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#14997 closed defect (duplicate)

ISOLDE: ResidueStepper references dead Structure

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

Description

The following bug report has been submitted:
Platform:        macOS-11.4-x86_64-i386-64bit
ChimeraX Version: 1.7rc202311302110 (2023-11-30 21:10:26 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.7rc202311302110 (2023-11-30)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Volumes/Transcend/Hashem'lab Results - New - updated/Shu-Bing Qian
> project/density map/15nu-pull down-high resolution/modeling /P17_J79 - with
> eIF3 model/auto refinment/P17_J79 model-step 9- map_refined-eIF5N-ter
> location from yeast model.cxs"

restore_snapshot for "NXmapHandler" returned None  

restore_snapshot for "FastVolumeSurface" returned None  

Exception ignored in: <function Drawing.__del__ at 0x10bde4680>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1215, in __del__  
if not self.was_deleted:  
^^^^^^^^^^^^^^^^  
AttributeError: 'MDFFMgr' object has no attribute 'was_deleted'  

restore_snapshot for "MDFFMgr" returned None  

Restoring stepper: P17_J79 model-step 7- map_refined-eIF5N-ter location from
yeast model.cif  
Log from Fri Apr 19 15:47:35 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "D:\\\Rafa\\\OneDrive\\\Desktop\\\P17_J79-witheIF3\\\P17_J79 model-step
> 8- map_refined-eIF5N-ter location from yeast model.cxs"

Opened cryosparc_P17_J79_003_volume_map_sharp (1).mrc as #1.1.1.1, grid size
500,500,500, pixel 0.93, shown at level 0.22, step 1, values float32  
Restoring stepper: P17_J79 model-step 7- map_refined-eIF5N-ter location from
yeast model.cif  
Log from Wed Apr 17 18:00:16 2024 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> "D:/Rafa/OneDrive/Desktop/P17_J79-witheIF3/cryosparc_P17_J79_003_volume_map_sharp
> (1).mrc" "D:/Rafa/OneDrive/Desktop/P17_J79-witheIF3/P17_J79 model-step 7-
> map_refined-eIF5N-ter location from yeast model.cif"

Summary of feedback from opening
D:/Rafa/OneDrive/Desktop/P17_J79-witheIF3/P17_J79 model-step 7- map_refined-
eIF5N-ter location from yeast model.cif  
---  
warnings | Unknown polymer entity '51' near line 262996  
Atom HO5' is not in the residue template for A /1:2  
Atom H6 is not in the residue template for T6A /1:37  
Atom HO5' is not in the residue template for U /2:1  
Atom H2' is not in the residue template for C4J /2:1244  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Opened cryosparc_P17_J79_003_volume_map_sharp (1).mrc as #1, grid size
500,500,500, pixel 0.93, shown at level 0.103, step 2, values float32  
Chain information for P17_J79 model-step 7- map_refined-eIF5N-ter location
from yeast model.cif #2  
---  
Chain | Description  
1 | initiator methionylated tRNA  
2 | 18S ribosomal RNA  
3 | beta-globin mRNA  
A | eukaryotic translation initiation factor 2 subunit alpha  
B | eukaryotic translation initiation factor 2 subunit gamma  
C | 40S ribosomal protein uS2  
D | 40S ribosomal protein eS1  
E | 40S ribosomal protein uS5  
F | 40S ribosomal protein uS3  
G | 40S ribosomal protein eS4  
H | 40S ribosomal protein uS7  
I | 40S ribosomal protein eS6  
J | ribosomal protein eS7  
K | 40S ribosomal protein eS8  
L | 40S ribosomal protein uS4  
M | 40S ribosomal protein eS10  
N | 40S ribosomal protein uS17  
O | 40S ribosomal protein eS12  
P | ribosomal protein uS15  
Q | 40S ribosomal protein uS11  
R | 40S ribosomal protein uS19  
S | 40S ribosomal protein uS9  
T | 40S ribosomal protein eS17  
U | 40S ribosomal protein uS13  
V | 40S ribosomal protein eS19  
W | 40S ribosomal protein uS10  
X | 40S ribosomal protein eS21  
Y | 40S ribosomal protein uS8  
Z | 40S ribosomal protein uS12  
a | 40S ribosomal protein eS24  
b | 40S ribosomal protein eS26  
c | 40S ribosomal protein eS27  
d | 40S ribosomal protein eS28  
e | ribosomal protein uS14  
f | ribosomal protein eS31  
g | ribosomal protein RACK1  
i | 40S ribosomal protein eS30  
j | eukaryotic translation initiation factor 1A  
k | ATP-binding cassette sub-family E member 1 (ABCE1)  
l | 60s ribosomal protein l41  
m | eukaryotic translation initiation factor 3 subunit d  
n | ribosomal protein eS25  
o | Eukaryotic translation initiation factor 5  
q | Eukaryotic translation initiation factor 3 subunit F  
r | eukaryotic translation initiation factor 3 subunit h  
s | Eukaryotic translation initiation factor 3 subunit K  
t | eukaryotic translation initiation factor 3 subunit l  
u | Eukaryotic translation initiation factor 3 subunit M  
v | Eukaryotic translation initiation factor 3 subunit C  
w | Eukaryotic translation initiation factor 3 subunit E  
y | Eukaryotic translation initiation factor 3 subunit A  
  

