ResidueStepper holding reference to closed structure

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.5.0-44-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/home/m05270nt/Documents/ISOLDE
> runs/ISOLDE_6i7t_451_attempt2.3_finalSimulation.cxs" format session

Opened LocScale_451_asymmetric.mrc as #2, grid size 320,320,320, pixel 1.06,
shown at level 0.143, step 1, values float32  
Opened 451_C1_4.12Angstrom.mrc as #1.1.1.1, grid size 320,320,320, pixel 1.06,
shown at level 0.00778, step 1, values float32  
Opened 451_C1_4.12Angstrom.mrc gaussian as #1.1.1.2, grid size 320,320,320,
pixel 1.06, shown at level 0.00176, step 1, values float32  
Restoring stepper: 6i7t_align.pdb  
Log from Mon Jul 29 14:50:52 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt2.2.cxs"
> format session

Opened LocScale_451_asymmetric.mrc as #2, grid size 320,320,320, pixel 1.06,
shown at level 0.143, step 1, values float32  
Opened 451_C1_4.12Angstrom.mrc as #1.1.1.1, grid size 320,320,320, pixel 1.06,
shown at level 0.00778, step 1, values float32  
Opened 451_C1_4.12Angstrom.mrc gaussian as #1.1.1.2, grid size 320,320,320,
pixel 1.06, shown at level 0.00176, step 1, values float32  
Restoring stepper: 6i7t_align.pdb  
Log from Mon Jul 29 14:02:40 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt1.9.cxs"
> format session

Opened LocScale_451_asymmetric.mrc as #2, grid size 320,320,320, pixel 1.06,
shown at level 0.143, step 1, values float32  
Opened 451_C1_4.12Angstrom.mrc as #1.1.1.1, grid size 320,320,320, pixel 1.06,
shown at level 0.0115, step 1, values float32  
Opened 451_C1_4.12Angstrom.mrc gaussian as #1.1.1.2, grid size 320,320,320,
pixel 1.06, shown at level 0.00176, step 1, values float32  
Restoring stepper: 6i7t_align.pdb  
Log from Sun Jul 28 23:21:25 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt1.6.cxs"

Opened LocScale_451_asymmetric.mrc as #2, grid size 320,320,320, pixel 1.06,
shown at level 0.143, step 1, values float32  
Opened 451_C1_4.12Angstrom.mrc as #1.1.1.1, grid size 320,320,320, pixel 1.06,
shown at level 0.0135, step 1, values float32  
Opened 451_C1_4.12Angstrom.mrc gaussian as #1.1.1.2, grid size 320,320,320,
pixel 1.06, shown at level 0.00376, step 1, values float32  
Restoring stepper: 6i7t_align.pdb  
Log from Mon Jul 22 17:07:41 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt1.6.cxs"
> format session

Opened LocScale_451_asymmetric.mrc as #2, grid size 320,320,320, pixel 1.06,
shown at level 0.143, step 1, values float32  
Opened 451_C1_4.12Angstrom.mrc as #1.1.1.1, grid size 320,320,320, pixel 1.06,
shown at level 0.0118, step 1, values float32  
Opened 451_C1_4.12Angstrom.mrc gaussian as #1.1.1.2, grid size 320,320,320,
pixel 1.06, shown at level 0.00441, step 1, values float32  
Restoring stepper: 6i7t_align.pdb  
Log from Mon Jul 22 15:18:33 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt1.5.cxs"
> format session

Opened LocScale_451_asymmetric.mrc as #2, grid size 320,320,320, pixel 1.06,
shown at level 0.143, step 1, values float32  
Opened 451_C1_4.12Angstrom.mrc as #1.1.1.1, grid size 320,320,320, pixel 1.06,
shown at level 0.0134, step 1, values float32  
Opened 451_C1_4.12Angstrom.mrc gaussian as #1.1.1.2, grid size 320,320,320,
pixel 1.06, shown at level 0.00679, step 1, values float32  
Restoring stepper: 6i7t_align.pdb  
Log from Mon Jul 22 13:22:45 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt1.4.cxs"

Opened LocScale_451_asymmetric.mrc as #2, grid size 320,320,320, pixel 1.06,
shown at level 0.143, step 1, values float32  
Opened 451_C1_4.12Angstrom.mrc as #1.1.1.1, grid size 320,320,320, pixel 1.06,
shown at level 0.0134, step 1, values float32  
Opened 451_C1_4.12Angstrom.mrc gaussian as #1.1.1.2, grid size 320,320,320,
pixel 1.06, shown at level 0.00679, step 1, values float32  
Restoring stepper: 6i7t_align.pdb  
Log from Thu Jun 13 22:40:35 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt1.3.cxs"
> format session

Opened LocScale_451_asymmetric.mrc as #2, grid size 320,320,320, pixel 1.06,
shown at level 0.143, step 1, values float32  
Opened 451_C1_4.12Angstrom.mrc as #1.1.1.1, grid size 320,320,320, pixel 1.06,
shown at level 0.0131, step 1, values float32  
Opened 451_C1_4.12Angstrom.mrc gaussian as #1.1.1.2, grid size 320,320,320,
pixel 1.06, shown at level 0.00665, step 1, values float32  
Restoring stepper: 6i7t_align.pdb  
Log from Thu Jun 13 20:43:40 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt1.2.cxs"
> format session

Opened LocScale_451_asymmetric.mrc as #2, grid size 320,320,320, pixel 1.06,
shown at level 0.143, step 1, values float32  
Opened 451_C1_4.12Angstrom.mrc as #1.1.1.1, grid size 320,320,320, pixel 1.06,
shown at level 0.0147, step 1, values float32  
Opened 451_C1_4.12Angstrom.mrc gaussian as #1.1.1.2, grid size 320,320,320,
pixel 1.06, shown at level 0.00772, step 1, values float32  
Restoring stepper: 6i7t_align.pdb  
Log from Thu Jun 13 14:14:23 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt1.1.cxs"
> format session

Opened LocScale_451_asymmetric.mrc as #2, grid size 320,320,320, pixel 1.06,
shown at level 0.143, step 1, values float32  
Opened 451_C1_4.12Angstrom.mrc as #1.1.1.1, grid size 320,320,320, pixel 1.06,
shown at level 0.0147, step 1, values float32  
Opened 451_C1_4.12Angstrom.mrc gaussian as #1.1.1.2, grid size 320,320,320,
pixel 1.06, shown at level 0.00772, step 1, values float32  
Restoring stepper: 6i7t_align.pdb  
Log from Tue Jun 11 16:59:34 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt1.cxs"
> format session

Opened LocScale_451_asymmetric.mrc as #2, grid size 320,320,320, pixel 1.06,
shown at level 0.143, step 1, values float32  
Opened 451_C1_4.12Angstrom.mrc as #1.1.1.1, grid size 320,320,320, pixel 1.06,
shown at level 0.0163, step 1, values float32  
Log from Tue Jun 11 15:47:39 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_4428_attempt2.1.cxs"

Opened emd_4428.map as #1.1.1.1, grid size 320,320,320, pixel 1.34, shown at
level 0.0818, step 1, values float32  
Opened emd_4428.map gaussian as #1.1.1.2, grid size 320,320,320, pixel 1.34,
shown at level 0.0671, step 1, values float32  
Restoring stepper: 6i7t  
Log from Mon Apr 8 13:50:44 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /home/m05270nt/Documents/ISOLDE_6i7t_4428_attempt2.cxs format session

Opened emd_4428.map as #1.1.1.1, grid size 320,320,320, pixel 1.34, shown at
level 0.0564, step 1, values float32  
Log from Mon Apr 8 10:59:13 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/home/m05270nt/Documents/eIF2 eIF2B structures
> chimera/6i7t_Adomavicius2019.cxs" format session

Log from Sat Apr 6 22:47:48 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> set bgColor transparent

Log from Sat Apr 6 21:38:13 2024 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
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 6i7t format mmcif fromDatabase pdb

6i7t title:  
eIF2B:eIF2 complex [more info...]  
  
