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#7305 closed defect (duplicate)

Basic Actions session save: 'QEventLoop' object has no attribute 'exec_'

Reported by:	tent.tangpradabkul@…	Owned by:	Zach Pearson
Priority:	normal	Milestone:
Component:	Sessions	Version:
Keywords:		Cc:	Tom Goddard, Eric Pettersen
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
I just recently installed Chimera X to my computer and when I tried to save the session, this error showed up and couldn't let me save the session. 


Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /Users/tenttiya/Downloads/miniPTC-Feb8.cxs format session

Not registering illegal selector name "tRNA-interacting nucleotides"  

Log from Tue Feb 8 17:23:45 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /Users/sarahsmaga/Desktop/miniPTC-7k00.cxs format session

registering illegal selector name "tRNA-interacting nucleotides"  

Log from Wed Jan 26 14:18:02 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /Users/sarahsmaga/Desktop/miniPTC-ribosome.cxs

registering illegal selector name "tRNA-interacting nucleotides"  

Log from Thu Jan 20 17:59:07 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /Users/sarahsmaga/Desktop/miniPTC-ribosome.cxs

Log from Thu Jan 20 10:12:13 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Updating list of available bundles failed: [Errno 61] Connection refused  

> open /Users/sarahsmaga/Downloads/Chimera/PDB/7K00.cif

Summary of feedback from opening
/Users/sarahsmaga/Downloads/Chimera/PDB/7K00.cif  
---  
notes | Fetching CCD PAR from http://ligand-
expo.rcsb.org/reports/P/PAR/PAR.cif  
Fetching CCD SPD from http://ligand-expo.rcsb.org/reports/S/SPD/SPD.cif  
Fetching CCD SPM from http://ligand-expo.rcsb.org/reports/S/SPM/SPM.cif  
Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif  
Fetching CCD G7M from http://ligand-expo.rcsb.org/reports/G/G7M/G7M.cif  
Fetching CCD UR3 from http://ligand-expo.rcsb.org/reports/U/UR3/UR3.cif  
Fetching CCD MA6 from http://ligand-expo.rcsb.org/reports/M/MA6/MA6.cif  
Fetching CCD IAS from http://ligand-expo.rcsb.org/reports/I/IAS/IAS.cif  
Fetching CCD D2T from http://ligand-expo.rcsb.org/reports/D/D2T/D2T.cif  
Fetching CCD 1MG from http://ligand-expo.rcsb.org/reports/1/1MG/1MG.cif  
Fetching CCD 6MZ from http://ligand-expo.rcsb.org/reports/6/6MZ/6MZ.cif  
Fetching CCD 3TD from http://ligand-expo.rcsb.org/reports/3/3TD/3TD.cif  
Fetching CCD OMG from http://ligand-expo.rcsb.org/reports/O/OMG/OMG.cif  
Fetching CCD H2U from http://ligand-expo.rcsb.org/reports/H/H2U/H2U.cif  
Fetching CCD OMC from http://ligand-expo.rcsb.org/reports/O/OMC/OMC.cif  
Fetching CCD 2MA from http://ligand-expo.rcsb.org/reports/2/2MA/2MA.cif  
Fetching CCD OMU from http://ligand-expo.rcsb.org/reports/O/OMU/OMU.cif  
Fetching CCD MEQ from http://ligand-expo.rcsb.org/reports/M/MEQ/MEQ.cif  
Fetching CCD 4D4 from http://ligand-expo.rcsb.org/reports/4/4D4/4D4.cif  
Fetching CCD MS6 from http://ligand-expo.rcsb.org/reports/M/MS6/MS6.cif  
  
7K00.cif title:  
Structure of the Bacterial Ribosome at 2 Angstrom Resolution [more info...]  
  
Chain information for 7K00.cif #1  
---  
Chain | Description  
0 | 50S ribosomal protein L33  
1 | 50S ribosomal protein L34  
2 | 50S ribosomal protein L35  
3 | 50S ribosomal protein L36  
4 | 50S ribosomal protein L31  
5 | E-site tRNA  
A | 16S rRNA  
B | 30S ribosomal protein S2  
C | 30S ribosomal protein S3  
D | 30S ribosomal protein S4  
E | 30S ribosomal protein S5  
F | 30S ribosomal protein S6  
G | 30S ribosomal protein S7  
H | 30S ribosomal protein S8  
I | 30S ribosomal protein S9  
J | 30S ribosomal protein S10  
K | 30S ribosomal protein S11  
L | 30S ribosomal protein S12  
M | 30S ribosomal protein S13  
N | 30S ribosomal protein S14  
O | 30S ribosomal protein S15  
P | 30S ribosomal protein S16  
Q | 30S ribosomal protein S17  
R | 30S ribosomal protein S18  
S | 30S ribosomal protein S19  
T | 30S ribosomal protein S20  
U | 30S ribosomal protein S21  
X | mRNA  
Y | A-site tRNA-val  
Z | P-site tRNA-fMet  
a | 23S rRNA  
b | 5S rRNA  
c | 50S ribosomal protein L2  
d | 50S ribosomal protein L3  
e | 50S ribosomal protein L4  
f | 50S ribosomal protein L5  
g | 50S ribosomal protein L6  
h | 50S ribosomal protein L9  
i | 50S ribosomal protein L13  
j | 50S ribosomal protein L14  
k | 50S ribosomal protein L15  
l | 50S ribosomal protein L16  
m | 50S ribosomal protein L17  
n | 50S ribosomal protein L18  
o | 50S ribosomal protein L19  
p | 50S ribosomal protein L20  
q | 50S ribosomal protein L21  
r | 50S ribosomal protein L22  
s | 50S ribosomal protein L23  
t | 50S ribosomal protein L24  
u | 50S ribosomal protein L25  
v | 50S ribosomal protein L27  
w | 50S ribosomal protein L28  
x | 50S ribosomal protein L29  
y | 50S ribosomal protein L30  
z | 50S ribosomal protein L32  
  