> clipper associate #1 toModel #2

Opened cryosparc_P17_J79_003_volume_map_sharp (1).mrc as #1.1.1.1, grid size
500,500,500, pixel 0.93, shown at level 0.22, step 1, values float32  
Chain information for P17_J79 model-step 7- map_refined-eIF5N-ter location
from yeast model.cif  
---  
Chain | Description  
1.2/1 | initiator methionylated tRNA  
1.2/2 | 18S ribosomal RNA  
1.2/3 | beta-globin mRNA  
1.2/A | eukaryotic translation initiation factor 2 subunit alpha  
1.2/B | eukaryotic translation initiation factor 2 subunit gamma  
1.2/C | 40S ribosomal protein uS2  
1.2/D | 40S ribosomal protein eS1  
1.2/E | 40S ribosomal protein uS5  
1.2/F | 40S ribosomal protein uS3  
1.2/G | 40S ribosomal protein eS4  
1.2/H | 40S ribosomal protein uS7  
1.2/I | 40S ribosomal protein eS6  
1.2/J | ribosomal protein eS7  
1.2/K | 40S ribosomal protein eS8  
1.2/L | 40S ribosomal protein uS4  
1.2/M | 40S ribosomal protein eS10  
1.2/N | 40S ribosomal protein uS17  
1.2/O | 40S ribosomal protein eS12  
1.2/P | ribosomal protein uS15  
1.2/Q | 40S ribosomal protein uS11  
1.2/R | 40S ribosomal protein uS19  
1.2/S | 40S ribosomal protein uS9  
1.2/T | 40S ribosomal protein eS17  
1.2/U | 40S ribosomal protein uS13  
1.2/V | 40S ribosomal protein eS19  
1.2/W | 40S ribosomal protein uS10  
1.2/X | 40S ribosomal protein eS21  
1.2/Y | 40S ribosomal protein uS8  
1.2/Z | 40S ribosomal protein uS12  
1.2/a | 40S ribosomal protein eS24  
1.2/b | 40S ribosomal protein eS26  
1.2/c | 40S ribosomal protein eS27  
1.2/d | 40S ribosomal protein eS28  
1.2/e | ribosomal protein uS14  
1.2/f | ribosomal protein eS31  
1.2/g | ribosomal protein RACK1  
1.2/i | 40S ribosomal protein eS30  
1.2/j | eukaryotic translation initiation factor 1A  
1.2/k | ATP-binding cassette sub-family E member 1 (ABCE1)  
1.2/l | 60s ribosomal protein l41  
1.2/m | eukaryotic translation initiation factor 3 subunit d  
1.2/n | ribosomal protein eS25  
1.2/o | Eukaryotic translation initiation factor 5  
1.2/q | Eukaryotic translation initiation factor 3 subunit F  
1.2/r | eukaryotic translation initiation factor 3 subunit h  
1.2/s | Eukaryotic translation initiation factor 3 subunit K  
1.2/t | eukaryotic translation initiation factor 3 subunit l  
1.2/u | Eukaryotic translation initiation factor 3 subunit M  
1.2/v | Eukaryotic translation initiation factor 3 subunit C  
1.2/w | Eukaryotic translation initiation factor 3 subunit E  
1.2/y | Eukaryotic translation initiation factor 3 subunit A  
  

> volume #1.1.1.1 style surface

> transparency 50

> select #1/1,3

3250 atoms, 3505 bonds, 68 pseudobonds, 100 residues, 2 models selected  

> select #1/1

2437 atoms, 2628 bonds, 63 pseudobonds, 75 residues, 2 models selected  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Done loading forcefield  

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  

> select #1/1

2437 atoms, 2628 bonds, 63 pseudobonds, 75 residues, 2 models selected  

> isolde sim start /1

Sim termination reason: None  
ISOLDE: stopped sim  
Loading residue template for GNP from internal database  

> setattr g display false

Assigning display attribute to 3 items  

> isolde ignore #1/2:1244

ISOLDE: currently ignoring 1 residues in model 1.2  

> select #1/1

2437 atoms, 2628 bonds, 63 pseudobonds, 75 residues, 2 models selected  

> isolde sim start /1

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select #1/3

813 atoms, 877 bonds, 25 residues, 1 model selected  

> isolde sim start /3

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> ui tool show "Ramachandran Plot"

> isolde sim start /j:66

ISOLDE: started sim  

> isolde pepflip /j:66

> isolde pepflip /j:67

> isolde pepflip /j:68

> isolde pepflip /j:69

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /u:108

ISOLDE: started sim  

> isolde pepflip /u:108

> isolde pepflip /u:109

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /r:291

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /k:320

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /k:325

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /k:319

ISOLDE: started sim  

> isolde pepflip /k:319

> isolde pepflip /k:320

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /k:328

ISOLDE: started sim  

> select clear

> isolde pepflip /k:328

> isolde pepflip /k:329

> isolde pepflip /k:332

> isolde pepflip /k:330

> isolde pepflip /k:331

> isolde pepflip /k:330

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /f:147

ISOLDE: started sim  

> select clear

> isolde pepflip /f:147

[Repeated 1 time(s)]

> isolde pepflip /f:148

[Repeated 1 time(s)]

> isolde pepflip /f:146

> select clear

> isolde pepflip /f:147

[Repeated 1 time(s)]