Chain information for 6i7t #1  
---  
Chain | Description | UniProt  
A B | Translation initiation factor eIF-2B subunit alpha | EI2BA_YEAST 1-305  
C D | Translation initiation factor eIF-2B subunit delta | EI2BD_YEAST 1-651  
E F | Translation initiation factor eIF-2B subunit beta | EI2BB_YEAST 1-381  
G H | Translation initiation factor eIF-2B subunit epsilon | EI2BE_YEAST 1-712  
I J | Translation initiation factor eIF-2B subunit gamma | EI2BG_YEAST 1-578  
K L | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
1-304  
M N | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
1-285  
O P | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
1-527  
  

> select /A:1-305

2393 atoms, 2437 bonds, 305 residues, 1 model selected  

> select clear

> select /A:1-305

2393 atoms, 2437 bonds, 305 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel forest green

> select /B:1-305

2393 atoms, 2437 bonds, 305 residues, 1 model selected  

> color sel forest green

> select /C:247-651

2677 atoms, 2720 bonds, 1 pseudobond, 342 residues, 2 models selected  

> color sel chartreuse

> color sel lime

> color sel spring green

> color sel lawn green

> color sel medium spring green

> color sel chartreuse

> select /D:247-651

2677 atoms, 2720 bonds, 1 pseudobond, 342 residues, 2 models selected  

> color sel chartreuse

> select /E:16-381

2797 atoms, 2846 bonds, 1 pseudobond, 354 residues, 2 models selected  

> color sel medium aquamarine

> select /C:247-651

2677 atoms, 2720 bonds, 1 pseudobond, 342 residues, 2 models selected  

> color sel green yellow

> select /D:247-651

2677 atoms, 2720 bonds, 1 pseudobond, 342 residues, 2 models selected  

> color sel green yellow

> select /E:16-381

2797 atoms, 2846 bonds, 1 pseudobond, 354 residues, 2 models selected  

> color sel pale green

> select /F:16-381

2797 atoms, 2846 bonds, 1 pseudobond, 354 residues, 2 models selected  

> color sel pale green

> select /A:1-305

2393 atoms, 2437 bonds, 305 residues, 1 model selected  

> color sel dark green

> select /B:1-305

2393 atoms, 2437 bonds, 305 residues, 1 model selected  

> color sel dark green

> select /G:24-433

3265 atoms, 3327 bonds, 410 residues, 1 model selected  

> color sel navy

> select /H:24-433

3265 atoms, 3327 bonds, 410 residues, 1 model selected  

> color sel navy

> select /I:2-415

2187 atoms, 2232 bonds, 3 pseudobonds, 268 residues, 2 models selected  

> color sel light blue

> select /J:2-415

2187 atoms, 2232 bonds, 3 pseudobonds, 268 residues, 2 models selected  

> color sel light blue

> select /K:3-265

2006 atoms, 2034 bonds, 2 pseudobonds, 249 residues, 2 models selected  

> color sel gold

> color sel yellow

> color sel gold

> color sel pale goldenrod

> color sel khaki

> color sel gold

> select /L:3-265

2006 atoms, 2034 bonds, 2 pseudobonds, 249 residues, 2 models selected  

> color sel gold

> select /M:127-143

143 atoms, 146 bonds, 17 residues, 1 model selected  

> color sel dark violet

> select /N:127-143

143 atoms, 146 bonds, 17 residues, 1 model selected  

> color sel dark violet

> select /O:98-519

3034 atoms, 3079 bonds, 3 pseudobonds, 396 residues, 2 models selected  

> color sel dark orange

> color sel orange red

> select /P:98-519

3034 atoms, 3079 bonds, 3 pseudobonds, 396 residues, 2 models selected  

> color sel orange red

> select /K:3-265

2006 atoms, 2034 bonds, 2 pseudobonds, 249 residues, 2 models selected  

> color sel goldenrod

> select /L:3-265

2006 atoms, 2034 bonds, 2 pseudobonds, 249 residues, 2 models selected  

> color sel goldenrod

> select clear

> save "/home/m05270nt/Documents/New Folder/6i7t_Adomavicius.cxs"

——— End of log from Sat Apr 6 21:38:13 2024 ———

opened ChimeraX session  

> graphics silhouettes true

> lighting shadows false

> lighting simple

> lighting shadows true

> graphics silhouettes false

> graphics silhouettes true

> set bgColor white

> set bgColor #ffffff00

> lighting simple

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true

> lighting shadows false

> lighting simple

> save "/home/m05270nt/Documents/eIF2 eIF2B structures
> chimera/6i7t_Adomavicius2019.cxs"

——— End of log from Sat Apr 6 22:47:48 2024 ———

opened ChimeraX session  

> show cartoons

> hide atoms

> show atoms

> style stick

Changed 37004 atom styles  

> save /home/m05270nt/Documents/ISOLDE_6i7t_4428_attempt2.cxs

> open /home/m05270nt/Documents/emd_4428.map

Opened emd_4428.map as #2, grid size 320,320,320, pixel 1.34, shown at level
0.0186, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.04684

> 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  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 212 residues in model #1 to IUPAC-IUB
standards.  

> clipper associate #2 toModel #1

Opened emd_4428.map as #1.1.1.1, grid size 320,320,320, pixel 1.34, shown at
step 1, values float32  

> volume #1.1.1.1 level 0.05645

> select /K/L

4012 atoms, 4068 bonds, 4 pseudobonds, 498 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel goldenrod

> select clear

> select /M/N

286 atoms, 292 bonds, 34 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel dark violet

