Opened 3 years ago

Closed 19 months ago

#8772 closed defect (fixed)

isolde residue stepper referencing dead structure

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

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /Users/ts387/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-3.cxs
> format session

Opened J332_component_000_frame_019.mrc as #1.1.1.1, grid size 128,128,128,
pixel 1.67, shown at level 0.686, step 1, values float32  
Restoring stepper: Frame_19.pdb  
Log from Mon Apr 3 03:08:16 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-3.cxs
> format session

Opened J332_component_000_frame_019.mrc as #1.1.1.1, grid size 128,128,128,
pixel 1.67, shown at level 0.441, step 1, values float32  
Restoring stepper: Frame_19.pdb  
Log from Sun Apr 2 23:33:41 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-2.cxs
> format session

Opened J332_component_000_frame_019.mrc as #1.1.1.1, grid size 128,128,128,
pixel 1.67, shown at level 0.517, step 1, values float32  
Restoring stepper: Frame_19.pdb  
Log from Sun Apr 2 23:19:42 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-1.cxs

Opened J332_component_000_frame_019.mrc as #1.1.1.1, grid size 128,128,128,
pixel 1.67, shown at level 0.5, step 1, values float32  
Restoring stepper: Frame_19.pdb  
Log from Sat Apr 1 21:28:32 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-1.cxs
> format session

Opened J332_component_000_frame_019.mrc as #1.1.1.1, grid size 128,128,128,
pixel 1.67, shown at level 0.5, step 1, values float32  
Restoring stepper: Frame_19.pdb  
Log from Sat Apr 1 21:18:35 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-0.cxs
> format session

Opened J332_component_000_frame_019.mrc as #1.1.1.1, grid size 128,128,128,
pixel 1.67, shown at level 0.5, step 1, values float32  
Log from Sat Apr 1 16:52:53 2023

> ui tool show "Hide Dust"

UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/Frame_19.pdb

Chain information for Frame_19.pdb #1  
---  
Chain | Description  
A C D F | No description available  
B E | No description available  
S | No description available  
  

> hide atoms

> show cartoons

> color bychain

> open /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/J332_component_000_frame_019.mrc

Opened J332_component_000_frame_019.mrc as #2, grid size 128,128,128, pixel
1.67, shown at level 0.787, step 1, values float32  

> volume #2 color #b2b2b23f

> volume #2 level 0.5005

> surface dust #2 size 10.02

> isolde start

> set selectionWidth 4

Populating font family aliases took 361 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

> ui tool show "Ramachandran Plot"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 103 residues in model #1 to IUPAC-IUB
standards.  
Chain information for Frame_19.pdb  
---  
Chain | Description  
1.2/A 1.2/C 1.2/D 1.2/F | No description available  
1.2/B 1.2/E | No description available  
1.2/S | No description available  
  

> clipper associate #2 toModel #1

Opened J332_component_000_frame_019.mrc as #1.1.1.1, grid size 128,128,128,
pixel 1.67, shown at step 1, values float32  

> addh #1.2

Summary of feedback from adding hydrogens to Frame_19.pdb #1.2  
---  
warning | Not adding hydrogens to /S DT 0 P because it is missing heavy-atom
bond partners  
notes | No usable SEQRES records for Frame_19.pdb (#1.2) chain A; guessing
termini instead  
No usable SEQRES records for Frame_19.pdb (#1.2) chain B; guessing termini
instead  
No usable SEQRES records for Frame_19.pdb (#1.2) chain C; guessing termini
instead  
No usable SEQRES records for Frame_19.pdb (#1.2) chain D; guessing termini
instead  
No usable SEQRES records for Frame_19.pdb (#1.2) chain E; guessing termini
instead  
2 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A LYS 266, /B THR 265, /C
LYS 266, /D LYS 266, /E THR 265, /F LYS 266  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ASP 627, /B ASP 627, /C ASP
627, /D ASP 627, /E ASP 627, /F ASP 627  
Chain-final residues that are not actual C termini:  
2106 hydrogen bonds  
18095 hydrogens added  
  
Loading residue template for ATP from internal database  

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

[Repeated 4 time(s)]

> select clear

> save /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-0.cxs
> includeMaps true

> volume #1.1.1.1 level 0.5001

> select clear

[Repeated 5 time(s)]