> isolde pepflip /f:148

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /b:46

ISOLDE: started sim  

> isolde pepflip /b:46

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /j:10

ISOLDE: started sim  

> select clear

> isolde pepflip /j:10

> isolde pepflip /j:12

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /R:52

ISOLDE: started sim  

> isolde pepflip /R:52

> isolde pepflip /R:50

> select clear

[Repeated 1 time(s)]

> isolde pepflip /R:49

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /u:193

ISOLDE: started sim  

> isolde pepflip /u:193

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /U:144

ISOLDE: started sim  

> isolde pepflip /U:144

> isolde pepflip /U:143

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /w:245

ISOLDE: started sim  

> isolde pepflip /w:245

> isolde pepflip /w:242

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /k:349

ISOLDE: started sim  

> isolde pepflip /k:349

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /Q:138

ISOLDE: started sim  

> isolde pepflip /Q:138

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /d:52

ISOLDE: started sim  

> isolde pepflip /d:52

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /d:47

ISOLDE: started sim  

> select clear

> isolde pepflip /d:47

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /a:101

ISOLDE: started sim  

> isolde pepflip /a:101

> isolde pepflip /a:105

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /r:227

ISOLDE: started sim  

> isolde pepflip /r:227

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /q:240

ISOLDE: started sim  

> isolde pepflip /q:240

> isolde pepflip /q:241

> isolde pepflip /q:239

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /r:53

ISOLDE: started sim  

> isolde sim pause

> isolde sim resume

> isolde pepflip /r:53

[Repeated 1 time(s)]

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /r:123

ISOLDE: started sim  

> isolde pepflip /r:123

> isolde pepflip /r:124

> select clear

> isolde pepflip /r:125

> isolde pepflip /r:126

> select clear

> isolde pepflip /r:125

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /O:81

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /O:107

ISOLDE: started sim  

> isolde pepflip /O:107

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /O:113

ISOLDE: started sim  

> isolde pepflip /O:114

> isolde pepflip /O:113

[Repeated 1 time(s)]

> isolde pepflip /O:112

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /T:92

ISOLDE: started sim  

> isolde pepflip /T:92

> select clear

> isolde pepflip /T:93

> isolde pepflip /T:94

> isolde pepflip /T:93

> isolde pepflip /T:92

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /F:197

ISOLDE: started sim  

> isolde pepflip /F:197

> isolde pepflip /F:192

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /O:119

ISOLDE: started sim  

> isolde pepflip /O:119

> isolde pepflip /O:118

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /U:89

ISOLDE: started sim  

> isolde pepflip /U:89

> isolde pepflip /U:90

[Repeated 1 time(s)]

> isolde pepflip /U:89

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /R:37

ISOLDE: started sim  

> isolde pepflip /R:38

[Repeated 1 time(s)]

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /g:264

ISOLDE: started sim  

> isolde pepflip /g:264

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /g:246

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /k:446

ISOLDE: started sim  

> isolde pepflip /k:446

[Repeated 1 time(s)]

> isolde pepflip /k:447

> isolde pepflip /k:295

[Repeated 1 time(s)]

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /y:219

ISOLDE: started sim  

> isolde pepflip /y:219

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /S:116

ISOLDE: started sim  

> isolde pepflip /S:110

[Repeated 1 time(s)]

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /S:110

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /j:17

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /j:21

ISOLDE: started sim  

> isolde pepflip /j:21

> select clear

> isolde pepflip /j:20

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /y:131

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /A:243

ISOLDE: started sim  

> isolde pepflip /A:244

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /u:132

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /k:194

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /k:277

ISOLDE: started sim  

> isolde pepflip /k:277

> isolde pepflip /k:111

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /k:111

ISOLDE: started sim  

> select clear

> isolde pepflip /k:111

> isolde pepflip /k:294

[Repeated 2 time(s)]

> isolde pepflip /k:295

Unable to flip peptide bond after 50 rounds. Giving up.  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /K:53

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /K:6

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /R:84

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /J:100

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save "D:/Rafa/OneDrive/Desktop/P17_J79-witheIF3/P17_J79 model-step 8-
> map_refined-eIF5N-ter location from yeast model.cif" relModel #1.2

Not saving entity_poly_seq for non-authoritative sequences  

> save "D:/Rafa/OneDrive/Desktop/P17_J79-witheIF3/P17_J79 model-step 8-
> map_refined-eIF5N-ter location from yeast model.cif"

Not saving entity_poly_seq for non-authoritative sequences  

> save "D:/Rafa/OneDrive/Desktop/P17_J79-witheIF3/P17_J79 model-step 8-
> map_refined-eIF5N-ter location from yeast model.cxs"

Taking snapshot of stepper: P17_J79 model-step 7- map_refined-eIF5N-ter
location from yeast model.cif  

> isolde sim start /R:50

ISOLDE: started sim  

> isolde pepflip /R:50

> isolde pepflip /R:51

[Repeated 1 time(s)]

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save "D:/Rafa/OneDrive/Desktop/P17_J79-witheIF3/P17_J79 model-step 8-
> map_refined-eIF5N-ter location from yeast model.cxs"

Taking snapshot of stepper: P17_J79 model-step 7- map_refined-eIF5N-ter
location from yeast model.cif  