> select /O/P

6068 atoms, 6158 bonds, 6 pseudobonds, 792 residues, 2 models selected  

> color sel orange red

> select /A/B

4786 atoms, 4874 bonds, 610 residues, 1 model selected  

> color sel dark green

> select /E/F

5594 atoms, 5692 bonds, 2 pseudobonds, 708 residues, 2 models selected  

> select /E/F

5594 atoms, 5692 bonds, 2 pseudobonds, 708 residues, 2 models selected  

> color sel pale green

> select /C/D

5354 atoms, 5440 bonds, 2 pseudobonds, 684 residues, 2 models selected  

> color sel green yellow

> select /G/H

6530 atoms, 6654 bonds, 820 residues, 1 model selected  

> color sel navy

> select /I/J

4374 atoms, 4464 bonds, 6 pseudobonds, 536 residues, 2 models selected  

> select /I/J

4374 atoms, 4464 bonds, 6 pseudobonds, 536 residues, 2 models selected  

> color sel light blue

> select clear

> save /home/m05270nt/Documents/ISOLDE_6i7t_4428_attempt2.cxs

——— End of log from Mon Apr 8 10:59:13 2024 ———

opened ChimeraX session  

> 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  

> isolde sim start /A,C-E,G,I-J,B,F,H,K,M,O,L,N,P

Sim termination reason: None  
ISOLDE: stopped sim  

> addh #1.2

Summary of feedback from adding hydrogens to 6i7t #1.2  
---  
warnings | Not adding hydrogens to /O TYR 183 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /P TYR 183 CB because it is missing heavy-atom bond
partners  
notes | Termini for 6i7t (#1.2) chain A determined from SEQRES records  
Termini for 6i7t (#1.2) chain C determined from SEQRES records  
Termini for 6i7t (#1.2) chain D determined from SEQRES records  
Termini for 6i7t (#1.2) chain E determined from SEQRES records  
Termini for 6i7t (#1.2) chain G determined from SEQRES records  
11 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A MET 1, /B MET 1  
Chain-initial residues that are not actual N termini: /C LEU 247, /C LYS 598,
/D LEU 247, /D LYS 598, /E SER 16, /E SER 142, /G GLU 24, /I SER 2, /I ALA 67,
/I GLY 107, /I GLY 382, /J SER 2, /J ALA 67, /J GLY 107, /J GLY 382, /F SER
16, /F SER 142, /H GLU 24, /K THR 3, /K VAL 182, /K VAL 218, /M VAL 127, /O
GLN 98, /O GLU 169, /O ILE 368, /O LYS 449, /L THR 3, /L VAL 182, /L VAL 218,
/N VAL 127, /P GLN 98, /P GLU 169, /P ILE 368, /P LYS 449  
Chain-final residues that are actual C termini: /A ASP 305, /C ALA 651, /D ALA
651, /E ALA 381, /B ASP 305, /F ALA 381  
Chain-final residues that are not actual C termini: /C ASN 534, /D ASN 534, /E
GLU 129, /G SER 433, /I GLY 10, /I ASP 88, /I GLN 309, /I THR 415, /J GLY 10,
/J ASP 88, /J GLN 309, /J THR 415, /F GLU 129, /H SER 433, /K SER 174, /K ASP
210, /K THR 265, /M ARG 143, /O GLU 152, /O THR 361, /O LYS 444, /O LYS 519,
/L SER 174, /L ASP 210, /L THR 265, /N ARG 143, /P GLU 152, /P THR 361, /P LYS
444, /P LYS 519  
2855 hydrogen bonds  
Adding 'H' to /C LEU 247  
Adding 'H' to /C LYS 598  
Adding 'H' to /D LEU 247  
Adding 'H' to /D LYS 598  
Adding 'H' to /E SER 16  
29 messages similar to the above omitted  
/G SER 433 is not terminus, removing H atom from 'C'  
/I THR 415 is not terminus, removing H atom from 'C'  
/J THR 415 is not terminus, removing H atom from 'C'  
/H SER 433 is not terminus, removing H atom from 'C'  
/K THR 265 is not terminus, removing H atom from 'C'  
5 messages similar to the above omitted  
37732 hydrogens added  
  

> isolde sim start /A,C-E,G,I-J,B,F,H,K,M,O,L,N,P

ISOLDE: started sim  

> ui tool show "Ramachandran Plot"

> isolde sim pause

> log metadata #1

No models had metadata

> log chains #1

Chain information for 6i7t #1.2  
---  
Chain | Description | UniProt  
A B | Translation initiation factor eIF-2B subunit alpha | EI2BA_YEAST 1-305  
C D | Translation initiation factor eIF-2B subunit delta | EI2BD_YEAST 1-651  
E F | Translation initiation factor eIF-2B subunit beta | EI2BB_YEAST 1-381  
G H | Translation initiation factor eIF-2B subunit epsilon | EI2BE_YEAST 1-712  
I J | Translation initiation factor eIF-2B subunit gamma | EI2BG_YEAST 1-578  
K L | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
1-304  
M N | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
1-285  
O P | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
1-527  
  

> select /K

4075 atoms, 4103 bonds, 2 pseudobonds, 249 residues, 2 models selected  

> select /L

4075 atoms, 4103 bonds, 2 pseudobonds, 249 residues, 2 models selected  

> select /K

4075 atoms, 4103 bonds, 2 pseudobonds, 249 residues, 2 models selected  

> select clear

> ui tool show "Volume Viewer"

> volume gaussian #1 bfactor 150

Opened emd_4428.map gaussian as #2, grid size 320,320,320, pixel 1.34, shown
at step 1, values float32  

> clipper associate #2 toModel #1

Opened emd_4428.map gaussian as #1.1.1.2, grid size 320,320,320, pixel 1.34,
shown at step 1, values float32  

> select clear

> select ~sel & ##selected

74735 atoms, 75374 bonds, 20 pseudobonds, 4682 residues, 2 models selected  

> select ~sel & ##selected

1 atom, 1 residue, 1 model selected  

> isolde stepto next

> isolde stepto /K:55

> isolde stepto next

> isolde stepto prev

> isolde sim resume

> ui tool show "Ramachandran Plot"

> isolde sim pause

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 120 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /K:55

ISOLDE: started sim  

> isolde sim pause

> select clear

> isolde sim stop discardTo start

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

> isolde stepto next

[Repeated 2 time(s)]

> isolde stepto prev

[Repeated 7 time(s)]

> isolde sim start /A:155

ISOLDE: started sim  

> isolde pepflip /A:155

> isolde pepflip /A:156

[Repeated 1 time(s)]

> isolde sim stop discardTo start

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

> isolde sim start /A:156

ISOLDE: started sim  

> isolde pepflip /A:156

> isolde sim pause

> isolde sim resume

> isolde stepto next

> isolde stepto prev

> isolde stepto next

> isolde stepto prev

> isolde stepto next

[Repeated 5 time(s)]

> isolde pepflip /A:161

[Repeated 1 time(s)]

> select clear

> isolde sim pause

> isolde sim resume

> isolde sim pause

> isolde sim resume

> isolde sim pause

> isolde sim resume

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/m05270nt/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/delayed_reaction.py", line 81, in callback  
self.ff(*self.ff_args)  
File "/home/m05270nt/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1531, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
^^^^^^^^^  
File "/home/m05270nt/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 103, in coords  
return self.smoothed_coords  
^^^^^^^^^^^^^^^^^^^^  
RuntimeError: clWaitForEvents  
  
Error processing trigger "new frame":  
RuntimeError: clWaitForEvents  
  
File "/home/m05270nt/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 103, in coords  
return self.smoothed_coords  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> select clear

[Repeated 2 time(s)]

> isolde sim pause

[Repeated 2 time(s)]

> save /home/m05270nt/Documents/ISOLDE_6i7t_4428_attempt2.1.cxs

Taking snapshot of stepper: 6i7t  

——— End of log from Mon Apr 8 13:50:44 2024 ———

opened ChimeraX session  

> select clear

[Repeated 2 time(s)]

> close session

> open /home/m05270nt/Documents/451_C1_4.12Angstrom.mrc

Opened 451_C1_4.12Angstrom.mrc as #1, grid size 320,320,320, pixel 1.06, shown
at level 0.00798, step 2, values float32  

> volume #1 step 1

> surface dust #1 size 10.6

> volume #1 level 0.008361

> volume #1 level 0.01066

> open /home/m05270nt/Documents/LocScale_451/453_relion_locres.mrc

Opened 453_relion_locres.mrc as #2, grid size 320,320,320, pixel 1, shown at
level 35.6, step 2, values float32  

> close #2

> open /home/m05270nt/Documents/LocScale_451/LocScale_451_asymmetric.mrc

Opened LocScale_451_asymmetric.mrc as #2, grid size 320,320,320, pixel 1.06,
shown at level 0.0915, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.1033

> volume #2 level 0.08191

> volume #1 level 0.01181

> open /home/m05270nt/Documents/6i7t_align.pdb

6i7t_align.pdb title:  
EIF2B:EIF2 complex [more info...]  
  
Chain information for 6i7t_align.pdb #3  
---  
Chain | Description | UniProt  
A B | translation initiation factor eif-2B subunit α | EI2BA_YEAST 1-305  
C D | translation initiation factor eif-2B subunit δ | EI2BD_YEAST 1-651  
E F | translation initiation factor eif-2B subunit β | EI2BB_YEAST 1-381  
G H | translation initiation factor eif-2B subunit ε | EI2BE_YEAST 1-712  
I J | translation initiation factor eif-2B subunit γ | EI2BG_YEAST 1-578  
K L | EIF-2-α | IF2A_YEAST 1-304  
M N | EIF-2-β | IF2B_YEAST 1-285  
O P | EIF-2-γ | IF2G_YEAST 1-527  
  

> hide atoms

> show cartoons

> 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  

> clipper associate #1 toModel #3

Opened 451_C1_4.12Angstrom.mrc as #1.1.1.1, grid size 320,320,320, pixel 1.06,
shown at level 0.0163, step 1, values float32  
6i7t_align.pdb title:  
EIF2B:EIF2 complex [more info...]  
  