Non-standard residues in 7K00.cif #1  
---  
MG — magnesium ion  
MS6 — (2S)-2-amino-4-(methylsulfanyl)butane-1-thiol  
PAR — paromomycin (paromomycin I; amminosidin; catenulin; crestomycin;
monomycin A; neomycin E)  
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))  
SPM — spermine  
ZN — zinc ion  
  

> sequence chain #1/a

Alignment identifier is 1/a  

> select /a:2043

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select /a:2043-2098

1191 atoms, 1331 bonds, 2 pseudobonds, 56 residues, 2 models selected  

> select /a:2043

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select /a:2043-2625

10521 atoms, 11770 bonds, 501 pseudobonds, 491 residues, 3 models selected  

> name frozen miniPTC sel

> select ~sel

138817 atoms, 142320 bonds, 5734 pseudobonds, 17228 residues, 4 models
selected  

> hide (#!1 & sel) target a

> select /a:2043

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select /a:2043-2064

475 atoms, 532 bonds, 22 residues, 1 model selected  

QGestureManager::deliverEvent: could not find the target for gesture  

> select /a:2043-2091,2228-2258,

Expected an objects specifier or a keyword  

> select /a:2043-2091,2228-2258

1712 atoms, 1912 bonds, 48 pseudobonds, 80 residues, 2 models selected  

> select /a:2043-2091,2228-2258,2426-2625

5991 atoms, 6696 bonds, 281 pseudobonds, 280 residues, 2 models selected  

> name frozen miniPTC-cut sel

> select ~sel

143347 atoms, 147394 bonds, 5954 pseudobonds, 17439 residues, 4 models
selected  

> hide (#!1 & sel) target a

> select /a:2470-2480

232 atoms, 258 bonds, 7 pseudobonds, 11 residues, 2 models selected  

> select /a:2470-2480, 2525-2535

473 atoms, 528 bonds, 11 pseudobonds, 22 residues, 2 models selected  

> color (#!1 & sel) red

> color (#!1 & sel) hot pink

> nucleotides sel atoms

> style nucleic & sel stick

Changed 473 atom styles  

> select

149338 atoms, 154090 bonds, 6235 pseudobonds, 17719 residues, 4 models
selected  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 97795 atom styles  

> nucleotides sel tube/slab shape box

> nucleotides sel tube/slab shape box

> nucleotides sel fill

> style nucleic & sel stick

Changed 97795 atom styles  

> nucleotides sel ladder

> nucleotides sel ladder

> nucleotides sel ladder

> nucleotides sel ladder

> style sel stick

Changed 149338 atom styles  

> style sel stick

Changed 149338 atom styles  

> hide sel atoms

> style sel stick

Changed 149338 atom styles  

> nucleotides sel ladder

> nucleotides sel ladder

> nucleotides sel tube/slab shape box

> nucleotides sel tube/slab shape box

> nucleotides sel tube/slab shape box

> nucleotides sel fill

> style nucleic & sel stick

Changed 97795 atom styles  

> show sel atoms

> show sel cartoons

> show sel cartoons

> select miniPTC-cut

5991 atoms, 6696 bonds, 281 pseudobonds, 280 residues, 2 models selected  

> select ~sel

143347 atoms, 147394 bonds, 5954 pseudobonds, 17439 residues, 4 models
selected  

> hide (#!1 & sel) target a

> cartoon hide (#!1 & sel)

> show sel cartoons

> select clear

> save /Users/sarahsmaga/Desktop/miniPTC-ribosome.cxs

——— End of log from Thu Jan 20 10:12:13 2022 ———

opened ChimeraX session  

> select miniPTC-cut

5991 atoms, 6696 bonds, 281 pseudobonds, 280 residues, 2 models selected  

> select ~sel

143347 atoms, 147394 bonds, 5954 pseudobonds, 17439 residues, 4 models
selected  

> hide (#!1 & sel) target a

> cartoon hide (#!1 & sel)

> select /a:2252

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /a:2252,2602

45 atoms, 49 bonds, 2 residues, 1 model selected  

> color sel cyan

> select clear

> lighting soft

> save /Users/sarahsmaga/Desktop/miniPTC-ribosome.cxs

Drag select of 4311 atoms, 280 residues, 281 pseudobonds, 4739 bonds, 708
shapes  

> select clear

> select /a:2590,2588.2618

Expected an objects specifier or a keyword  

> select /a:2590,2588,2618

68 atoms, 74 bonds, 3 residues, 1 model selected  

> select /a:2555,2553,2583

66 atoms, 71 bonds, 3 residues, 1 model selected  

> select /a:2555,2553,2583, 2585,2551,2552,2451

149 atoms, 161 bonds, 7 residues, 1 model selected  

> name frozen "tRNA-interacting nucleotides" sel

registering illegal selector name "tRNA-interacting nucleotides"  