——— End of log from Wed Apr 17 18:00:16 2024 ———

opened ChimeraX session  

> select #1&protein

162209 atoms, 163626 bonds, 9958 residues, 1 model selected  

> hide sel cartoons

> ui tool show "Volume Viewer"

> volume #1.1.1.1 level 0.1362

> volume #1.1.1.1 level 0.2167

> volume #1.1.1.1 level 0.1398

> volume #1.1.1.1 level 0.1871

> select #1/m

5859 atoms, 5919 bonds, 365 residues, 1 model selected  

> show sel cartoons

> select /j:70@CD2

1 atom, 1 residue, 1 model selected  

> select up

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

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  

> select up

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

> isolde sim start /j:70

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select up

22 atoms, 21 bonds, 1 residue, 2 models selected  

> select #1/m

5859 atoms, 5919 bonds, 365 residues, 1 model selected  

> select up

221546 atoms, 227622 bonds, 11806 residues, 1 model selected  

> isolde sim start /j:16

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select up

34 atoms, 36 bonds, 1 residue, 1 model selected  

> isolde sim start /3:153

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select #1/o

2337 atoms, 2361 bonds, 147 residues, 1 model selected  

> show sel cartoons

> volume #1.1.1.1 level 0.1052

> select clear

> hide #!1.1 models

> select #1

221546 atoms, 227622 bonds, 1622 pseudobonds, 11806 residues, 27 models
selected  

> hide sel atoms

> select clear

> show atoms

> show #!1.1 models

> volume #1.1.1.1 level 0.2296

> save "D:/Rafa/OneDrive/Desktop/P17_J79-witheIF3/P17_J79 model-step 9-
> map_refined-eIF5N-ter location from yeast model.cif"

Not saving entity_poly_seq for non-authoritative sequences  

> save "D:/Rafa/OneDrive/Desktop/P17_J79-witheIF3/P17_J79 model-step 9-
> map_refined-eIF5N-ter location from yeast model.cxs"

Taking snapshot of stepper: P17_J79 model-step 7- map_refined-eIF5N-ter
location from yeast model.cif  

——— End of log from Fri Apr 19 15:47:35 2024 ———

opened ChimeraX session  

> save "/Volumes/Transcend/Hashem'lab Results - New - updated/Shu-Bing Qian
> project/density map/15nu-pull down-high resolution/modeling /P17_J79 - with
> eIF3 model/auto refinment/P17_J79 model-step 9.cif"

Not saving entity_poly_seq for non-authoritative sequences  

> close session

> open "/Volumes/Transcend/Hashem'lab Results - New - updated/Shu-Bing Qian
> project/density map/15nu-pull down-high resolution/modeling /P17_J79 - with
> eIF3 model/auto refinment/P17_J79 model-step 9.cif"

Summary of feedback from opening /Volumes/Transcend/Hashem'lab Results - New -
updated/Shu-Bing Qian project/density map/15nu-pull down-high
resolution/modeling /P17_J79 - with eIF3 model/auto refinment/P17_J79 model-
step 9.cif  
---  
warnings | Unknown polymer entity '51' near line 262996  
Atom HO5' is not in the residue template for A /1:2  
Atom H6 is not in the residue template for T6A /1:37  
Atom HO5' is not in the residue template for U /2:1  
Atom H2' is not in the residue template for C4J /2:1244  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for P17_J79 model-step 9.cif #1  
---  
Chain | Description  
1 | initiator methionylated tRNA  
2 | 18S ribosomal RNA  
3 | beta-globin mRNA  
A | eukaryotic translation initiation factor 2 subunit alpha  
B | eukaryotic translation initiation factor 2 subunit gamma  
C | 40S ribosomal protein uS2  
D | 40S ribosomal protein eS1  
E | 40S ribosomal protein uS5  
F | 40S ribosomal protein uS3  
G | 40S ribosomal protein eS4  
H | 40S ribosomal protein uS7  
I | 40S ribosomal protein eS6  
J | ribosomal protein eS7  
K | 40S ribosomal protein eS8  
L | 40S ribosomal protein uS4  
M | 40S ribosomal protein eS10  
N | 40S ribosomal protein uS17  
O | 40S ribosomal protein eS12  
P | ribosomal protein uS15  
Q | 40S ribosomal protein uS11  
R | 40S ribosomal protein uS19  
S | 40S ribosomal protein uS9  
T | 40S ribosomal protein eS17  
U | 40S ribosomal protein uS13  
V | 40S ribosomal protein eS19  
W | 40S ribosomal protein uS10  
X | 40S ribosomal protein eS21  
Y | 40S ribosomal protein uS8  
Z | 40S ribosomal protein uS12  
a | 40S ribosomal protein eS24  
b | 40S ribosomal protein eS26  
c | 40S ribosomal protein eS27  
d | 40S ribosomal protein eS28  
e | ribosomal protein uS14  
f | ribosomal protein eS31  
g | ribosomal protein RACK1  
i | 40S ribosomal protein eS30  
j | eukaryotic translation initiation factor 1A  
k | ATP-binding cassette sub-family E member 1 (ABCE1)  
l | 60s ribosomal protein l41  
m | eukaryotic translation initiation factor 3 subunit d  
n | ribosomal protein eS25  
o | Eukaryotic translation initiation factor 5  
q | Eukaryotic translation initiation factor 3 subunit F  
r | eukaryotic translation initiation factor 3 subunit h  
s | Eukaryotic translation initiation factor 3 subunit K  
t | eukaryotic translation initiation factor 3 subunit l  
u | Eukaryotic translation initiation factor 3 subunit M  
v | Eukaryotic translation initiation factor 3 subunit C  
w | Eukaryotic translation initiation factor 3 subunit E  
y | Eukaryotic translation initiation factor 3 subunit A  
  