Chain information for 6i7t_align.pdb  
---  
Chain | Description | UniProt  
1.2/A 1.2/B | translation initiation factor eif-2B subunit α | EI2BA_YEAST
1-305  
1.2/C 1.2/D | translation initiation factor eif-2B subunit δ | EI2BD_YEAST
1-651  
1.2/E 1.2/F | translation initiation factor eif-2B subunit β | EI2BB_YEAST
1-381  
1.2/G 1.2/H | translation initiation factor eif-2B subunit ε | EI2BE_YEAST
1-712  
1.2/I 1.2/J | translation initiation factor eif-2B subunit γ | EI2BG_YEAST
1-578  
1.2/K 1.2/L | EIF-2-α | IF2A_YEAST 1-304  
1.2/M 1.2/N | EIF-2-β | IF2B_YEAST 1-285  
1.2/O 1.2/P | EIF-2-γ | IF2G_YEAST 1-527  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 212 residues in model #1.2 to IUPAC-IUB
standards.  

> select clear

> volume #2 level 0.1838

> clipper associate #1 toModel #3

Invalid "toModel" argument: Must specify 1 model, got 0  

> clipper spotlight

> select clear

> volume #2 level 0.1435

> addh

Summary of feedback from adding hydrogens to 6i7t_align.pdb #1.2  
---  
warnings | Not adding hydrogens to /O TYR 183 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /P TYR 183 CB because it is missing heavy-atom bond
partners  
notes | Termini for 6i7t_align.pdb (#1.2) chain A determined from SEQRES
records  
Termini for 6i7t_align.pdb (#1.2) chain B determined from SEQRES records  
Termini for 6i7t_align.pdb (#1.2) chain C determined from SEQRES records  
Termini for 6i7t_align.pdb (#1.2) chain D determined from SEQRES records  
Termini for 6i7t_align.pdb (#1.2) chain E determined from SEQRES records  
11 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A MET 1, /B MET 1  
Chain-initial residues that are not actual N termini: /C LEU 247, /C LYS 598,
/D LEU 247, /D LYS 598, /E SER 16, /E SER 142, /F SER 16, /F SER 142, /G GLU
24, /H GLU 24, /I SER 2, /I ALA 67, /I GLY 107, /I GLY 382, /J SER 2, /J ALA
67, /J GLY 107, /J GLY 382, /K THR 3, /K VAL 182, /K VAL 218, /L THR 3, /L VAL
182, /L VAL 218, /M VAL 127, /N VAL 127, /O GLN 98, /O GLU 169, /O ILE 368, /O
LYS 449, /P GLN 98, /P GLU 169, /P ILE 368, /P LYS 449  
Chain-final residues that are actual C termini: /A ASP 305, /B ASP 305, /C ALA
651, /D ALA 651, /E ALA 381, /F ALA 381  
Chain-final residues that are not actual C termini: /C ASN 534, /D ASN 534, /E
GLU 129, /F GLU 129, /G SER 433, /H SER 433, /I GLY 10, /I ASP 88, /I GLN 309,
/I THR 415, /J GLY 10, /J ASP 88, /J GLN 309, /J THR 415, /K SER 174, /K ASP
210, /K THR 265, /L SER 174, /L ASP 210, /L THR 265, /M ARG 143, /N ARG 143,
/O GLU 152, /O THR 361, /O LYS 444, /O LYS 519, /P GLU 152, /P THR 361, /P LYS
444, /P LYS 519  
2853 hydrogen bonds  
Adding 'H' to /C LEU 247  
Adding 'H' to /C LYS 598  
Adding 'H' to /D LEU 247  
Adding 'H' to /D LYS 598  
Adding 'H' to /E SER 16  
29 messages similar to the above omitted  
/G SER 433 is not terminus, removing H atom from 'C'  
/H SER 433 is not terminus, removing H atom from 'C'  
/I THR 415 is not terminus, removing H atom from 'C'  
/J THR 415 is not terminus, removing H atom from 'C'  
/K THR 265 is not terminus, removing H atom from 'C'  
5 messages similar to the above omitted  
37732 hydrogens added  
  

> isolde restrain ligands #3

Must specify at least one atomic structure!  

> isolde restrain ligands #1

[Repeated 1 time(s)]

> ui tool show "Ramachandran Plot"

> save "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt1.cxs"

> isolde sim start /A,C-E,G,I-J,B,F,H,K,M,O,L,N,P

ISOLDE: started sim  

> isolde sim pause

> isolde sim stop discardTo start

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

> save "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt1.cxs"

——— End of log from Tue Jun 11 15:47:39 2024 ———

opened ChimeraX session  

> 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  

> ui tool show "Ramachandran Plot"

[Repeated 2 time(s)]

> isolde sim start /A,C-E,G,I-J,B,F,H,K,M,O,L,N,P

ISOLDE: started sim  

> isolde sim pause

> isolde sim resume

> isolde sim pause

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 141 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde stepto prev

[Repeated 4 time(s)]

> isolde stepto next

> volume gaussian #1 bfactor 150

Opened 451_C1_4.12Angstrom.mrc gaussian as #3, grid size 320,320,320, pixel
1.06, shown at step 1, values float32  

> clipper associate #3 toModel #1

Opened 451_C1_4.12Angstrom.mrc gaussian as #1.1.1.2, grid size 320,320,320,
pixel 1.06, shown at step 1, values float32  

> select clear

> isolde stepto next

> isolde stepto prev

> isolde stepto next

[Repeated 4 time(s)]

> isolde stepto prev

> isolde stepto next

[Repeated 1 time(s)]

> isolde stepto prev

> isolde sim start /K:8

ISOLDE: started sim  

> isolde pepflip /K:8

[Repeated 3 time(s)]

> isolde stepto next

> isolde sim pause

> isolde sim stop

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

> save "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt1.1.cxs"

Taking snapshot of stepper: 6i7t_align.pdb  

——— End of log from Tue Jun 11 16:59:34 2024 ———

opened ChimeraX session  

> save "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt1.2.cxs"

Taking snapshot of stepper: 6i7t_align.pdb  

——— End of log from Thu Jun 13 14:14:23 2024 ———

opened ChimeraX session  

> 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  

> isolde sim start /K:9

ISOLDE: started sim  

> ui tool show "Side View"

> save /home/m05270nt/Desktop/image1.png supersample 3

> save /home/m05270nt/Desktop/image2.png supersample 3

> save /home/m05270nt/Desktop/image3.png supersample 3

> save /home/m05270nt/Desktop/image4.png supersample 3

> select clear

> isolde stepto next

> select clear

> save /home/m05270nt/Desktop/image5.png supersample 3

> select clear

> isolde pepflip /K:10

[Repeated 1 time(s)]

> isolde pepflip /K:11

[Repeated 1 time(s)]

> save /home/m05270nt/Desktop/image6.png supersample 3

> isolde pepflip /K:10

[Repeated 7 time(s)]

> save /home/m05270nt/Desktop/image7.png supersample 3

> save /home/m05270nt/Desktop/image8.png supersample 3

> isolde stepto next

[Repeated 1 time(s)]

> save /home/m05270nt/Desktop/image9.png supersample 3

> isolde pepflip /K:12

[Repeated 3 time(s)]

> isolde stepto prev

> isolde stepto next

[Repeated 1 time(s)]

> isolde pepflip /K:13

[Repeated 1 time(s)]