Drag select of 2013 atoms, 143 residues, 121 pseudobonds, 2208 bonds, 345
shapes  

> color (#!1 & sel) cornflower blue

> select up

3090 atoms, 3443 bonds, 121 pseudobonds, 147 residues, 2 models selected  

> select up

3155 atoms, 3520 bonds, 121 pseudobonds, 147 residues, 2 models selected  

> select up

59130 atoms, 66225 bonds, 121 pseudobonds, 2753 residues, 2 models selected  

> select up

63520 atoms, 66364 bonds, 121 pseudobonds, 7004 residues, 2 models selected  

> select up

149338 atoms, 154090 bonds, 4727 pseudobonds, 17719 residues, 2 models
selected  

> color (#!1 & sel) cornflower blue

> select clear

> select /a:2555,2553,2583, 2585,2551,2552,2451

149 atoms, 161 bonds, 7 residues, 1 model selected  

> name frozen tRNA-int sel

> color sel hot pink

> select clear

> select /a:2471-2479,2527-2535

384 atoms, 428 bonds, 8 pseudobonds, 18 residues, 2 models selected  

> color (#!1 & sel) purple

> select clear

> ui tool show "Basic Actions"

> show /X target c

> show /X target c

> show /X target c

> show /X target c

> hide /X target c

> hide /X target c

> show /Y target c

> show /Y target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> show /Z target c

> show /Z target c

> color /Y #abd0c1 target abp

> color /Y #abd0c1 target abp

> color /Y #abd0c1 target c

> color /Y #abd0c1 target c

> color /Z #a5c7df target c

> color /Z #a5c7df target c

> select /Y:74-76

62 atoms, 68 bonds, 3 residues, 1 model selected  

> select /Y:74-76, Z:74-76

62 atoms, 68 bonds, 3 residues, 1 model selected  

> select /Y:74-76 / Z:74-76

124 atoms, 136 bonds, 6 residues, 1 model selected  

> name frozen CCAends sel

> hide CCAends target abp

> hide CCAends target abp

> hide CCAends target abp

> show sel atoms

> hide /Y target c

> hide /Y target c

> hide /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> nucleotides sel atoms

> style nucleic & sel stick

Changed 124 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 124 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 124 atom styles  

> select /Y:74-76

62 atoms, 68 bonds, 3 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel #abd0c1ff

> select /Z:74-76

62 atoms, 68 bonds, 3 residues, 1 model selected  

> color sel #a5c7dfff

> hide /Y target c

> hide /Y target c

> hide /Y target c

> hide /Y target c

> hide /Y target c

> hide /Y target c

> hide /Y target c

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> hide /Y target c

> hide /Y target c

> hide /Y target c

> hide /Y target c

> hide /Y target c

> hide /Y target c

JS console(basic_actions.js:166:warning): Throttling navigation to prevent the
browser from hanging. See https://crbug.com/882238. Command line switch
--disable-ipc-flooding-protection can be used to bypass the protection  

> hide /Y target c

> hide /Y target c

> hide /Y target c

> hide /Y target c

> hide /Y target c

> hide /Y target c

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> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

JS console(basic_actions.js:166:warning): Throttling navigation to prevent the
browser from hanging. See https://crbug.com/882238. Command line switch
--disable-ipc-flooding-protection can be used to bypass the protection  

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

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> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> hide /Z target c

> nucleotides sel atoms

> style nucleic & sel stick

Changed 62 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 62 atom styles  

> style sel stick

Changed 62 atom styles  

> style sel stick

Changed 62 atom styles  

> style sel ball

Changed 62 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 62 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 62 atom styles  

> hide sel cartoons

> show sel cartoons

> nucleotides sel atoms

> style nucleic & sel stick

Changed 62 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 62 atom styles  

> style sel stick

Changed 62 atom styles  

> style sel stick

Changed 62 atom styles  

> style sel sphere

Changed 62 atom styles  

> style sel ball

Changed 62 atom styles  

> style sel stick

Changed 62 atom styles  

> style sel stick

Changed 62 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 62 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 62 atom styles  

> select /Y:74-76

62 atoms, 68 bonds, 3 residues, 1 model selected  

> style sel stick

Changed 62 atom styles  

> show sel cartoons

> select tRNA-int

149 atoms, 161 bonds, 7 residues, 1 model selected  

> select up

59130 atoms, 66225 bonds, 2753 residues, 1 model selected  

> select up

63520 atoms, 66364 bonds, 7004 residues, 1 model selected  

> select down

59130 atoms, 66225 bonds, 2753 residues, 1 model selected  

> select down

149 atoms, 161 bonds, 7 residues, 1 model selected  

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

> show /Y target c

JS console(basic_actions.js:166:warning): Throttling navigation to prevent the
browser from hanging. See https://crbug.com/882238. Command line switch
--disable-ipc-flooding-protection can be used to bypass the protection  

> show /Z target c

> show /Z target c

> show /Z target c

> show /Z target c

> show /Z target c

> show /Z target c

> show /Z target c

> show /Z target c

> show /Z target c

> show /Z target c

> show /Z target c

> show /Z target c

> show /Z target c

> show /Z target c

> show /Z target c

> show /Z target c

> show /Z target c

> show /Z target c

> show /Z target c

> show /Z target c

> show /Z target c

> show /Z target c

> show /Z target c

> show /Z target c

> select /Y

1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected  

> select /Z

1642 atoms, 1813 bonds, 72 pseudobonds, 95 residues, 2 models selected  

> select /Y

1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected  

> nucleotides sel fill

> style nucleic & sel stick

Changed 1579 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 1579 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 1579 atom styles  