> open "/Volumes/Transcend/Hashem'lab Results - New - updated/Shu-Bing Qian
> project/density map/15nu-pull down-high
> resolution/48SIC+eIF3/cryosparc_P17_J79_003_volume_map_sharp (1).mrc"

Opened cryosparc_P17_J79_003_volume_map_sharp (1).mrc as #2, grid size
500,500,500, pixel 0.93, shown at level 0.103, step 2, values float32  

> select add #1

221546 atoms, 227622 bonds, 1622 pseudobonds, 11806 residues, 4 models
selected  

> select subtract #1

Nothing selected  

> select add #1

221546 atoms, 227622 bonds, 1622 pseudobonds, 11806 residues, 4 models
selected  

> hide sel atoms

> show sel cartoons

> set bgColor white

> color sel light salmon

> select /2:892

30 atoms, 31 bonds, 1 residue, 1 model selected  

> select up

55980 atoms, 60373 bonds, 1743 residues, 1 model selected  

> color sel gold

> select clear

Drag select of 14 residues  

> select up

1231 atoms, 1240 bonds, 79 residues, 1 model selected  

> select up

9531 atoms, 9618 bonds, 595 residues, 1 model selected  

> color sel forest green

> select /y:90

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select up

563 atoms, 563 bonds, 35 residues, 1 model selected  

> select up

10038 atoms, 10126 bonds, 603 residues, 1 model selected  

> color sel red

> select /v:458

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select up

277 atoms, 277 bonds, 16 residues, 1 model selected  

> select up

9044 atoms, 9123 bonds, 554 residues, 1 model selected  

> color sel blue

> select /w:306

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

> select up

256 atoms, 256 bonds, 16 residues, 1 model selected  

> select up

6921 atoms, 6994 bonds, 419 residues, 1 model selected  

> color sel lime

> select /u:40

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select up

204 atoms, 204 bonds, 15 residues, 1 model selected  

> select up

5878 atoms, 5923 bonds, 365 residues, 1 model selected  

> color sel pink

> select /s:8

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

> select down

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

> select up

148 atoms, 147 bonds, 9 residues, 1 model selected  

> select up

3449 atoms, 3484 bonds, 215 residues, 1 model selected  

> color sel brown

> select /t:493

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

> select up

189 atoms, 190 bonds, 10 residues, 1 model selected  

> select up

6205 atoms, 6281 bonds, 372 residues, 1 model selected  

> color sel purple

> select /r:102

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select up

263 atoms, 264 bonds, 15 residues, 1 model selected  

> select up

5228 atoms, 5279 bonds, 324 residues, 1 model selected  

> color sel cyan

> select /q:188

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select up

222 atoms, 225 bonds, 13 residues, 1 model selected  

> select up

4227 atoms, 4265 bonds, 272 residues, 1 model selected  

> color sel cyan

> select /r:143

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

> select up

242 atoms, 244 bonds, 15 residues, 1 model selected  

> select up

5228 atoms, 5279 bonds, 324 residues, 1 model selected  

> color sel yellow

> select /A:117

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select up

473 atoms, 476 bonds, 29 residues, 1 model selected  

> select up

4344 atoms, 4375 bonds, 266 residues, 1 model selected  

> color sel purple

> select /B:146

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select up

174 atoms, 175 bonds, 10 residues, 1 model selected  

> select up

6580 atoms, 6633 bonds, 422 residues, 1 model selected  

> color sel orange

> select /o:121

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

> select up

76 atoms, 75 bonds, 6 residues, 1 model selected  

> select up

2337 atoms, 2361 bonds, 147 residues, 1 model selected  

> color sel light blue

> select /j:106

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

> select up

175 atoms, 175 bonds, 12 residues, 1 model selected  

> select up

1791 atoms, 1801 bonds, 109 residues, 1 model selected  

> color sel blue

> select /1:50

33 atoms, 35 bonds, 1 residue, 1 model selected  

> select up

2437 atoms, 2628 bonds, 75 residues, 1 model selected  

> color sel magenta

> lighting simple

> select /3:146

34 atoms, 36 bonds, 1 residue, 1 model selected  

> select up

813 atoms, 877 bonds, 25 residues, 1 model selected  

> color sel dark red

> select clear

[Repeated 1 time(s)]

> select /y:13

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

> select up

220 atoms, 220 bonds, 14 residues, 1 model selected  

> view sel

> show sel atoms

> style sel stick

Changed 220 atom styles  

> select add /D:76

234 atoms, 233 bonds, 15 residues, 1 model selected  

> select add /D:40

248 atoms, 246 bonds, 16 residues, 1 model selected  

> select up

689 atoms, 691 bonds, 43 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 689 atom styles  

