/drornoy/Documents/Presentations/Technion Food Eng. 2021/Chl
> proteins"

Current working directory is: /Users/drornoy/Documents/Presentations/Technion
Food Eng. 2021/Chl proteins  

> save LHC1_closeup.png supersample 3 transparentBackground true

> save LHC1_closeup.png supersample 3 transparentBackground true

> save "/Users/drornoy/Documents/Presentations/Technion Food Eng. 2021/Chl
> proteins/LHC1 closeup.cxs"

> select /4:xat

44 atoms, 47 bonds, 1 residue, 1 model selected  

> save "/Users/drornoy/Documents/Presentations/Technion Food Eng. 2021/Chl
> proteins/LHC1 closeup.cxs"

> close session

> open 1rwt

1rwt title:  
Crystal Structure of Spinach Major Light-harvesting complex at 2.72 Angstrom
Resolution [more info...]  
  
Chain information for 1rwt #1  
---  
Chain | Description  
A B C D E F G H I J | Chlorophyll A-B binding protein, chloroplast  
  
Non-standard residues in 1rwt #1  
---  
BNG — nonyl beta-D-glucopyranoside  
CHL — chlorophyll B  
CLA — chlorophyll A  
DGD — digalactosyl diacyl glycerol (DGDG)  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
((3R,3'R)-β,β-carotene-3,3'-diol; lutein)  
NA — sodium ion  
NEX —
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol
((3S,5R,6R,3'S,5'R,6'S)-5',6'-epoxy-6,7-didehydro-
5,6,5',6'-tetrahydro-β,β-carotene-3,5,3'-triol; 9'-cis-neoxanthin)  
XAT — (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-
tetrahydro-β,β-carotene-3,3'-diol (violaxanthin)  
  
1rwt mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> sym #1 assembly 1

> view

> hide #!2 models

> show #!2 models

> select ~#2/B,F,G

49348 atoms, 50125 bonds, 1192 pseudobonds, 5242 residues, 4 models selected  

> hide sel & #!2 cartoons

> hide sel & #!2 atoms

> hide #!2 models

> show #!1 models

> hide #2.1 models

> show #!2 models

> windowsize 800 800

> windowsize

window size 987 800  

> windowsize 1200 800

> windowsize 1000 800

> close #2

> ~select #1

Nothing selected  

> select /B,F,G

8730 atoms, 8853 bonds, 210 pseudobonds, 940 residues, 2 models selected  

> select ~/B,F,G

20309 atoms, 20636 bonds, 491 pseudobonds, 2151 residues, 2 models selected  

> hide sel atoms

> select protein

16619 atoms, 17139 bonds, 2181 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select ~/B,F,G

20309 atoms, 20636 bonds, 491 pseudobonds, 2151 residues, 2 models selected  

> hide sel cartoons

> select :WAT

Nothing selected  

> select :HOH

699 atoms, 699 residues, 1 model selected  

> hide sel atoms

> cartoon style sel modeHelix tube sides 20

> select :CLA

5010 atoms, 5330 bonds, 320 pseudobonds, 80 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel lime

> color sel byhetero

> select :CHL

3630 atoms, 3870 bonds, 240 pseudobonds, 60 residues, 2 models selected  

> color sel spring green

> color sel byhetero

> select :NEX,LUT,XAT

1720 atoms, 1790 bonds, 40 residues, 1 model selected  

> color sel dark orange

> color sel byhetero

> lighting flat

> save "/Users/drornoy/Documents/Presentations/Technion Food Eng. 2021/Chl
> proteins/LHCII trimer.cxs"

> save LHC2_closeup.png supersample 3 transparentBackground true

> select :DGD

660 atoms, 670 bonds, 10 residues, 1 model selected  

> hide sel atoms

> select :BNG

210 atoms, 210 bonds, 10 residues, 1 model selected  

> hide sel atoms

> select :BNG,LHG,NA

701 atoms, 690 bonds, 21 residues, 1 model selected  

> hide sel atoms

> save "/Users/drornoy/Documents/Presentations/Technion Food Eng. 2021/Chl
> proteins/LHCII trimer.cxs"

> save LHC2_closeup.png supersample 3 transparentBackground true

> save "/Users/drornoy/Documents/Presentations/Technion Food Eng. 2021/Chl
> proteins/LHCII trimer.cxs"

——— End of log from Mon Jan 18 13:01:26 2021 ———

opened ChimeraX session  

> select #1/F-G

5709 atoms, 5791 bonds, 140 pseudobonds, 621 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> select #1/B