> show sel atoms

> select /Y

1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected  

> select /Z

1642 atoms, 1813 bonds, 72 pseudobonds, 95 residues, 2 models selected  

> show sel atoms

> nucleotides sel fill

> style nucleic & sel stick

Changed 1623 atom styles  

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

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> hide /Z target abp

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> hide /Z target abp

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> hide /Z target abp

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> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

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> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

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> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

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> hide /Z target abp

> hide /Z target abp

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> hide /Z target abp

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> hide /Z target abp

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> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

> hide /Z target abp

JS console(basic_actions.js:166:warning): Throttling navigation to prevent the
browser from hanging. See https://crbug.com/882238. Command line switch
--disable-ipc-flooding-protection can be used to bypass the protection  

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show sel atoms

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

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> show /Z target abp

> show /Z target abp

> show /Z target abp

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> show /Z target abp

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> show /Z target abp

> show /Z target abp

> show /Z target abp

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> show /Z target abp

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> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> show /Z target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

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> color /Z #a5c7df target abp

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> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> nucleotides sel fill

> style nucleic & sel stick

Changed 1623 atom styles  

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> color /Z #a5c7df target abp

> select /Y

1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected  

> show sel atoms

> show sel atoms

> hide sel atoms

> hide sel atoms

> hide sel cartoons

> show sel cartoons

> show sel atoms

> select /Y

1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected  

> select /Y

1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected  

> color sel bynucleotide

> select /Z

1642 atoms, 1813 bonds, 72 pseudobonds, 95 residues, 2 models selected  

> select /Y

1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected  

> color sel bychain

> select /Z

1642 atoms, 1813 bonds, 72 pseudobonds, 95 residues, 2 models selected  

> select /Y

1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected  

> select clear

> select /Y

1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected  

> nucleotides sel fill

> style nucleic & sel stick

Changed 1579 atom styles  

> show sel atoms

> hide sel atoms

> show sel atoms

> nucleotides sel tube/slab shape box

> nucleotides sel tube/slab shape box

> nucleotides sel tube/slab shape box

> nucleotides sel fill

> style nucleic & sel stick

Changed 1579 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 1579 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 1579 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 1579 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 1579 atom styles  

> nucleotides sel tube/slab shape box

> nucleotides sel atoms

> style nucleic & sel stick

Changed 1579 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 1579 atom styles  

> nucleotides sel slab

> style nucleic & sel stick

Changed 1579 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 1579 atom styles  

> save /Users/sarahsmaga/Desktop/miniPTC-ribosome.cxs

——— End of log from Thu Jan 20 17:59:07 2022 ———

opened ChimeraX session  

> save "/Users/sarahsmaga/Desktop/mini PTC.pdb" displayedOnly true relModel #1

> select clear

Drag select of 13 atoms, 4 residues, 2 pseudobonds, 8 shapes, 20 bonds  
Drag select of 2 residues  

> select clear

Drag select of 1 residues, 1 shapes  

> select clear

> select :a 2552,2551

Expected a keyword  

> select :a 2552,2551

Expected a keyword  

> select :a/2552,2551

25586 atoms, 28274 bonds, 143 pseudobonds, 1163 residues, 2 models selected  

> select /a:2552,2551

41 atoms, 44 bonds, 2 residues, 1 model selected  

> select /a:2252,2251

47 atoms, 52 bonds, 2 residues, 1 model selected  

> select :a

25586 atoms, 28274 bonds, 143 pseudobonds, 1163 residues, 2 models selected  

> select miniPTC-cut

5991 atoms, 6696 bonds, 281 pseudobonds, 280 residues, 2 models selected  
Drag select of 611 atoms, 44 residues, 38 pseudobonds, 110 shapes, 674 bonds  

> select clear

> select tRNA-int

149 atoms, 161 bonds, 7 residues, 1 model selected  

> select tRNA-int

149 atoms, 161 bonds, 7 residues, 1 model selected  

> select /Y

1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected  

> select /Z

1642 atoms, 1813 bonds, 72 pseudobonds, 95 residues, 2 models selected  

> select /Y

1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected  

> select :Y,Z

Nothing selected  

> select /Y,Z

3234 atoms, 3577 bonds, 139 pseudobonds, 182 residues, 3 models selected  

> hide sel atoms

> hide sel cartoons

> hide sel cartoons

Drag select of 1460 atoms, 112 residues, 78 pseudobonds, 1620 bonds, 255
shapes  

> color (#!1 & sel) cornflower blue

> select clear

> select /Y,Z

3234 atoms, 3577 bonds, 139 pseudobonds, 182 residues, 3 models selected  

> show sel cartoons

> show sel atoms

> hide sel cartoons

> hide sel atoms

> select /Y,Z:70-76

293 atoms, 325 bonds, 14 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 293 atom styles  