> select H

102262 atoms, 11803 residues, 1 model selected  

> hide sel atoms

> select /y:17@CG

1 atom, 1 residue, 1 model selected  
Drag select of 158 atoms, 96 residues, 126 bonds  

> volume #2 level 0.1637

> volume zone #2 nearAtoms sel range 2

> volume #2 step 1

> volume zone #2 nearAtoms sel range 3

> volume #2 color #b2b2b20d

> graphics silhouettes true

> show sel atoms

> style sel stick

Changed 1588 atom styles  

> select H

102262 atoms, 11803 residues, 1 model selected  

> hide sel atoms

> volume #2 level 0.2

> select clear

> select /y:24@CD

1 atom, 1 residue, 1 model selected  

> cofr sel

> select /y:48@CG

1 atom, 1 residue, 1 model selected  

> cofr sel

> volume #2 level 0.1357

> select /2:1114

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

> select add /2:1107

61 atoms, 63 bonds, 2 residues, 1 model selected  

> select add /2:1108

91 atoms, 94 bonds, 3 residues, 1 model selected  

> select add /2:1110

121 atoms, 125 bonds, 4 residues, 1 model selected  

> select add /2:1111

151 atoms, 156 bonds, 5 residues, 1 model selected  

> select add /2:1109

184 atoms, 191 bonds, 6 residues, 1 model selected  

> select add /2:1113

215 atoms, 223 bonds, 7 residues, 1 model selected  

> select add /2:1112

246 atoms, 255 bonds, 8 residues, 1 model selected  

> select add /v:399

263 atoms, 271 bonds, 9 residues, 1 model selected  

> select up

56328 atoms, 60724 bonds, 1764 residues, 1 model selected  

> select down

263 atoms, 271 bonds, 9 residues, 1 model selected  

> select /v:399

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select up

348 atoms, 351 bonds, 21 residues, 1 model selected  

> select up

9044 atoms, 9123 bonds, 554 residues, 1 model selected  

> select add /2:1115

9077 atoms, 9158 bonds, 555 residues, 1 model selected  

> select add /2:1114

9108 atoms, 9190 bonds, 556 residues, 1 model selected  

> select add /2:1113

9139 atoms, 9222 bonds, 557 residues, 1 model selected  

> select add /2:1112

9170 atoms, 9254 bonds, 558 residues, 1 model selected  

> select add /2:1111

9200 atoms, 9285 bonds, 559 residues, 1 model selected  

> select add /2:1110

9230 atoms, 9316 bonds, 560 residues, 1 model selected  

> select add /2:1109

9263 atoms, 9351 bonds, 561 residues, 1 model selected  

> select add /2:1107

9293 atoms, 9382 bonds, 562 residues, 1 model selected  

> select add /2:1108

9323 atoms, 9413 bonds, 563 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 9323 atom styles  

> select H

102262 atoms, 11803 residues, 1 model selected  

> hide sel atoms

> volume zone #2 nearAtoms sel range 3

> select clear

Drag select of 1110 atoms, 290 residues, 948 bonds  

> volume zone #2 nearAtoms sel range 3

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select up

125 atoms, 124 bonds, 7 residues, 1 model selected  

> view sel

> select /v:336

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select up

191 atoms, 190 bonds, 11 residues, 1 model selected  

> view sel

> select /v:373

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

> select up

280 atoms, 282 bonds, 16 residues, 1 model selected  

> view sel

> volume #2 color #b2b2b2

> volume zone #2 nearAtoms sel & #1 range 5.58

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume #2 style surface

> lighting soft

> volume #2 level 0.25

> volume #2 change image level -0.03107,0 level 0.1025,0.8 level 1.157,1

> graphics silhouettes false

> view

> select clear

> select /m:361

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

> select up

164 atoms, 167 bonds, 8 residues, 1 model selected  

> select up

5859 atoms, 5919 bonds, 365 residues, 1 model selected  

> color sel hot pink

> view sel

> volume zone #2 nearAtoms sel range 7

> show sel atoms

> style sel stick

Changed 5859 atom styles  

> select H

102262 atoms, 11803 residues, 1 model selected  

> hide sel atoms

> select clear

> volume #2 color #b2b2b20d

> lighting simple

> graphics silhouettes true

> volume #2 level 0.2

> volume #2 level 0.15

> select /m:455

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

> select /d:14

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select /A:53

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

> select up

293 atoms, 292 bonds, 15 residues, 1 model selected  

> view sel

> show sel atoms

> style sel stick

Changed 293 atom styles  

> select H

102262 atoms, 11803 residues, 1 model selected  

> hide sel atoms

> volume zone #2 nearAtoms sel range 7

> select /A:52

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

> select up

56 atoms, 55 bonds, 4 residues, 1 model selected  

> select /A:54

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

> select up

293 atoms, 292 bonds, 15 residues, 1 model selected  

> volume zone #2 nearAtoms sel range 7

[Repeated 1 time(s)]

> select /A:54@NH1

1 atom, 1 residue, 1 model selected  

> select up

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

> view sel

> select /3:143

34 atoms, 36 bonds, 1 residue, 1 model selected  

> select add /3:142

64 atoms, 67 bonds, 2 residues, 1 model selected  

> select add /3:141

97 atoms, 102 bonds, 3 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 97 atom styles  