3021 atoms, 3062 bonds, 70 pseudobonds, 319 residues, 2 models selected  

> hide sel cartoons

> select #1:CLA@CHB

80 atoms, 80 residues, 1 model selected  

> style sel ball

Changed 80 atom styles  

> color sel white

> undo

> undo

> select #1:CLA@CAA

80 atoms, 80 residues, 1 model selected  

> style sel ball

Changed 80 atom styles  

> color sel white

> select #1:CHL@CAA

60 atoms, 60 residues, 1 model selected  

> style sel ball

Changed 60 atom styles  

> color sel white

> close session

> open 7ah0

Summary of feedback from opening 7ah0 fetched from pdb  
---  
note | Fetching compressed mmCIF 7ah0 from
http://files.rcsb.org/download/7ah0.cif  
  
7ah0 title:  
Crystal structure of the de novo designed two-heme binding protein, 4D2 [more
info...]  
  
Chain information for 7ah0 #1  
---  
Chain | Description  
A | 4D2  
  
Non-standard residues in 7ah0 #1  
---  
HEM — protoporphyrin IX containing Fe (HEME)  
  

> help help:user

> ribbon #1 style arrows true

> cartoon #1 style arrows true

Expected a keyword  

> ribbon style arrows true

> ribbon style arrows true

> ribbon style arrowsHelix true

> show atoms

> rainbow

> color byhetero

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> surface #1 enclose :1-109

> mlp

Map values for surface "7ah0_A SES surface": minimum -27.32, mean -3.789,
maximum 21.76  
To also show corresponding color key, enter the above mlp command and add key
true  

> close #1.3

> surface #1 enclose :1-25

> mlp

Map values for surface "7ah0_A SES surface": minimum -27.32, mean -3.789,
maximum 21.76  
To also show corresponding color key, enter the above mlp command and add key
true  

> close #1.3

> surface #1 enclose :1-25

> surface #1 enclose :30-52

> surface #1 enclose :61-82

> surface #1 enclose :88-109

> mlp #1.3

mlp: no amino acids specified  

> help help:user

> mlp :1-25 surfaces #1.3

Map values for surface "Surface :1-25": minimum -21.09, mean -3.088, maximum
20.16  

> mlp :30-52 surfaces #1.4

Map values for surface "Surface :30-52": minimum -20.52, mean -3.135, maximum
19.79  

> mlp :61-82 surfaces #1.5

Map values for surface "Surface :61-82": minimum -22.77, mean -2.935, maximum
19.91  

> mlp :88-109 surfaces #1.6

Map values for surface "Surface :88-109": minimum -21.93, mean -3.519, maximum
19.24  

> ui tool show "Side View"

> select :HEM

86 atoms, 92 bonds, 8 pseudobonds, 2 residues, 2 models selected  

> style sel sphere

Changed 86 atom styles  

> select clear

> save "/Users/drornoy/Documents/Protein Designs/Heme binding 4HB/Ross Heme
> binder.cxs"

> hide #!1.3 models

> hide #!1.4 models

> hide #!1.5 models

> hide #!1.6 models

> open 2dre

2dre title:  
Crystal structure of Water-soluble chlorophyll protein from lepidium
virginicum at 2.00 angstrom resolution [more info...]  
  
Chain information for 2dre #2  
---  
Chain | Description  
A B C D | Water-soluble chlorophyll protein  
  
Non-standard residues in 2dre #2  
---  
CLA — chlorophyll A  
  

> align #2/A:CLA@C[1234][ABCD]@N[ABCD] toAtoms #1:202@C[1234][ABCD]@N[ABCD]
> matchAtomNames true

RMSD between 20 atom pairs is 0.151 angstroms  

> select #2

6168 atoms, 5758 bonds, 22 pseudobonds, 1258 residues, 3 models selected  

> select #2

6168 atoms, 5758 bonds, 22 pseudobonds, 1258 residues, 3 models selected  

> hide sel cartoons

> hide sel atoms

> select #2/A:CLA

65 atoms, 69 bonds, 4 pseudobonds, 1 residue, 2 models selected  

> show sel atoms

> select #1/A:202

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

> style sel stick

Changed 43 atom styles  

> align #2/B:CLA@C[1234][ABCD]@N[ABCD] toAtoms #1:201@C[1234][ABCD]@N[ABCD]
> matchAtomNames true move chains