> isolde modify his sel NE

Set protonation of HIS #1.2/A:513 to NE  

> isolde modify his sel NE

Set protonation of HIS #1.2/B:513 to NE  

> isolde modify his sel NE

Set protonation of HIS #1.2/E:513 to NE  

> save /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-0.cxs
> includeMaps true

——— End of log from Sat Apr 1 16:52:53 2023 ———

opened ChimeraX session  

> select clear

> isolde restrain ligands #1

> select clear

> ui tool show "Ramachandran Plot"

> ui tool show "Volume Viewer"

> select #1

36033 atoms, 36412 bonds, 2187 residues, 15 models selected  

> isolde set gpuDeviceIndex 2

> isolde sim start sel

Loading residue template for ATP from internal database  

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

[Repeated 4 time(s)]ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 47 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-1.cxs
> includeMaps true

Taking snapshot of stepper: Frame_19.pdb  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-1.cxs
> includeMaps true

Taking snapshot of stepper: Frame_19.pdb  

——— End of log from Sat Apr 1 21:18:35 2023 ———

opened ChimeraX session  

> isolde start

> set selectionWidth 4

Populating font family aliases took 337 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

> ui tool show "Volume Viewer"

> ui tool show "Ramachandran Plot"

> isolde sim start sel

Loading residue template for ATP from internal database  
ISOLDE: started sim  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-1.cxs
> includeMaps true

Taking snapshot of stepper: Frame_19.pdb  

——— End of log from Sat Apr 1 21:28:32 2023 ———

opened ChimeraX session  

> isolde start

> set selectionWidth 4

Populating font family aliases took 440 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

> ui tool show "Ramachandran Plot"

> ui tool show "Volume Viewer"

> select clear

> isolde set gpuDeviceIndex 2

> select clear

> isolde sim start sel

Loading residue template for ATP from internal database  
ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.8427

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.7438

> volume #1.1.1.1 level 0.4984

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde sim stop

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  

> volume #1.1.1.1 level 0.589

> view #1.2/A:513

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.5464

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.6787

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> view #1.2/B:540

> volume #1.1.1.1 level 0.5566

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> volume #1.1.1.1 level 0.7449

> volume #1.1.1.1 level 0.5769

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-1.cxs
> includeMaps true

Taking snapshot of stepper: Frame_19.pdb  

> view #1.2/A:513

> view #1.2/B:540

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> volume #1.1.1.1 level 0.6894

> volume #1.1.1.1 level 0.5053

> select clear

[Repeated 1 time(s)]

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde sim pause

> isolde sim resume

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.7354

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select clear

[Repeated 1 time(s)]

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.5885

> select clear

> isolde sim stop

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 clear

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.3968

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  
Residue does not have an N-terminal peptide bond!  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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  

> volume #1.1.1.1 level 0.7486

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

> volume #1.1.1.1 level 0.4368

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

> volume #1.1.1.1 level 0.8156

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

> volume #1.1.1.1 level 0.6865

> volume #1.1.1.1 level 0.5279

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-2.cxs
> includeMaps true

Taking snapshot of stepper: Frame_19.pdb  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.8253

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.5955

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-2.cxs
> includeMaps true

Taking snapshot of stepper: Frame_19.pdb  

> volume #1.1.1.1 level 0.7081

> volume #1.1.1.1 level 0.618

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.7487

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.564

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.6611

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

> volume #1.1.1.1 level 0.301

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.382

> volume #1.1.1.1 level 0.3052

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.5591

> volume #1.1.1.1 level 0.4343

> volume #1.1.1.1 level 0.2837

> volume #1.1.1.1 level 0.2235

> select clear

[Repeated 1 time(s)]

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.5916

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

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  

> volume #1.1.1.1 level 0.6417

> volume #1.1.1.1 level 0.2704

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.2621

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.5416

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.3049

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.1242

> volume #1.1.1.1 level 0.1586

> volume #1.1.1.1 level 0.1844

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.7659

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.6128

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.4849

> volume #1.1.1.1 level 0.6175

> volume #1.1.1.1 level 0.4896

> volume #1.1.1.1 level 0.5512

> volume #1.1.1.1 level 0.4754

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.5367

> volume #1.1.1.1 level 0.6697

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-2.cxs
> includeMaps true

Taking snapshot of stepper: Frame_19.pdb  

> save /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-2.cxs
> includeMaps true