> style sel stick

Changed 293 atom styles  

> style sel stick

Changed 293 atom styles  

> style sel stick

Changed 293 atom styles  

> style sel ball

Changed 293 atom styles  

> style sel stick

Changed 293 atom styles  

> select clear

> select /Y,Z:70-76

293 atoms, 325 bonds, 14 residues, 1 model selected  

> select /Y:70-76

144 atoms, 159 bonds, 7 residues, 1 model selected  

> select /Z:70-76

149 atoms, 166 bonds, 7 residues, 1 model selected  

> color sel orange

> color sel purple

> select /Y:70-76

144 atoms, 159 bonds, 7 residues, 1 model selected  

> color sel light sea green

> select clear

Drag select of 108 atoms, 7 residues, 117 bonds, 21 shapes  

> select up

192 atoms, 213 bonds, 9 residues, 1 model selected  

> select up

59130 atoms, 66225 bonds, 2753 residues, 1 model selected  

> select down

192 atoms, 213 bonds, 9 residues, 1 model selected  

> select up

59130 atoms, 66225 bonds, 2753 residues, 1 model selected  

> select down

192 atoms, 213 bonds, 9 residues, 1 model selected  
Drag select of 288 atoms, 22 residues, 13 pseudobonds, 316 bonds, 52 shapes  

> color (#!1 & sel) cornflower blue

> color (#!1 & sel) red

> select clear

> select CCAends

124 atoms, 136 bonds, 6 residues, 1 model selected  

> select CCAends

124 atoms, 136 bonds, 6 residues, 1 model selected  

> select CCAends

124 atoms, 136 bonds, 6 residues, 1 model selected  

> select sel :< 5

634 atoms, 693 bonds, 13 pseudobonds, 32 residues, 2 models selected  

> select clear

> select CCAends

124 atoms, 136 bonds, 6 residues, 1 model selected  

> select sel :< 3

428 atoms, 468 bonds, 12 pseudobonds, 21 residues, 2 models selected  

> select sel :< 3

959 atoms, 1025 bonds, 30 pseudobonds, 72 residues, 3 models selected  

> select clear

> select /Y, Z

3234 atoms, 3577 bonds, 139 pseudobonds, 182 residues, 3 models selected  

> hide sel surfaces

> hide sel cartoons

> hide sel atoms

> hide sel atoms

> select CCAends

124 atoms, 136 bonds, 6 residues, 1 model selected  

> hide CCAends target abp

> show CCAends target abp

> select sel :< 3

428 atoms, 468 bonds, 12 pseudobonds, 21 residues, 2 models selected  

> color (#!1 & sel) light sea green

> color (#!1 & sel) hot pink

> color (#!1 & sel) magenta

> select sel :< 3

959 atoms, 1025 bonds, 30 pseudobonds, 72 residues, 3 models selected  

> select clear

> select CCAends

124 atoms, 136 bonds, 6 residues, 1 model selected  

> select /Y, Z:70-76

293 atoms, 325 bonds, 14 residues, 1 model selected  

> hide sel atoms

> show sel atoms

> select /Y,

Expected an objects specifier or a keyword  

> select /Y

1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected  

> ui tool show "Color Actions"

> color sel pale green

> color sel aquamarine

> select /Z

1642 atoms, 1813 bonds, 72 pseudobonds, 95 residues, 2 models selected  

> color sel plum

> select clear

> select CCAends

124 atoms, 136 bonds, 6 residues, 1 model selected  

> select up

3202 atoms, 3577 bonds, 150 residues, 1 model selected  

> select CCAends

124 atoms, 136 bonds, 6 residues, 1 model selected  

> select sel :< 3

428 atoms, 468 bonds, 12 pseudobonds, 21 residues, 2 models selected  

> select sel :< 3

959 atoms, 1025 bonds, 30 pseudobonds, 72 residues, 3 models selected  

> select CCAends

124 atoms, 136 bonds, 6 residues, 1 model selected  

> select CCAends

124 atoms, 136 bonds, 6 residues, 1 model selected  

> select sel :< 3

428 atoms, 468 bonds, 12 pseudobonds, 21 residues, 2 models selected  

> select subtract CCAends

304 atoms, 332 bonds, 12 pseudobonds, 15 residues, 2 models selected  

> select subtract /Y

281 atoms, 307 bonds, 12 pseudobonds, 13 residues, 2 models selected  

> select subtract /Z

259 atoms, 282 bonds, 12 pseudobonds, 12 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel khaki

> color sel goldenrod

> color sel gold

> select clear

> show miniPTC target abp

> hide miniPTC target abp

> save /Users/sarahsmaga/Desktop/miniPTC-7k00.cxs

——— End of log from Wed Jan 26 14:18:02 2022 ———

opened ChimeraX session  

> ui tool show "Show Sequence Viewer"

> sequence chain /a

Alignment identifier is 1/a  

> select /a:2450

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select /a:2450

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select /a:2191-2317

2724 atoms, 3047 bonds, 79 pseudobonds, 127 residues, 2 models selected  

> select /a:2317

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select /a:2191-2317

2724 atoms, 3047 bonds, 79 pseudobonds, 127 residues, 2 models selected  

> select clear

> select /a:2555

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select /a:2555

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select /a:2502-2503

46 atoms, 51 bonds, 2 residues, 1 model selected  

> select /a:2502-2517

339 atoms, 377 bonds, 16 residues, 1 model selected  

> select /a:2502-2517,2567-2593

922 atoms, 1029 bonds, 28 pseudobonds, 43 residues, 2 models selected  

> select /a:2502-2517,2567-2610

1286 atoms, 1436 bonds, 50 pseudobonds, 60 residues, 2 models selected  

> select clear

> select a:2058-2079,2241-2258,2427-2463,2487-2522,2543-2609

Expected an objects specifier or a keyword  

> select /a:2058-2079,2241-2258,2427-2463,2487-2522,2543-2609

3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected  

> name frozen Yonath_A2P2 sel

registering illegal selector name "Yonath_A2P2"  