RMSD between 20 atom pairs is 0.132 angstroms  

> select #1/A:201

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

> style sel stick

Changed 43 atom styles  

> select #2/B:CLA

65 atoms, 69 bonds, 4 pseudobonds, 1 residue, 2 models selected  

> show sel atoms

> help help:user

> select #1

925 atoms, 936 bonds, 13 pseudobonds, 111 residues, 7 models selected  

> show sel atoms

> save "/Users/drornoy/Documents/Protein Designs/Heme binding 4HB/Heme4HB with
> Chls.pdb" displayedOnly true

> open "/Users/drornoy/Documents/Protein Designs/Heme binding 4HB/Heme4HB with
> Chls.pdb"

Summary of feedback from opening /Users/drornoy/Documents/Protein Designs/Heme
binding 4HB/Heme4HB with Chls.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 SER A 2
LYS A 25 1 24  
Start residue of secondary structure not found: HELIX 2 2 SER A 30 LEU A 52 1
23  
Start residue of secondary structure not found: HELIX 3 3 PRO A 61 LEU A 82 1
22  
Start residue of secondary structure not found: HELIX 4 4 SER A 88 MET A 109 1
22  
  
Chain information for Heme4HB with Chls.pdb  
---  
Chain | Description  
3.1/A | No description available  
  

> hide #!3.2 models

> show #!3.2 models

> hide #!1 models

> hide #!2 models

> show #!2 models

> show #!1 models

> close #3

> select #1:HEM

86 atoms, 92 bonds, 8 pseudobonds, 2 residues, 2 models selected  

> hide sel atoms

> save "/Users/drornoy/Documents/Protein Designs/Heme binding 4HB/Heme4HB with
> Chls.pdb" displayedOnly true

> open "/Users/drornoy/Documents/Protein Designs/Heme binding 4HB/Heme4HB with
> Chls.pdb"

Summary of feedback from opening /Users/drornoy/Documents/Protein Designs/Heme
binding 4HB/Heme4HB with Chls.pdb  
---  
warnings | Cannot find LINK/SSBOND residue HEM (201 )  
Cannot find LINK/SSBOND residue HEM (202 )  
Cannot find LINK/SSBOND residue HEM (201 )  
Cannot find LINK/SSBOND residue HEM (202 )  
Start residue of secondary structure not found: HELIX 1 1 SER A 2 LYS A 25 1
24  
Start residue of secondary structure not found: HELIX 2 2 SER A 30 LEU A 52 1
23  
Start residue of secondary structure not found: HELIX 3 3 PRO A 61 LEU A 82 1
22  
Start residue of secondary structure not found: HELIX 4 4 SER A 88 MET A 109 1
22  
  
Chain information for Heme4HB with Chls.pdb  
---  
Chain | Description  
3.1/A | No description available  
  

> hide #!2 models

> hide #!1 models

> rainbow #!3.1-2

> show #!3.1-2 atoms

> color #!3.1-2 byhetero

> hide #!3.2 models

> show #!3.2 models

> hide #!3.1 models

> show #!3.1 models

> select #3:CLA

130 atoms, 138 bonds, 8 pseudobonds, 2 residues, 2 models selected  

> color (#!3.2 & sel) forest green

> color sel byhetero

> color (#!3.2 & sel) light sea green

> ui tool show "Color Actions"

> color sel olive drab

> color sel cadet blue

> color sel medium aquamarine

> color sel teal

> color sel dark cyan

> color sel teal

> color sel byhetero

> select Mg

6 atoms, 6 residues, 2 models selected  

> select clear

> save "/Users/drornoy/Documents/Protein Designs/Heme binding 4HB/Ross Heme
> binder with LvWSCP Chls.cxs"

> close #3

> close #2

> show #!1 models

> open 5hpz

5hpz title:  
type II water soluble Chl binding proteins [more info...]  
  
Chain information for 5hpz #2  
---  
Chain | Description  
A B | Water-soluble chlorophyll protein  
  
Non-standard residues in 5hpz #2  
---  
68G — 13'2-hydroxyl-Chlorophyll a  
  
5hpz mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> align #2/A:68G@C[1234][ABCD]@N[ABCD] toAtoms #1:202@C[1234][ABCD]@N[ABCD]
> matchAtomNames true

RMSD between 20 atom pairs is 0.155 angstroms  

> select #1:HEM

86 atoms, 92 bonds, 8 pseudobonds, 2 residues, 2 models selected  

> show sel atoms

> align #2/B:68G@C[1234][ABCD]@N[ABCD] toAtoms #1:201@C[1234][ABCD]@N[ABCD]
> matchAtomNames true move chains