> select /3:140

34 atoms, 36 bonds, 1 residue, 1 model selected  

> select add /3:139

67 atoms, 71 bonds, 2 residues, 1 model selected  

> select add /3:138

101 atoms, 107 bonds, 3 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 101 atom styles  

> save /Users/hashem-lab/Desktop/Shu-Bing/Focus-mRNA/With-eIF3/With-eIF3.cxs

Taking snapshot of stepper: P17_J79 model-step 7- map_refined-eIF5N-ter
location from yeast model.cif  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1417, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 360, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif': Error
while saving session data for 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif'  
  
ValueError: error processing: 'isolde residue stepper 0' -> -> 'P17_J79 model-
step 7- map_refined-eIF5N-ter location from yeast model.cif': Error while
saving session data for 'isolde residue stepper 0' -> -> 'P17_J79 model-step
7- map_refined-eIF5N-ter location from yeast model.cif'  
  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, 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-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1417, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 360, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif': Error
while saving session data for 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif'  
  
ValueError: error processing: 'isolde residue stepper 0' -> -> 'P17_J79 model-
step 7- map_refined-eIF5N-ter location from yeast model.cif': Error while
saving session data for 'isolde residue stepper 0' -> -> 'P17_J79 model-step
7- map_refined-eIF5N-ter location from yeast model.cif'  
  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> view

> save /Users/hashem-lab/Desktop/Shu-Bing/Focus-mRNA/With-eIF3/With-eIF3.cxs

Taking snapshot of stepper: P17_J79 model-step 7- map_refined-eIF5N-ter
location from yeast model.cif  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1417, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 360, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif': Error
while saving session data for 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif'  
  
ValueError: error processing: 'isolde residue stepper 0' -> -> 'P17_J79 model-
step 7- map_refined-eIF5N-ter location from yeast model.cif': Error while
saving session data for 'isolde residue stepper 0' -> -> 'P17_J79 model-step
7- map_refined-eIF5N-ter location from yeast model.cif'  
  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, 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-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1417, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 360, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif': Error
while saving session data for 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif'  
  
ValueError: error processing: 'isolde residue stepper 0' -> -> 'P17_J79 model-
step 7- map_refined-eIF5N-ter location from yeast model.cif': Error while
saving session data for 'isolde residue stepper 0' -> -> 'P17_J79 model-step
7- map_refined-eIF5N-ter location from yeast model.cif'  
  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save /Users/hashem-lab/Desktop/image14.png supersample 3

> save /Users/hashem-lab/Desktop/image15.png supersample 3

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume #2 style surface

> graphics silhouettes false

> volume #2 color #b2b2b2

> vop gaussian #2 sdev 2.79

Opened cryosparc_P17_J79_003_volume_map_sharp (1).mrc gaussian as #3, grid
size 500,500,500, pixel 0.93, shown at step 1, values float32  

> volume #3 level 0.003973

> view

> volume #3 level 0.03626

> volume #3 level 0.01581

> close #3

> save "/Users/hashem-lab/Desktop/Shu-Bing/Focus-mRNA/With-eIF3/P17_J79-step
> 9.cxs"

Taking snapshot of stepper: P17_J79 model-step 7- map_refined-eIF5N-ter
location from yeast model.cif  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1417, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 360, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif': Error
while saving session data for 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif'  
  
ValueError: error processing: 'isolde residue stepper 0' -> -> 'P17_J79 model-
step 7- map_refined-eIF5N-ter location from yeast model.cif': Error while
saving session data for 'isolde residue stepper 0' -> -> 'P17_J79 model-step
7- map_refined-eIF5N-ter location from yeast model.cif'  
  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, 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-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1417, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 360, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif': Error
while saving session data for 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif'  
  
ValueError: error processing: 'isolde residue stepper 0' -> -> 'P17_J79 model-
step 7- map_refined-eIF5N-ter location from yeast model.cif': Error while
saving session data for 'isolde residue stepper 0' -> -> 'P17_J79 model-step
7- map_refined-eIF5N-ter location from yeast model.cif'  
  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save "/Users/hashem-lab/Desktop/Shu-Bing/Focus-mRNA/With-eIF3/P17_J79 model-
> step 9.cif"

Not saving entity_poly_seq for non-authoritative sequences  

> open "/Users/hashem-lab/Desktop/Shu-Bing/Focus-mRNA/With-eIF3/P17_J79 model-
> step 9.cif"