> isolde stepto prev

> ui tool show "Ramachandran Plot"

> isolde pepflip /K:12

[Repeated 5 time(s)]

> select clear

> isolde stepto next

> isolde pepflip /K:13

[Repeated 1 time(s)]

> isolde stepto prev

[Repeated 1 time(s)]

> isolde stepto next

> isolde pepflip /K:12

[Repeated 1 time(s)]

> isolde stepto next

[Repeated 6 time(s)]

> isolde stepto prev

[Repeated 2 time(s)]

> isolde stepto next

[Repeated 4 time(s)]

> isolde stepto prev

[Repeated 2 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  

> select /D

5466 atoms, 5509 bonds, 1 pseudobond, 342 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel yellow green

> undo

> isolde sim start /K:24

ISOLDE: started sim  

> isolde sim pause

> isolde sim resume

> save /home/m05270nt/Desktop/image10.png supersample 3

> save /home/m05270nt/Desktop/image11.png supersample 3

> isolde pepflip /K:24

[Repeated 1 time(s)]

> isolde stepto next

> isolde stepto prev

> isolde stepto next

[Repeated 2 time(s)]

> isolde stepto prev

[Repeated 3 time(s)]

> isolde stepto next

[Repeated 6 time(s)]

> isolde pepflip /K:25

> save /home/m05270nt/Desktop/image12.png supersample 3

> isolde pepflip /K:24

[Repeated 1 time(s)]

> isolde pepflip /K:25

[Repeated 2 time(s)]

> save /home/m05270nt/Desktop/image13.png supersample 3

> save /home/m05270nt/Desktop/image14.png supersample 3

> isolde stepto next

[Repeated 2 time(s)]

> isolde stepto prev

> isolde stepto next

[Repeated 8 time(s)]

> isolde sim pause

> isolde sim stop

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

> isolde sim start /K:35

ISOLDE: started sim  

> save /home/m05270nt/Desktop/image15.png supersample 3

> isolde stepto next

[Repeated 2 time(s)]

> save /home/m05270nt/Desktop/image1.png supersample 3

> isolde pepflip /K:38

[Repeated 1 time(s)]

> save /home/m05270nt/Desktop/image2.png supersample 3

> save /home/m05270nt/Desktop/image3.png supersample 3

> isolde pepflip /K:38

> save /home/m05270nt/Desktop/image4.png supersample 3

> save /home/m05270nt/Desktop/image5.png supersample 3

> save /home/m05270nt/Desktop/image6.png supersample 3

> isolde stepto next

[Repeated 5 time(s)]

> isolde stepto prev

> isolde stepto next

[Repeated 2 time(s)]

> save /home/m05270nt/Desktop/image1.png supersample 3

> save /home/m05270nt/Desktop/image2.png supersample 3

> isolde stepto next

[Repeated 1 time(s)]

> save /home/m05270nt/Desktop/image1.png supersample 3

> isolde pepflip /K:48

[Repeated 1 time(s)]

> save /home/m05270nt/Desktop/image2.png supersample 3

> select clear

> isolde stepto next

[Repeated 1 time(s)]

> isolde stepto prev

[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 stepto next

[Repeated 2 time(s)]

> isolde stepto prev

[Repeated 1 time(s)]

> isolde stepto next

[Repeated 1 time(s)]

> isolde sim start /K:51

ISOLDE: started sim  

> select clear

> isolde stepto next

> save /home/m05270nt/Desktop/image1.png supersample 3

> save /home/m05270nt/Desktop/image2.png supersample 3

> isolde pepflip /K:52

[Repeated 1 time(s)]

> isolde stepto next

[Repeated 2 time(s)]

> isolde stepto prev

> isolde stepto next

> isolde sim stop

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

> isolde sim start /K:55

ISOLDE: started sim  

> save /home/m05270nt/Desktop/image1.png supersample 3

> select clear

> save /home/m05270nt/Desktop/image2.png supersample 3

> save /home/m05270nt/Desktop/image3.png supersample 3

> isolde pepflip /K:55

[Repeated 1 time(s)]

> isolde pepflip /K:56

[Repeated 1 time(s)]

> save /home/m05270nt/Desktop/image4.png supersample 3

> save /home/m05270nt/Desktop/image5.png supersample 3

> save /home/m05270nt/Desktop/image6.png supersample 3

> isolde stepto next

[Repeated 1 time(s)]

> save /home/m05270nt/Desktop/image1.png supersample 3

> save /home/m05270nt/Desktop/image2.png supersample 3

> save /home/m05270nt/Desktop/image3.png supersample 3

> save /home/m05270nt/Desktop/image4.png supersample 3

> isolde stepto next

[Repeated 2 time(s)]

> save /home/m05270nt/Desktop/image1.png supersample 3

> select clear

[Repeated 1 time(s)]

> isolde sim pause

> isolde sim resume

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/m05270nt/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/delayed_reaction.py", line 81, in callback  
self.ff(*self.ff_args)  
File "/home/m05270nt/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1531, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
^^^^^^^^^  
File "/home/m05270nt/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 103, in coords  
return self.smoothed_coords  
^^^^^^^^^^^^^^^^^^^^  
RuntimeError: clWaitForEvents  
  
Error processing trigger "new frame":  
RuntimeError: clWaitForEvents  
  
File "/home/m05270nt/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 103, in coords  
return self.smoothed_coords  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> isolde sim pause

> save "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt1.3.cxs"

Taking snapshot of stepper: 6i7t_align.pdb  

——— End of log from Thu Jun 13 20:43:40 2024 ———

opened ChimeraX session  

> 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  

> isolde sim start /K:60

ISOLDE: started sim  

> select clear

> view

[Repeated 1 time(s)]

> ui tool show "Side View"

> save /home/m05270nt/Desktop/image2.png supersample 3

> save /home/m05270nt/Desktop/image3.png supersample 3

> save /home/m05270nt/Desktop/image4.png supersample 3

> save /home/m05270nt/Desktop/image5.png supersample 3

> save /home/m05270nt/Desktop/image6.png supersample 3

> isolde stepto prev

> select clear

> save /home/m05270nt/Desktop/image7.png supersample 3

> save /home/m05270nt/Desktop/image8.png supersample 3

> isolde stepto next

[Repeated 1 time(s)]

> isolde stepto prev

[Repeated 2 time(s)]

> isolde stepto next

[Repeated 1 time(s)]

> select clear

> save /home/m05270nt/Desktop/image1.png supersample 3

> save /home/m05270nt/Desktop/image2.png supersample 3

> select clear

> isolde pepflip /K:61

[Repeated 1 time(s)]

> save /home/m05270nt/Desktop/image3.png supersample 3

> select clear

[Repeated 1 time(s)]

> save /home/m05270nt/Desktop/image4.png supersample 3

> save /home/m05270nt/Desktop/image5.png supersample 3

> isolde stepto prev

[Repeated 3 time(s)]

> isolde stepto next

> isolde pepflip /K:58

[Repeated 1 time(s)]

> select clear

> isolde stepto next

[Repeated 3 time(s)]

> isolde stepto prev

[Repeated 1 time(s)]

> isolde stepto next

[Repeated 1 time(s)]

> isolde stepto prev

[Repeated 1 time(s)]

> isolde stepto next

> save /home/m05270nt/Desktop/image6.png supersample 3

> save /home/m05270nt/Desktop/image7.png supersample 3

> select clear

> isolde stepto next

[Repeated 2 time(s)]

> select clear

> save /home/m05270nt/Desktop/image8.png supersample 3

> select clear

> save /home/m05270nt/Desktop/image9.png supersample 3

> select clear

> isolde stepto prev

> select clear

> isolde stepto next

[Repeated 3 time(s)]