RMSD between 20 atom pairs is 0.199 angstroms  

> select up

925 atoms, 936 bonds, 8 pseudobonds, 111 residues, 2 models selected  

> select up

925 atoms, 936 bonds, 12 pseudobonds, 111 residues, 6 models selected  

> select #2

2722 atoms, 2741 bonds, 10 pseudobonds, 411 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> select #2:68G

132 atoms, 140 bonds, 8 pseudobonds, 2 residues, 2 models selected  

> show sel atoms

> close #2

> style sphere

Changed 925 atom styles  

> style stick

Changed 925 atom styles  

> show #!1.3 models

> show #!1.4 models

> hide #!1.4 models

> show #!1.5 models

> hide #!1.5 models

> hide #!1.3 models

> show #!1.4 models

> show #!1.6 models

> hide #!1.6 models

> show #!1.6 models

> show #!1.5 models

> show #!1.3 models

> hide #!1.3 models

> hide #!1.5 models

> hide #!1.6 models

> hide #!1.4 models

> open 1kzu

Summary of feedback from opening 1kzu fetched from pdb  
---  
notes | Fetching compressed mmCIF 1kzu from
http://files.rcsb.org/download/1kzu.cif  
Fetching CCD RG1 from http://ligand-expo.rcsb.org/reports/R/RG1/RG1.cif  
  
1kzu title:  
Integral membrane peripheral light harvesting complex from rhodopseudomonas
acidophila strain 10050 [more info...]  
  
Chain information for 1kzu #2  
---  
Chain | Description  
A D G | light harvesting protein B-800/850  
B E H | light harvesting protein B-800/850  
  
Non-standard residues in 1kzu #2  
---  
BCL — bacteriochlorophyll A  
RG1 — Rhodopin b-D-glucoside ((3E)-3,4-didehydro-1',2'-dihydro-psi,psi-
caroten-1'-yl beta-D-glucopyranoside)  
  
1kzu mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> hide #!1 models

> show #!2 cartoons

> style #!2 stick

Changed 2961 atom styles  

> show #!2 cartoons

> select #2/A:BCL

132 atoms, 140 bonds, 8 pseudobonds, 2 residues, 2 models selected  

> show #!1 models

> align #2/A:BCL@C[1234][ABCD]@N[ABCD] toAtoms #1:201@C[1234][ABCD]@N[ABCD]
> matchAtomNames true move chains

Pairing dropped 20 atoms and 0 reference atoms  
RMSD between 20 atom pairs is 0.124 angstroms  

> color sel byhetero

> select #2

2961 atoms, 3009 bonds, 45 pseudobonds, 336 residues, 2 models selected  

> color sel byhetero

> align #2/B:BCL@C[1234][ABCD]@N[ABCD] toAtoms #1:202@C[1234][ABCD]@N[ABCD]
> matchAtomNames true move chains

RMSD between 20 atom pairs is 0.171 angstroms  

> select #2

2961 atoms, 3009 bonds, 45 pseudobonds, 336 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> select #2/A-B:BCL

198 atoms, 210 bonds, 12 pseudobonds, 3 residues, 2 models selected  

> show sel atoms

> hide #!1 models

> select #2/A:BCL

132 atoms, 140 bonds, 8 pseudobonds, 2 residues, 2 models selected  

> select #2/A

539 atoms, 548 bonds, 10 pseudobonds, 63 residues, 2 models selected  

> show sel cartoons

> show #!1 models

> select #2/A-B:56

66 atoms, 70 bonds, 4 pseudobonds, 1 residue, 2 models selected  

> hide sel atoms

> select #2/A-B

985 atoms, 1003 bonds, 15 pseudobonds, 110 residues, 2 models selected  

> hide sel cartoons

> help help:user

> select #2/A &backbone

196 atoms, 195 bonds, 49 residues, 1 model selected  

> select #2/A@C@CA@O@N

207 atoms, 195 bonds, 60 residues, 1 model selected  

> select #2/A@C

49 atoms, 49 residues, 1 model selected  

> select #2/A@CA

49 atoms, 49 residues, 1 model selected  

> select #2/A@C@CA@O@N

207 atoms, 195 bonds, 60 residues, 1 model selected  

> show sel cartoons

> align #2/C:12-37@C@O@N@CA toAtoms #1:61-82@C@N@O@CA matchAtomNames true move
> chains