Taking snapshot of stepper: Frame_19.pdb  

> volume #1.1.1.1 level 0.4416

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim pause

> select clear

[Repeated 1 time(s)]

> isolde sim resume

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> select clear

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-2.cxs
> includeMaps true

Taking snapshot of stepper: Frame_19.pdb  

> volume #1.1.1.1 level 0.8507

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> select clear

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

> volume #1.1.1.1 level 0.5439

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.7433

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.5694

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.8191

> volume #1.1.1.1 level 0.6297

> select clear

> volume #1.1.1.1 level 0.2983

> volume #1.1.1.1 level 0.195

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim pause

> isolde sim resume

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.6757

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.5223

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> select clear

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 2 time(s)]

> isolde sim stop

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 sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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  

> volume #1.1.1.1 level 0.4542

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.4622

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.5263

> volume #1.1.1.1 level 0.4943

> volume #1.1.1.1 level 0.4983

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.4462

> volume #1.1.1.1 level 0.5023

> volume #1.1.1.1 level 0.4662

> volume #1.1.1.1 level 0.4903

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.5023

> select clear

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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 sel

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> volume #1.1.1.1 level 0.9929

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.8035

> select clear

> isolde sim stop

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  

> volume #1.1.1.1 level 0.7677

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

> volume #1.1.1.1 level 0.9672

> volume #1.1.1.1 level 0.8189

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.7677

> select clear

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.7156

> volume #1.1.1.1 level 0.7962

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.5689

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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 sel

ISOLDE: started sim  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> volume #1.1.1.1 level 0.8304

> isolde sim stop

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 sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.6367

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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 sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.5254

> volume #1.1.1.1 level 0.4808

> isolde sim stop

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 sel

ISOLDE: started sim  

> isolde sim pause

> isolde sim resume

> select clear

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

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 sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.307

> volume #1.1.1.1 level 0.5473

> isolde sim stop

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 sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> volume #1.1.1.1 level 0.3997

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

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 sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.3997

> volume #1.1.1.1 level 0.5867

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.4322

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

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 sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.6888

> volume #1.1.1.1 level 0.7276

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.5519

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.4163

> volume #1.1.1.1 level 0.547

> volume #1.1.1.1 level 0.4599

> volume #1.1.1.1 level 0.4114

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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 sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-2.cxs
> includeMaps true

Taking snapshot of stepper: Frame_19.pdb  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 3 time(s)]

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.5129

> volume #1.1.1.1 level 0.4973

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.3997

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.5498

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.4578

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 3 time(s)]

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.3642

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.4666

> isolde sim stop

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  

> volume #1.1.1.1 level 0.8675

> volume #1.1.1.1 level 0.7339

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> volume #1.1.1.1 level 0.6144

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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 sel

ISOLDE: started sim  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.7013

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.8905

> volume #1.1.1.1 level 0.6758

> volume #1.1.1.1 level 0.8189

> volume #1.1.1.1 level 0.8445

> select clear

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.6911

> volume #1.1.1.1 level 0.5735

> select clear

[Repeated 1 time(s)]

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.8701

> volume #1.1.1.1 level 0.4865

> volume #1.1.1.1 level 0.328

> volume #1.1.1.1 level 0.5172

> select clear

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-2.cxs
> includeMaps true

Taking snapshot of stepper: Frame_19.pdb  

> save /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-2.cxs
> includeMaps true

Taking snapshot of stepper: Frame_19.pdb  

——— End of log from Sun Apr 2 23:19:42 2023 ———

opened ChimeraX session  

> isolde start

> set selectionWidth 4

> ui tool show "Volume Viewer"

> volume #1.1.1.1 level 0.9532

> select clear

> volume #1.1.1.1 level 0.6555

> volume #1.1.1.1 level 0.8265

> volume #1.1.1.1 level 0.5615

> isolde set gpuDeviceIndex 2

> ui tool show "Ramachandran Plot"

> select clear

> volume #1.1.1.1 level 0.5386

> isolde sim start sel

Loading residue template for ATP from internal database  
ISOLDE: started sim  

> volume #1.1.1.1 level 0.4363

> volume #1.1.1.1 level 0.4926

> volume #1.1.1.1 level 0.5437

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> volume #1.1.1.1 level 0.4414