Summary of feedback from opening /Users/hashem-lab/Desktop/Shu-Bing/Focus-
mRNA/With-eIF3/P17_J79 model-step 9.cif  
---  
warnings | Unknown polymer entity '51' near line 262996  
Atom HO5' is not in the residue template for A /1:2  
Atom H6 is not in the residue template for T6A /1:37  
Atom HO5' is not in the residue template for U /2:1  
Atom H2' is not in the residue template for C4J /2:1244  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for P17_J79 model-step 9.cif #3  
---  
Chain | Description  
1 | initiator methionylated tRNA  
2 | 18S ribosomal RNA  
3 | beta-globin mRNA  
A | eukaryotic translation initiation factor 2 subunit alpha  
B | eukaryotic translation initiation factor 2 subunit gamma  
C | 40S ribosomal protein uS2  
D | 40S ribosomal protein eS1  
E | 40S ribosomal protein uS5  
F | 40S ribosomal protein uS3  
G | 40S ribosomal protein eS4  
H | 40S ribosomal protein uS7  
I | 40S ribosomal protein eS6  
J | ribosomal protein eS7  
K | 40S ribosomal protein eS8  
L | 40S ribosomal protein uS4  
M | 40S ribosomal protein eS10  
N | 40S ribosomal protein uS17  
O | 40S ribosomal protein eS12  
P | ribosomal protein uS15  
Q | 40S ribosomal protein uS11  
R | 40S ribosomal protein uS19  
S | 40S ribosomal protein uS9  
T | 40S ribosomal protein eS17  
U | 40S ribosomal protein uS13  
V | 40S ribosomal protein eS19  
W | 40S ribosomal protein uS10  
X | 40S ribosomal protein eS21  
Y | 40S ribosomal protein uS8  
Z | 40S ribosomal protein uS12  
a | 40S ribosomal protein eS24  
b | 40S ribosomal protein eS26  
c | 40S ribosomal protein eS27  
d | 40S ribosomal protein eS28  
e | ribosomal protein uS14  
f | ribosomal protein eS31  
g | ribosomal protein RACK1  
i | 40S ribosomal protein eS30  
j | eukaryotic translation initiation factor 1A  
k | ATP-binding cassette sub-family E member 1 (ABCE1)  
l | 60s ribosomal protein l41  
m | eukaryotic translation initiation factor 3 subunit d  
n | ribosomal protein eS25  
o | Eukaryotic translation initiation factor 5  
q | Eukaryotic translation initiation factor 3 subunit F  
r | eukaryotic translation initiation factor 3 subunit h  
s | Eukaryotic translation initiation factor 3 subunit K  
t | eukaryotic translation initiation factor 3 subunit l  
u | Eukaryotic translation initiation factor 3 subunit M  
v | Eukaryotic translation initiation factor 3 subunit C  
w | Eukaryotic translation initiation factor 3 subunit E  
y | Eukaryotic translation initiation factor 3 subunit A  
  

> hide sel atoms

> show sel cartoons

[Repeated 1 time(s)]

> hide #!1 models

> select add #3

221647 atoms, 227729 bonds, 1622 pseudobonds, 11809 residues, 5 models
selected  

> show sel & #!3 cartoons

> hide sel & #!3 atoms

> hide #!2 models

> select subtract #3

101 atoms, 107 bonds, 3 residues, 1 model selected  

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!3 models

> close #3

> show #!1 models

> select add #1

221546 atoms, 227622 bonds, 1622 pseudobonds, 11806 residues, 4 models
selected  

> select subtract #1

Nothing selected  

> select add #1

221546 atoms, 227622 bonds, 1622 pseudobonds, 11806 residues, 4 models
selected  

> select subtract #1

Nothing selected  

> save "/Users/hashem-lab/Desktop/Shu-Bing/Focus-mRNA/With-eIF3/P17_J79 model-
> step 9.cxs"

Taking snapshot of stepper: P17_J79 model-step 7- map_refined-eIF5N-ter
location from yeast model.cif  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1417, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 360, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif': Error
while saving session data for 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif'  
  
ValueError: error processing: 'isolde residue stepper 0' -> -> 'P17_J79 model-
step 7- map_refined-eIF5N-ter location from yeast model.cif': Error while
saving session data for 'isolde residue stepper 0' -> -> 'P17_J79 model-step
7- map_refined-eIF5N-ter location from yeast model.cif'  
  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, 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-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1417, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 360, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif': Error
while saving session data for 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x152c220d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x14bb9f250> 'P17_J79
model-step 7- map_refined-eIF5N-ter location from yeast model.cif'  
  
ValueError: error processing: 'isolde residue stepper 0' -> -> 'P17_J79 model-
step 7- map_refined-eIF5N-ter location from yeast model.cif': Error while
saving session data for 'isolde residue stepper 0' -> -> 'P17_J79 model-step
7- map_refined-eIF5N-ter location from yeast model.cif'  
  
File
"/Applications/ChimeraX-1.7-rc2023.11.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-16.4.5
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro12,1
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 2,7 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 3 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 427.0.0.0.0
      SMC Version (system): 2.28f7

Software:

    System Software Overview:

      System Version: macOS 11.4 (20F71)
      Kernel Version: Darwin 20.5.0
      Time since boot: 22:02

Graphics/Displays:

    Intel Iris Graphics 6100:

      Chipset Model: Intel Iris Graphics 6100
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x162b
      Revision ID: 0x0009
      Metal Family: Supported, Metal GPUFamily macOS 1
      Displays:
        ASUS VG278HE:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: E1LMTF071883
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: Apple Mini DisplayPort To VGA Adapter
          Automatically Adjust Brightness: Yes
          Adapter Firmware Version: 1,03
        DELL U3223QE:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440 @ 30.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 1L43CP3     
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.13.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.2
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7rc202311302110
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.7rc1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.45.1
    funcparserlib: 2.0.0a0
    glfw: 2.6.3
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.0
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.7
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.0.0
    prompt-toolkit: 3.0.41
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.1
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.8.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by Eric Pettersen, 18 months ago

Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → ISOLDE: ResidueStepper references dead Structure

comment:2 by Eric Pettersen, 18 months ago

Resolution:	→ duplicate
Status:	assigned → closed

Duplicate of #14631

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