Pairing dropped 0 atoms and 88 reference atoms  
No atoms paired for alignment  

> select #2/C:12-37@C@O@N@CA

Nothing selected  

> align #2/D:12-37@C@O@N@CA toAtoms #1:61-82@C@N@O@CA matchAtomNames true move
> chains

Pairing dropped 16 atoms and 0 reference atoms  
RMSD between 88 atom pairs is 0.592 angstroms  

> select #2/D

539 atoms, 548 bonds, 10 pseudobonds, 63 residues, 2 models selected  

> show sel cartoons

> show sel atoms

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select #2/A-B:BCL

198 atoms, 210 bonds, 12 pseudobonds, 3 residues, 2 models selected  

> show #!2 models

> select #2

2961 atoms, 3009 bonds, 45 pseudobonds, 336 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> select #2/A-B:BCL

198 atoms, 210 bonds, 12 pseudobonds, 3 residues, 2 models selected  

> show sel atoms

> select #2/A-B:56

66 atoms, 70 bonds, 4 pseudobonds, 1 residue, 2 models selected  

> hide sel atoms

> select #1:HEM

86 atoms, 92 bonds, 8 pseudobonds, 2 residues, 2 models selected  

> hide sel atoms

> save "/Users/drornoy/Documents/Protein Designs/Heme binding 4HB/Heme4HB with
> BChls.pdb" displayedOnly true

> save "/Users/drornoy/Documents/Protein Designs/Heme binding 4HB/Ross Heme
> binder with LH2 BChls.cxs"

——— End of log from Wed Jan 19 19:30:16 2022 ———

opened ChimeraX session  

> select :HEM

86 atoms, 92 bonds, 8 pseudobonds, 2 residues, 2 models selected  

> show sel atoms

> hide #!1 models

> show #!1 models

> select #1 &protein

834 atoms, 844 bonds, 1 pseudobond, 104 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> select #1:HEM@FE

2 atoms, 2 residues, 1 model selected  

> style sel sphere

Changed 2 atom styles  

> select #2:BCL@MG

9 atoms, 9 residues, 1 model selected  

> style sel sphere

Changed 9 atom styles  

> select #2:BCL@MG :<3.5 &HIS

Expected a keyword  

> select #2:BCL@MG :<3.5 &:HIS

100 atoms, 100 bonds, 10 residues, 2 models selected  

> show sel atoms

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> select #2/B

446 atoms, 455 bonds, 5 pseudobonds, 47 residues, 2 models selected  

> show sel cartoons

> select up

2961 atoms, 3009 bonds, 45 pseudobonds, 336 residues, 2 models selected  

> select #1 &protein

834 atoms, 844 bonds, 1 pseudobond, 104 residues, 2 models selected  

> show sel cartoons

> hide #!1 models

> hide #!2 cartoons

> show #!1 models

> select #1 &protein

834 atoms, 844 bonds, 1 pseudobond, 104 residues, 2 models selected  

> hide sel cartoons

> save "/Users/drornoy/Documents/Protein Designs/Heme binding 4HB/Ross Heme
> binder with LH2 BChls.cxs"

——— End of log from Tue Feb 1 10:38:31 2022 ———

opened ChimeraX session  




OpenGL version: 3.3.0 NVIDIA 418.67
OpenGL renderer: Quadro K5200/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision Tower 7910
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
Virutal Machine: none
CPU: 48 Intel(R) Xeon(R) CPU E5-2670 v3 @ 2.30GHz
Cache Size: 30720 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           125G        4.0G        114G         54M        6.9G        120G
	Swap:          2.0G        754M        1.3G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK110GL [Quadro K5200] [10de:103c] (rev a1)	
	Subsystem: NVIDIA Corporation GK110GL [Quadro K5200] [10de:1095]	
	Kernel driver in use: nvidia
Locale: ('en_IL', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
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    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
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    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

[Eric Pettersen]

Probable garbage-collection crash

[Tom Goddard]

User was restoring a session that had been dragged and dropped on ChimeraX application. Was in msgpack_deserialize()

def msgpack_deserialize(stream):
    try:
        return next(stream)
    except StopIteration:
        return None

getting the next item from the stream (in the body of the try). I am a bit surprised the drag and drop did not log a command before this crash happened,

[Tom Goddard]

Actually the session restore was initialized by clicking cxcmd link in an html page in the help viewer.

[Tom Goddard]

This is ChimeraX 1.2.5 before the command log for the crash was put into the bug report. So that is why I didn't see the session open command logged.