> isolde sim pause

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-3.cxs
> includeMaps true

Taking snapshot of stepper: Frame_19.pdb  

——— End of log from Sun Apr 2 23:33:41 2023 ———

opened ChimeraX session  

> ui tool show "Volume Viewer"

> select clear

> isolde set gpuDeviceIndex 2

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde sim pause

> isolde sim resume

> volume #1.1.1.1 level 0.4926

> volume #1.1.1.1 level 0.5028

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> volume #1.1.1.1 level 0.4619

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde sim stop

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 sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.4313

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.5876

> volume #1.1.1.1 level 0.6013

> volume #1.1.1.1 level 0.4864

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

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 sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.4099

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.6755

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> volume #1.1.1.1 level 0.5422

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

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 sel

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde sim stop

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 sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.4412

> isolde sim stop

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 sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.6304

> volume #1.1.1.1 level 0.4412

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 2 time(s)]

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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 sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.5179

> volume #1.1.1.1 level 0.2878

> isolde sim stop

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 clear

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde sim stop

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 sel

ISOLDE: started sim  

> select clear

> isolde sim stop

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  

> volume #1.1.1.1 level 0.3857

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 3 time(s)]

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.4968

> save /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-2.cxs
> includeMaps true

Taking snapshot of stepper: Frame_19.pdb  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

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 sel

ISOLDE: started sim  

> select clear

> isolde sim stop

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 sel

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

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 sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

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  

> save /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-2.cxs
> includeMaps true

Taking snapshot of stepper: Frame_19.pdb  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim pause

> isolde sim resume

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

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 sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

Chain , residue 800 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-2.cxs
> includeMaps true

Taking snapshot of stepper: Frame_19.pdb  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.6861

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select clear

[Repeated 1 time(s)]

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-2.cxs
> includeMaps true

Taking snapshot of stepper: Frame_19.pdb  

> save /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-3.cxs
> includeMaps true

Taking snapshot of stepper: Frame_19.pdb  

> save /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-2.cxs
> includeMaps true

Taking snapshot of stepper: Frame_19.pdb  

> save /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-3.cxs
> includeMaps true

Taking snapshot of stepper: Frame_19.pdb  

——— End of log from Mon Apr 3 03:08:16 2023 ———

opened ChimeraX session  

> close session

> open /Users/ts387/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/Frame_19-3_edit.pdb

Chain information for Frame_19-3_edit.pdb #1  
---  
Chain | Description  
A C D F | No description available  
B E | No description available  
S | No description available  
  

> style stick

Changed 36033 atom styles  

> color bychain

> color byhetero

> hide atoms

> show cartoons

> select ::name="ATP"

258 atoms, 270 bonds, 6 residues, 1 model selected  

> show sel atoms

> select #1/B:540

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

> show sel atoms

> select #1/A:540

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

> show sel atoms

> select #1/A:498

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

> show sel atoms

> select #1/540

Nothing selected  

> select #1/A-F:540

144 atoms, 138 bonds, 6 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> select #1/A-F:498

144 atoms, 138 bonds, 6 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> select #1/A-F:418

132 atoms, 126 bonds, 6 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> open /Users/ts387/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/J332_component_000_frame_019.mrc

Opened J332_component_000_frame_019.mrc as #2, grid size 128,128,128, pixel
1.67, shown at level 0.787, step 1, values float32  

> volume #2 level 0.5

> ui tool show "Hide Dust"

> surface dust #2 size 10.02

> volume #2 color #b2b2b240

> volume #2 style mesh

> select up

753 atoms, 756 bonds, 39 residues, 1 model selected  

> select #1/A-F:540

144 atoms, 138 bonds, 6 residues, 1 model selected  

> show sel atoms

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for Frame_19-3_edit.pdb  
---  
Chain | Description  
1.2/A 1.2/C 1.2/D 1.2/F | No description available  
1.2/B 1.2/E | No description available  
1.2/S | No description available  
  

> clipper associate #2 toModel #1

Opened J332_component_000_frame_019.mrc as #1.1.1.1, grid size 128,128,128,
pixel 1.67, shown at step 1, values float32  
Loading residue template for ATP from internal database  