> name frozen Yonath_A2P2 sel

registering illegal selector name "Yonath_A2P2"  

> name frozen Yonath_A2P2 sel

registering illegal selector name "Yonath_A2P2"  

> name frozen A2P2 sel

> select miniPTC-cut

5991 atoms, 6696 bonds, 281 pseudobonds, 280 residues, 2 models selected  

> color (#!1 & sel) cornflower blue

> select A2P2

3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected  

> color (#!1 & sel) purple

> select miniPTC-cut

5991 atoms, 6696 bonds, 281 pseudobonds, 280 residues, 2 models selected  

> color (#!1 & sel) gray

> select A2P2

3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected  

> color (#!1 & sel) cornflower blue

> select clear

> set bgColor white

> lighting simple

> lighting soft

> lighting full

> lighting soft

> lighting shadows true intensity 0.5

> lighting full

> lighting simple

> lighting simple

> lighting flat

> lighting soft

> lighting simple

> lighting soft

> save /Users/sarahsmaga/Desktop/image21.png supersample 3

> save /Users/sarahsmaga/Downloads/miniPTC.cxs

> set bgColor transparent

> save /Users/sarahsmaga/Desktop/image22.png supersample 3

> set bg, transparent

Expected a keyword  

> set bgColor

Missing "bgColor" keyword's argument  

> set bgColor transparent

> save /Users/sarahsmaga/Desktop/image23.png supersample 3

> set bgColor nonesparent

Invalid "bgColor" argument: Invalid color name or specifier  

> set bgColor none

Invalid "bgColor" argument: Invalid color name or specifier  

> set background color none

Expected a keyword  

> set background none

Expected a keyword  

> set bgColor none

Invalid "bgColor" argument: Invalid color name or specifier  

> set bgtransparency

Expected a keyword  

> set bgColor transparent

> ui windowfill toggle

> ui windowfill toggle

> show #!1 target m

> select #1

149338 atoms, 154090 bonds, 6235 pseudobonds, 17719 residues, 4 models
selected  

> hide sel cartoons

> show sel cartoons

> select clear

> select #1

149338 atoms, 154090 bonds, 6235 pseudobonds, 17719 residues, 4 models
selected  

> select miniPTC-cut

5991 atoms, 6696 bonds, 281 pseudobonds, 280 residues, 2 models selected  

> select ~sel

143347 atoms, 147394 bonds, 5954 pseudobonds, 17439 residues, 4 models
selected  

> hide sel cartoons

> select clear

> set bgColor white

> select /a:2058-2075,2434-2463,2487-2522,2543-2609

3226 atoms, 3602 bonds, 147 pseudobonds, 151 residues, 2 models selected  

> name frozen A1P1 sel

> name frozen A1P1 sel

> select A2P2

3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected  

> color (#!1 & sel) gray

> select miniPTC-cut

5991 atoms, 6696 bonds, 281 pseudobonds, 280 residues, 2 models selected  

> color (#!1 & sel) light gray

> select A2P2

3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected  

> color (#!1 & sel) cornflower blue

> select A2P2

3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected  

> select A2P2

3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected  

> select A2P2

3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected  

> select A1P1

3226 atoms, 3602 bonds, 147 pseudobonds, 151 residues, 2 models selected  

> select A2P2

3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected  

> select A1P1

3226 atoms, 3602 bonds, 147 pseudobonds, 151 residues, 2 models selected  

> select A2P2

3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected  

> select A1P1

3226 atoms, 3602 bonds, 147 pseudobonds, 151 residues, 2 models selected  

> select A2P2

3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected  

> select A1P1

3226 atoms, 3602 bonds, 147 pseudobonds, 151 residues, 2 models selected  

> select A1P1

3226 atoms, 3602 bonds, 147 pseudobonds, 151 residues, 2 models selected  

> select A2P2

3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected  

> color (#!1 & sel) light gray

> select A1P1

3226 atoms, 3602 bonds, 147 pseudobonds, 151 residues, 2 models selected  

> color (#!1 & sel) cornflower blue

> select clear

> save /Users/sarahsmaga/Downloads/miniPTC-Feb8.cxs

> select /a:2058-2075,2434-2463,2487-2517,2567-2609

2612 atoms, 2917 bonds, 118 pseudobonds, 122 residues, 2 models selected  

> name frozen A1P1 sel

> name frozen A1P1 sel

> name frozen A1P1 sel

> select A2P2

3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected  

> color (#!1 & sel) light gray

> select A1P1

2612 atoms, 2917 bonds, 118 pseudobonds, 122 residues, 2 models selected  

> color (#!1 & sel) cornflower blue

> select /a:2058-2075,2434-2463,2487-2517,2567-2609

2612 atoms, 2917 bonds, 118 pseudobonds, 122 residues, 2 models selected  

> save /Users/sarahsmaga/Downloads/miniPTC-Feb8.cxs