> save /home/m05270nt/Desktop/image10.png supersample 3

> save /home/m05270nt/Desktop/image11.png supersample 3

> save /home/m05270nt/Desktop/image12.png supersample 3

> save /home/m05270nt/Desktop/image13.png supersample 3

> save /home/m05270nt/Desktop/image14.png supersample 3

> save /home/m05270nt/Desktop/image10.png supersample 3

> save /home/m05270nt/Desktop/image11.png supersample 3

> save /home/m05270nt/Desktop/image12.png supersample 3

> save /home/m05270nt/Desktop/image1.png supersample 3

> isolde stepto next

[Repeated 3 time(s)]

> isolde stepto prev

[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 4 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt1.4.cxs"

Taking snapshot of stepper: 6i7t_align.pdb  

——— End of log from Thu Jun 13 22:40:35 2024 ———

opened ChimeraX session  

> save "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt1.5.cxs"

Taking snapshot of stepper: 6i7t_align.pdb  

——— End of log from Mon Jul 22 13:22:45 2024 ———

opened ChimeraX session  

> 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 clear

> isolde sim start /K:64

ISOLDE: started sim  

> isolde stepto next

[Repeated 2 time(s)]

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Asp69_1.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Asp69_2.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Asp69_3.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde stepto next

> isolde sim pause

> isolde sim stop

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

> isolde sim start /K:70

ISOLDE: started sim  

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Val70_1.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Val70_2.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Val70_3.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Val70_4.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde sim pause

> save "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt1.5.cxs"

Taking snapshot of stepper: 6i7t_align.pdb  

> isolde sim resume

> isolde stepto next

[Repeated 2 time(s)]

> isolde stepto prev

[Repeated 1 time(s)]

> isolde stepto next

[Repeated 2 time(s)]

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Leu74_1.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde pepflip /K:74

[Repeated 1 time(s)]

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Leu74_2.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde stepto next

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Arg75_1.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Arg75_2.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Arg75_3.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Arg75_4.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Arg75_5.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Arg75_6.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Arg75_7.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Arg75_8.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Arg75_9.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Arg75_10.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde stepto next

[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 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /K:77

ISOLDE: started sim  

> isolde sim pause

> isolde sim resume

> isolde stepto prev

> isolde stepto next

[Repeated 2 time(s)]

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Glu79_1.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Glu79_2.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde pepflip /K:79

[Repeated 3 time(s)]

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Glu79_3.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde stepto prev

> isolde pepflip /K:78

[Repeated 1 time(s)]

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Lys78_vs_Glu79.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde stepto next

> isolde pepflip /K:79

[Repeated 4 time(s)]

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Lys78_vs_Glu79_2.png" width 1289 height
> 803 supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Lys78_vs_Glu79_3.png" width 1289 height
> 803 supersample 3 transparentBackground true

> isolde pepflip /K:79

[Repeated 1 time(s)]

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Lys78_vs_Glu79_4.png" width 1289 height
> 803 supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Lys78_vs_Glu79_5.png" width 1289 height
> 803 supersample 3 transparentBackground true

> isolde sim pause

> isolde sim stop

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

> save "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt1.6.cxs"

Taking snapshot of stepper: 6i7t_align.pdb  

——— End of log from Mon Jul 22 15:18:33 2024 ———

opened ChimeraX session  

> 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  

> isolde sim start /K:79

ISOLDE: started sim  

> isolde stepto next

[Repeated 4 time(s)]

> isolde stepto prev

[Repeated 1 time(s)]

> isolde stepto next

> isolde sim stop

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

> isolde sim start /K:85

ISOLDE: started sim  

> isolde stepto next

[Repeated 3 time(s)]

> isolde stepto prev

[Repeated 1 time(s)]

> isolde stepto next

[Repeated 7 time(s)]

> isolde stepto prev

[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 /K:91

ISOLDE: started sim  

> isolde stepto next

[Repeated 5 time(s)]

> isolde stepto prev

> isolde stepto next

> isolde stepto prev

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Ile98_1.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Ile98_2.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Ile98_3.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde pepflip /K:96

[Repeated 1 time(s)]

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Ile98_4.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde stepto next

[Repeated 1 time(s)]

> isolde stepto prev

[Repeated 1 time(s)]

> isolde stepto next

[Repeated 1 time(s)]

> isolde stepto prev

> isolde stepto next

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Cys98_1.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde pepflip /K:98

[Repeated 1 time(s)]

> isolde stepto next

> isolde pepflip /K:99

[Repeated 3 time(s)]

> isolde stepto prev

> isolde sim stop

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

> isolde sim start /K:98

ISOLDE: started sim  

> isolde stepto next

> isolde stepto prev

> isolde sim pause

> isolde sim stop

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

> isolde sim start /K:98

ISOLDE: started sim  

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Cys98_2.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/220724_Images/K_Cys98_3.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde stepto next

> isolde sim stop

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

> save "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt1.6.cxs"

Taking snapshot of stepper: 6i7t_align.pdb  

——— End of log from Mon Jul 22 17:07:41 2024 ———

opened ChimeraX session  

> save "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt1.7.cxs"

Taking snapshot of stepper: 6i7t_align.pdb  

> 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  

> isolde sim start /K:99

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:96-102

ISOLDE: started sim  

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/Glu99_image1.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde pepflip /K:99

[Repeated 5 time(s)]

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Glu99_2.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde stepto prev

> isolde stepto next

> isolde stepto prev

> isolde stepto next

[Repeated 1 time(s)]

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Glu100_1.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde pepflip /K:100

[Repeated 1 time(s)]

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Glu100_2.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde stepto next

[Repeated 5 time(s)]

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Lys106_1.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde sim pause

> isolde sim resume

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Lys106_2.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Lys106_3.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde stepto next

[Repeated 5 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 /K:112

ISOLDE: started sim  

> isolde stepto next

> isolde stepto prev

> isolde stepto next

[Repeated 3 time(s)]

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Ala116_1.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde pepflip /K:116

[Repeated 1 time(s)]

> isolde stepto next

[Repeated 6 time(s)]

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Leu123_1.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Leu123_2.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Leu123_3.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Leu123_4.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde stepto next

[Repeated 4 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 /K:128

ISOLDE: started sim  

> isolde stepto next

[Repeated 3 time(s)]

> isolde sim pause

> isolde sim resume

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Trp132_1.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde pepflip /K:132

[Repeated 1 time(s)]

> isolde stepto next

> isolde pepflip /K:133

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

> isolde pepflip /K:133

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

> isolde stepto prev

> isolde stepto next

> isolde cisflip /K:133

[Repeated 1 time(s)]

> isolde stepto prev

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Trp132_2.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde stepto next

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Pro133_1.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde pepflip /K:133

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

> isolde pepflip /K:133

[Repeated 1 time(s)]

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Pro133_2.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde stepto next

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Leu134_1.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Leu134_2.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Leu134_3.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde stepto next

[Repeated 3 time(s)]

> isolde stepto prev

> isolde sim stop

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

> isolde sim start /K:137

ISOLDE: started sim  

> isolde stepto next

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Phe138_1.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Phe138_2.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde stepto next

> isolde stepto prev

[Repeated 1 time(s)]

> isolde stepto next

[Repeated 5 time(s)]

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Glu143_1.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Glu143_2.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Glu143_3.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde stepto next

[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 /K:145

ISOLDE: started sim  

> isolde stepto next

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Lys146_1.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Lys146_2.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde stepto next

[Repeated 3 time(s)]

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Ile150_1.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Ile150_2.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde stepto next

[Repeated 5 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 /K:156

ISOLDE: started sim  

> isolde stepto prev

> isolde stepto next

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Glu152_1.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt1.8.cxs"
> includeMaps true