——— End of log from Tue Feb 8 17:23:45 2022 ———

opened ChimeraX session  

> color miniPTC #d6d6d6 target c

> select /a:2466

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select /a:2466-2468

62 atoms, 68 bonds, 3 residues, 1 model selected  

> select /a:2469

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select /a:2469

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select /a:2468-2469

44 atoms, 49 bonds, 2 residues, 1 model selected  

> select /a:2468-2472

112 atoms, 126 bonds, 5 residues, 1 model selected  

> select /a:2468

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select /a:2468

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select /a:2458

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /a:2458

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /a:2441

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select /a:2441

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select /a:2441

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select /a:2441,2458

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select /a:2070,2441,2458

65 atoms, 70 bonds, 2 pseudobonds, 3 residues, 2 models selected  

> select /a:2070,2441,2458

65 atoms, 70 bonds, 2 pseudobonds, 3 residues, 2 models selected  

> select /a:2070,2083,2441,2458

88 atoms, 95 bonds, 2 pseudobonds, 4 residues, 2 models selected  

> select /a:2070,2083,2237,2441,2458

111 atoms, 120 bonds, 2 pseudobonds, 5 residues, 2 models selected  

> select /a:2070,2083,2237,2253-2254,2441,2458

154 atoms, 167 bonds, 2 pseudobonds, 7 residues, 2 models selected  

> select /a:2043,2070,2083,2237,2253-2254,2441,2458

174 atoms, 188 bonds, 2 pseudobonds, 8 residues, 2 models selected  

> select /a:2043,2070,2083,2237,2253-2254,2441,2458,2625

197 atoms, 213 bonds, 5 pseudobonds, 9 residues, 2 models selected  

> select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2625

240 atoms, 260 bonds, 5 pseudobonds, 11 residues, 2 models selected  

> select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2625

240 atoms, 260 bonds, 5 pseudobonds, 11 residues, 2 models selected  

> select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2625

240 atoms, 260 bonds, 5 pseudobonds, 11 residues, 2 models selected  

> select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2625

240 atoms, 260 bonds, 5 pseudobonds, 11 residues, 2 models selected  

> select /a:746,955,1911,1917,2457,2504,2580,2604-2605

180 atoms, 190 bonds, 9 residues, 1 model selected  

> select /a:746,955,1911,1917,2457,2504,2580,2604-2605

180 atoms, 190 bonds, 9 residues, 1 model selected  

> select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2625

240 atoms, 260 bonds, 5 pseudobonds, 11 residues, 2 models selected  

> select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2625

240 atoms, 260 bonds, 5 pseudobonds, 11 residues, 2 models selected  

> select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2508,2625

283 atoms, 308 bonds, 5 pseudobonds, 13 residues, 2 models selected  

> select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2508,2625

283 atoms, 308 bonds, 5 pseudobonds, 13 residues, 2 models selected  

> select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2508,2625

283 atoms, 308 bonds, 5 pseudobonds, 13 residues, 2 models selected  

> select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2508,2625

283 atoms, 308 bonds, 5 pseudobonds, 13 residues, 2 models selected  

> select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2508,2625

283 atoms, 308 bonds, 5 pseudobonds, 13 residues, 2 models selected  

> select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2509,2625

306 atoms, 334 bonds, 5 pseudobonds, 14 residues, 2 models selected  

> select /a:2516

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select /a:2516

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2625

240 atoms, 260 bonds, 5 pseudobonds, 11 residues, 2 models selected  

> select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2625

240 atoms, 260 bonds, 5 pseudobonds, 11 residues, 2 models selected  

> select /a:2516

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select /a:2516

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2625

240 atoms, 260 bonds, 5 pseudobonds, 11 residues, 2 models selected  

> select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2516,2625

262 atoms, 284 bonds, 5 pseudobonds, 12 residues, 2 models selected  

> select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2516,2568,2625

282 atoms, 305 bonds, 7 pseudobonds, 13 residues, 2 models selected  

> name frozen PTC_1-1 sel

[Repeated 1 time(s)]