Taking snapshot of stepper: 6i7t_align.pdb  

> isolde sim pause

> isolde sim resume

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Glu156_2.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Glu156_3.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Glu156_4.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde stepto next

[Repeated 3 time(s)]

> isolde stepto prev

> isolde stepto next

[Repeated 2 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 /K:162

ISOLDE: started sim  

> isolde stepto next

[Repeated 6 time(s)]

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Leu169_1.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Leu169_2.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde stepto next

> isolde stepto prev

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Leu169_3.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde stepto next

[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 /K:171

ISOLDE: started sim  

> isolde stepto next

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Tyr172_1.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Tyr172_2.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde sim pause

> isolde sim resume

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/280724_images/K_Tyr172_3_reverted.png" width 1289 height
> 803 supersample 3 transparentBackground true

> isolde stepto next

[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 "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt1.9.cxs"
> includeMaps true

Taking snapshot of stepper: 6i7t_align.pdb  

——— End of log from Sun Jul 28 23:21:25 2024 ———

opened ChimeraX session  

> isolde sim start /A:42

ISOLDE: started sim  

> isolde stepto next

> isolde stepto prev

> isolde sim stop discardTo start

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

> isolde sim start /A:41

ISOLDE: started sim  

> isolde stepto /A:41

> save "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt2.1.cxs"

Taking snapshot of stepper: 6i7t_align.pdb  

> isolde stepto next

[Repeated 1 time(s)]

> isolde stepto prev

[Repeated 1 time(s)]

> isolde stepto next

[Repeated 4 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 /A:46

ISOLDE: started sim  

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/290724_images/A_Ile46_1.cxs"

Taking snapshot of stepper: 6i7t_align.pdb  

> isolde stepto next

[Repeated 1 time(s)]

> isolde stepto prev

[Repeated 1 time(s)]

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/290724_images/A_Ile46_2.cxs"

Taking snapshot of stepper: 6i7t_align.pdb  

> isolde stepto next

[Repeated 5 time(s)]

> isolde stepto prev

[Repeated 2 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 /A:304

ISOLDE: started sim  

> isolde stepto /A:304

> isolde stepto next

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/290724_images/A_305_1.cxs"

Taking snapshot of stepper: 6i7t_align.pdb  

> isolde sim pause

> isolde stepto /A:75

> isolde sim resume

> isolde stepto next

[Repeated 8 time(s)]

> isolde stepto prev

> isolde sim stop

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

> isolde stepto /A:84

> isolde sim start /A:84

ISOLDE: started sim  

> isolde stepto next

[Repeated 1 time(s)]

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/290724_images/A_Asp86.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde sim pause

> isolde stepto prev

[Repeated 21 time(s)]

> isolde sim stop

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

> isolde stepto prev

[Repeated 21 time(s)]

> isolde stepto next

> isolde sim start /A:43

ISOLDE: started sim  

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/290724_images/A_Ala42_Ala43.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde sim pause

> isolde stepto next

[Repeated 6 time(s)]

> isolde sim resume

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/290724_images/A_Lys50.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde sim pause

> isolde sim stop

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

> isolde stepto /A:304

> isolde stepto next

> isolde sim start /A:305

ISOLDE: started sim  

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/290724_images/A_Asp305.png" width 1289 height 803
> supersample 3 transparentBackground true

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/290724_images/A_Asp305_2.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde sim stop

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

> isolde stepto /D:650

> isolde sim start /D:650

ISOLDE: started sim  

> isolde stepto prev

[Repeated 3 time(s)]

> save "/home/m05270nt/Documents/ISOLDE
> runs/451_attempt1/290724_images/D_Glu646_1.png" width 1289 height 803
> supersample 3 transparentBackground true

> isolde sim pause

> 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 stepto /D:377

> save "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_451_attempt2.2.cxs"
> includeMaps true

Taking snapshot of stepper: 6i7t_align.pdb  

——— End of log from Mon Jul 29 14:02:40 2024 ———

opened ChimeraX session  

> save "/home/m05270nt/Documents/ISOLDE
> runs/ISOLDE_6i7t_451_attempt2.3_finalSimulation.cxs" includeMaps true

Taking snapshot of stepper: 6i7t_align.pdb  

——— End of log from Mon Jul 29 14:50:52 2024 ———

opened ChimeraX session  

> 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  

> isolde sim start /A,C-E,G,I-J,B,F,H,K,M,O,L,N,P

ISOLDE: started sim  

> save "/home/m05270nt/Documents/ISOLDE runs/451_attempt1/290724_images/full
> structure simulation.png" width 1289 height 803 supersample 3
> transparentBackground true

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 72 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_290724(2).pdb"

> save "/home/m05270nt/Documents/ISOLDE
> runs/ISOLDE_6i7t_451_attempt2.3_finalSimulation.cxs" includeMaps true

Taking snapshot of stepper: 6i7t_align.pdb  

> close session

> open "/home/m05270nt/Documents/ISOLDE runs/ISOLDE_6i7t_290724(2).pdb"

ISOLDE_6i7t_290724(2).pdb title:  
EIF2B:EIF2 complex [more info...]  
  
Chain information for ISOLDE_6i7t_290724(2).pdb #1  
---  
Chain | Description | UniProt  
A B | translation initiation factor eif-2B subunit α | EI2BA_YEAST 1-305  
C D | translation initiation factor eif-2B subunit δ | EI2BD_YEAST 1-651  
E F | translation initiation factor eif-2B subunit β | EI2BB_YEAST 1-381  
G H | translation initiation factor eif-2B subunit ε | EI2BE_YEAST 1-712  
I J | translation initiation factor eif-2B subunit γ | EI2BG_YEAST 1-578  
K L | EIF-2-α | IF2A_YEAST 1-304  
M N | EIF-2-β | IF2B_YEAST 1-285  
O P | EIF-2-γ | IF2G_YEAST 1-527  
  

> show cartoons

> hide atoms

> open /home/m05270nt/Documents/451_C1_4.12Angstrom.mrc

Opened 451_C1_4.12Angstrom.mrc as #2, grid size 320,320,320, pixel 1.06, shown
at level 0.00798, step 2, values float32  

> surface dust #2 size 10.6

> hide #!1 models

> color #2 #d9ace59d models

> show #!1 models

> hide #!2 models

> color #1 light gray

> select /K

4075 atoms, 4103 bonds, 2 pseudobonds, 249 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel goldenrod

> select /A

4809 atoms, 4853 bonds, 305 residues, 1 model selected  

> color sel dark green

> select /D

5466 atoms, 5509 bonds, 1 pseudobond, 342 residues, 2 models selected  

> color sel green yellow

> select clear

[Repeated 1 time(s)]

> open 6i7t fromDatabase pdb format mmcif

6i7t title:  
eIF2B:eIF2 complex [more info...]  
  
Chain information for 6i7t #3  
---  
Chain | Description | UniProt  
A B | Translation initiation factor eIF-2B subunit alpha | EI2BA_YEAST 1-305  
C D | Translation initiation factor eIF-2B subunit delta | EI2BD_YEAST 1-651  
E F | Translation initiation factor eIF-2B subunit beta | EI2BB_YEAST 1-381  
G H | Translation initiation factor eIF-2B subunit epsilon | EI2BE_YEAST 1-712  
I J | Translation initiation factor eIF-2B subunit gamma | EI2BG_YEAST 1-578  
K L | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
1-304  
M N | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
1-285  
O P | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
1-527  
  

> close #3

> open /home/m05270nt/Documents/6i7t_align.pdb

6i7t_align.pdb title:  
EIF2B:EIF2 complex [more info...]  
  