> select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2516,2568,2625

282 atoms, 305 bonds, 7 pseudobonds, 13 residues, 2 models selected  

> select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2516,2568,2625

282 atoms, 305 bonds, 7 pseudobonds, 13 residues, 2 models selected  

> select /a:2504

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select /a:2504-2506

63 atoms, 69 bonds, 3 residues, 1 model selected  

> select /a:2508

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /a:2506-2508

63 atoms, 69 bonds, 3 residues, 1 model selected  

> select /a:2505

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /a:2505

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /a:2505,2516-2517

65 atoms, 71 bonds, 3 residues, 1 model selected  

> select /a:2505

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /a:2505-2506

43 atoms, 47 bonds, 2 residues, 1 model selected  

> select /a:2505-2506

43 atoms, 47 bonds, 2 residues, 1 model selected  

> select /a:2507-2508

43 atoms, 47 bonds, 2 residues, 1 model selected  

> select /a:2507-2510

86 atoms, 95 bonds, 4 residues, 1 model selected  

> select /a:2505,2507-2510

109 atoms, 120 bonds, 5 residues, 1 model selected  

> select /a:2510-2511

40 atoms, 43 bonds, 2 residues, 1 model selected  

> select /a:2507-2511

106 atoms, 117 bonds, 5 residues, 1 model selected  

> select /a:2508-2509

46 atoms, 51 bonds, 2 residues, 1 model selected  

> select /a:2508-2511

86 atoms, 95 bonds, 4 residues, 1 model selected  

> select /a:2506

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select /a:2506-2508

63 atoms, 69 bonds, 3 residues, 1 model selected  

> select /a:2506-2507

40 atoms, 43 bonds, 2 residues, 1 model selected  

> select /a:2506-2508

63 atoms, 69 bonds, 3 residues, 1 model selected  

> select /a:2506-2507

40 atoms, 43 bonds, 2 residues, 1 model selected  

> select /a:2506-2508

63 atoms, 69 bonds, 3 residues, 1 model selected  

> select /a:2505

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /a:2505

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /a:2505,2516

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select /a:2505,2516,2625

68 atoms, 74 bonds, 3 residues, 1 model selected  

> select /a:2441,2505,2516,2625

88 atoms, 95 bonds, 4 residues, 1 model selected  

> select /a:2253-2254,2441,2505,2516,2625

131 atoms, 142 bonds, 6 residues, 1 model selected  

> select /a:2253-2254,2441,2458,2505,2516,2625

154 atoms, 167 bonds, 7 residues, 1 model selected  

> select /a:2237,2253-2254,2441,2458,2505,2516,2625

177 atoms, 192 bonds, 8 residues, 1 model selected  

> select /a:2083,2237,2253-2254,2441,2458,2505,2516,2625

200 atoms, 217 bonds, 9 residues, 1 model selected  

> select /a:2043,2083,2237,2253-2254,2441,2458,2505,2516,2625

220 atoms, 238 bonds, 3 pseudobonds, 10 residues, 2 models selected  

> select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505,2516,2625

242 atoms, 262 bonds, 5 pseudobonds, 11 residues, 2 models selected  

> select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505,2516,2568,2625

262 atoms, 283 bonds, 7 pseudobonds, 12 residues, 2 models selected  

> name frozen 1-1_mut sel

Not registering illegal selector name "1-1_mut"  

> name frozen 1-1_mut sel

Not registering illegal selector name "1-1_mut"  

> name frozen 1-1_mut sel

Not registering illegal selector name "1-1_mut"  

> name frozen 1-1 sel

Not registering illegal selector name "1-1"  

> name frozen 1-1 sel

Not registering illegal selector name "1-1"  

> name frozen mut sel

[Repeated 1 time(s)]

> select mut

262 atoms, 283 bonds, 7 pseudobonds, 12 residues, 2 models selected  

> select PTC_1-1

282 atoms, 305 bonds, 7 pseudobonds, 13 residues, 2 models selected  

> save /Users/tenttiya/Desktop/1-1.cxs

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 225, in take_snapshot  
self.add_webview_state(data)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 260, in add_webview_state  
event_loop.exec_()  
AttributeError: 'QEventLoop' object has no attribute 'exec_'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd8e8514f10> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7fd8dbd98c70> 'Basic
Actions'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fd8e8514f10> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x7fd8dbd98c70> 'Basic Actions': Error while saving session data for 'tools'
-> <chimerax.core.tools.Tools object at 0x7fd8e8514f10> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7fd8dbd98c70> 'Basic
Actions'  
  

Populating font family aliases took 294 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.  

ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 225, in take_snapshot  
self.add_webview_state(data)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 260, in add_webview_state  
event_loop.exec_()  
AttributeError: 'QEventLoop' object has no attribute 'exec_'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd8e8514f10> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7fd8dbd98c70> 'Basic
Actions'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fd8e8514f10> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x7fd8dbd98c70> 'Basic Actions': Error while saving session data for 'tools'
-> <chimerax.core.tools.Tools object at 0x7fd8e8514f10> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7fd8dbd98c70> 'Basic
Actions'  
  
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save /Users/tenttiya/Desktop/PTC_1-1.cxs

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 225, in take_snapshot  
self.add_webview_state(data)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 260, in add_webview_state  
event_loop.exec_()  
AttributeError: 'QEventLoop' object has no attribute 'exec_'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd8e8514f10> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7fd8dbd98c70> 'Basic
Actions'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fd8e8514f10> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x7fd8dbd98c70> 'Basic Actions': Error while saving session data for 'tools'
-> <chimerax.core.tools.Tools object at 0x7fd8e8514f10> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7fd8dbd98c70> 'Basic
Actions'  
  
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 225, in take_snapshot  
self.add_webview_state(data)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 260, in add_webview_state  
event_loop.exec_()  
AttributeError: 'QEventLoop' object has no attribute 'exec_'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd8e8514f10> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7fd8dbd98c70> 'Basic
Actions'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fd8e8514f10> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x7fd8dbd98c70> 'Basic Actions': Error while saving session data for 'tools'
-> <chimerax.core.tools.Tools object at 0x7fd8e8514f10> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7fd8dbd98c70> 'Basic
Actions'  
  
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 10
      L2 Cache: 20 MB
      Memory: 16 GB

Software:

    System Software Overview:

      System Version: macOS 12.1 (21C52)
      Kernel Version: Darwin 21.2.0
      Time since boot: 1 day 16:24

Graphics/Displays:

    Apple G13X:

      Chipset Model: Apple G13X
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc:	Tom Goddard Eric Pettersen added
Component:	Unassigned → Sessions
Owner:	set to Zach Pearson
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Basic Actions session save: 'QEventLoop' object has no attribute 'exec_'

comment:2 by Eric Pettersen, 3 years ago

Resolution:	→ duplicate
Status:	assigned → closed

Hi Tent,

Thanks for reporting this problem. It has been fixed and the fix is in the daily build, so if you use that you won't run into it anymore. Alternatively, if you close the Basic Actions tool before saving a session, that will work too.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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