Chain information for 6i7t_align.pdb #3  
---  
Chain | Description | UniProt  
A B | translation initiation factor eif-2B subunit α | EI2BA_YEAST 1-305  
C D | translation initiation factor eif-2B subunit δ | EI2BD_YEAST 1-651  
E F | translation initiation factor eif-2B subunit β | EI2BB_YEAST 1-381  
G H | translation initiation factor eif-2B subunit ε | EI2BE_YEAST 1-712  
I J | translation initiation factor eif-2B subunit γ | EI2BG_YEAST 1-578  
K L | EIF-2-α | IF2A_YEAST 1-304  
M N | EIF-2-β | IF2B_YEAST 1-285  
O P | EIF-2-γ | IF2G_YEAST 1-527  
  

> hide #!1 models

> show #!3 cartoons

> hide #!3 atoms

> color #3 dark gray

> show #!1 models

> show #!2 models

> volume #2 step 1

> hide #!2 models

> select add #1

74736 atoms, 75374 bonds, 20 pseudobonds, 4682 residues, 2 models selected  

> select subtract #1

Nothing selected  

> graphics silhouettes false

> graphics silhouettes true

> lighting flat

[Repeated 1 time(s)]

> lighting full

> lighting soft

> lighting full

> graphics silhouettes false

> graphics silhouettes true

> select #1/K

4075 atoms, 4103 bonds, 2 pseudobonds, 249 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 4075 atom styles  

> color sel byhetero

> select #3/K

2006 atoms, 2034 bonds, 2 pseudobonds, 249 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 2006 atom styles  

> color sel byhetero

> select clear

> hide #!1 models

> color #3 dark gray

> show #!1 models

> show #!2 models

> volume #2 level 0.00951

> volume #2 level 0.01066

> ui tool show "Side View"

> log metadata #1

Metadata for ISOLDE_6i7t_290724(2).pdb #1  
---  
Title | EIF2B:EIF2 complex  
Citation | The structural basis of translational control by
EIF2PHOSPHORYLATION. PMID: 31086188  
Gene source | Saccharomyces cerevisiae (baker's yeast)  
Experimental method | Electron microscopy  
Resolution | 4.61Å  
  
> log chains #1

Chain information for ISOLDE_6i7t_290724(2).pdb #1  
---  
Chain | Description | UniProt  
A B | translation initiation factor eif-2B subunit α | EI2BA_YEAST 1-305  
C D | translation initiation factor eif-2B subunit δ | EI2BD_YEAST 1-651  
E F | translation initiation factor eif-2B subunit β | EI2BB_YEAST 1-381  
G H | translation initiation factor eif-2B subunit ε | EI2BE_YEAST 1-712  
I J | translation initiation factor eif-2B subunit γ | EI2BG_YEAST 1-578  
K L | EIF-2-α | IF2A_YEAST 1-304  
M N | EIF-2-β | IF2B_YEAST 1-285  
O P | EIF-2-γ | IF2G_YEAST 1-527  
  

> ui tool show "Side View"

> hide #!1 models

> show #!1 models

> hide #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> select #1/A:305

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

> show sel atoms

> style sel stick

Changed 13 atom styles  

> color sel byhetero

> select clear

> ui tool show H-Bonds

> ui tool show Contacts

> show #!3 models

> select #3/A:305

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

> show sel atoms

> style sel stick

Changed 9 atom styles  

> save "/home/m05270nt/Documents/6i7t vs ISOLDE 290724(2).cxs" includeMaps
> true

Taking snapshot of stepper: 6i7t_align.pdb  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1417, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/models.py", line 361, 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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/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 1'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x742f0f26cf50> ->
<chimerax.atomic.structure.AtomicStructure object at 0x742f2150ef90>
'6i7t_align.pdb'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax/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 1' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x742f0f26cf50> ->
<chimerax.atomic.structure.AtomicStructure object at 0x742f2150ef90>
'6i7t_align.pdb': Error while saving session data for 'isolde residue stepper
1' -> <chimerax.isolde.navigate.ResidueStepper object at 0x742f0f26cf50> ->
<chimerax.atomic.structure.AtomicStructure object at 0x742f2150ef90>
'6i7t_align.pdb'  
  
ValueError: error processing: 'isolde residue stepper 1' -> ->
'6i7t_align.pdb': Error while saving session data for 'isolde residue stepper
1' -> -> '6i7t_align.pdb'  
  
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1417, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/models.py", line 361, 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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/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 1'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x742f0f26cf50> ->
<chimerax.atomic.structure.AtomicStructure object at 0x742f2150ef90>
'6i7t_align.pdb'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax/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 1' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x742f0f26cf50> ->
<chimerax.atomic.structure.AtomicStructure object at 0x742f2150ef90>
'6i7t_align.pdb': Error while saving session data for 'isolde residue stepper
1' -> <chimerax.isolde.navigate.ResidueStepper object at 0x742f0f26cf50> ->
<chimerax.atomic.structure.AtomicStructure object at 0x742f2150ef90>
'6i7t_align.pdb'  
  
ValueError: error processing: 'isolde residue stepper 1' -> ->
'6i7t_align.pdb': Error while saving session data for 'isolde residue stepper
1' -> -> '6i7t_align.pdb'  
  
File "/usr/lib/ucsf-chimerax/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 "/home/m05270nt/Documents/6i7t vs ISOLDE 290724(2).cxs"

Taking snapshot of stepper: 6i7t_align.pdb  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1417, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/models.py", line 361, 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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/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 1'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x742f0f26cf50> ->
<chimerax.atomic.structure.AtomicStructure object at 0x742f2150ef90>
'6i7t_align.pdb'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax/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 1' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x742f0f26cf50> ->
<chimerax.atomic.structure.AtomicStructure object at 0x742f2150ef90>
'6i7t_align.pdb': Error while saving session data for 'isolde residue stepper
1' -> <chimerax.isolde.navigate.ResidueStepper object at 0x742f0f26cf50> ->
<chimerax.atomic.structure.AtomicStructure object at 0x742f2150ef90>
'6i7t_align.pdb'  
  
ValueError: error processing: 'isolde residue stepper 1' -> ->
'6i7t_align.pdb': Error while saving session data for 'isolde residue stepper
1' -> -> '6i7t_align.pdb'  
  
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1417, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/models.py", line 361, 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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/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 1'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x742f0f26cf50> ->
<chimerax.atomic.structure.AtomicStructure object at 0x742f2150ef90>
'6i7t_align.pdb'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax/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 1' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x742f0f26cf50> ->
<chimerax.atomic.structure.AtomicStructure object at 0x742f2150ef90>
'6i7t_align.pdb': Error while saving session data for 'isolde residue stepper
1' -> <chimerax.isolde.navigate.ResidueStepper object at 0x742f0f26cf50> ->
<chimerax.atomic.structure.AtomicStructure object at 0x742f2150ef90>
'6i7t_align.pdb'  
  
ValueError: error processing: 'isolde residue stepper 1' -> ->
'6i7t_align.pdb': Error while saving session data for 'isolde residue stepper
1' -> -> '6i7t_align.pdb'  
  
File "/usr/lib/ucsf-chimerax/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: 3.3.0 NVIDIA 535.183.01
OpenGL renderer: NVIDIA RTX A1000 6GB Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_GB.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: HP
Model: HP ZBook Power 15.6 inch G10 Mobile Workstation PC
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 13th Gen Intel(R) Core(TM) i7-13700H
Cache Size: 24576 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            30Gi       4.2Gi        13Gi       545Mi        13Gi        25Gi
	Swap:          7.8Gi          0B       7.8Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:a720] (rev 04)	
	DeviceName: Onboard IGD	
	Subsystem: Hewlett-Packard Company Device [103c:8bef]

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    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: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    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: 0.22.4
    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: 1.7.1
    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: 1.7.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    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: 2.6.1
    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: 1.5.14
    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: 1.0.4
    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: 1.12.4
    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: 1.33.3
    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: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    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: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    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: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    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: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    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: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9