> save /Users/ts387/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-4.cxs
> includeMaps true

Taking snapshot of stepper: Frame_19.pdb  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1391, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 208, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 344, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 1'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x7fd7e0636640> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7fd7ee496610>
'Frame_19.pdb'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 1' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7fd7e0636640> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7fd7ee496610>
'Frame_19.pdb': Error while saving session data for 'isolde residue stepper 1'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x7fd7e0636640> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7fd7ee496610>
'Frame_19.pdb'  
  
ValueError: error processing: 'isolde residue stepper 1' -> -> 'Frame_19.pdb':
Error while saving session data for 'isolde residue stepper 1' -> ->
'Frame_19.pdb'  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1391, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 208, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 344, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 1'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x7fd7e0636640> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7fd7ee496610>
'Frame_19.pdb'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 1' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7fd7e0636640> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7fd7ee496610>
'Frame_19.pdb': Error while saving session data for 'isolde residue stepper 1'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x7fd7e0636640> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7fd7ee496610>
'Frame_19.pdb'  
  
ValueError: error processing: 'isolde residue stepper 1' -> -> 'Frame_19.pdb':
Error while saving session data for 'isolde residue stepper 1' -> ->
'Frame_19.pdb'  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> close session

> open /Users/ts387/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/Frame_19-3_edit.pdb

Chain information for Frame_19-3_edit.pdb #1  
---  
Chain | Description  
A C D F | No description available  
B E | No description available  
S | No description available  
  

> style stick

Changed 36033 atom styles  

> color bychain

> color byhetero

> hide atoms

> show cartoons

> select ::name="ATP"

258 atoms, 270 bonds, 6 residues, 1 model selected  

> show sel atoms

> open /Users/ts387/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/J332_component_000_frame_019.mrc

Opened J332_component_000_frame_019.mrc as #2, grid size 128,128,128, pixel
1.67, shown at level 0.787, step 1, values float32  

> volume #2 level 0.5

> volume #2 style mesh

> ui tool show "Hide Dust"

> surface dust #2 size 10.02

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for Frame_19-3_edit.pdb  
---  
Chain | Description  
1.2/A 1.2/C 1.2/D 1.2/F | No description available  
1.2/B 1.2/E | No description available  
1.2/S | No description available  
  

> clipper associate #2 toModel #1

Opened J332_component_000_frame_019.mrc as #1.1.1.1, grid size 128,128,128,
pixel 1.67, shown at step 1, values float32  

> save /Users/ts387/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_000/cs_P18_J332_component_000_frame_019-3.cxs
> includeMaps true

Taking snapshot of stepper: Frame_19.pdb  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1391, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 208, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 344, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 1'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x7fd7e0636640> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7fd7ee496610>
'Frame_19.pdb'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 1' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7fd7e0636640> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7fd7ee496610>
'Frame_19.pdb': Error while saving session data for 'isolde residue stepper 1'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x7fd7e0636640> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7fd7ee496610>
'Frame_19.pdb'  
  
ValueError: error processing: 'isolde residue stepper 1' -> -> 'Frame_19.pdb':
Error while saving session data for 'isolde residue stepper 1' -> ->
'Frame_19.pdb'  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1391, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 208, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 344, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 1'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x7fd7e0636640> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7fd7ee496610>
'Frame_19.pdb'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 1' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7fd7e0636640> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7fd7ee496610>
'Frame_19.pdb': Error while saving session data for 'isolde residue stepper 1'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x7fd7e0636640> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7fd7ee496610>
'Frame_19.pdb'  
  
ValueError: error processing: 'isolde residue stepper 1' -> -> 'Frame_19.pdb':
Error while saving session data for 'isolde residue stepper 1' -> ->
'Frame_19.pdb'  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.9.51
OpenGL renderer: AMD Radeon Pro 5300 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac20,1
      Processor Name: 6-Core Intel Core i5
      Processor Speed: 3.3 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 12 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0)
      OS Loader Version: 564.40.4~66

Software:

    System Software Overview:

      System Version: macOS 13.2.1 (22D68)
      Kernel Version: Darwin 22.3.0
      Time since boot: 2 days, 19 hours, 5 minutes

Graphics/Displays:

    AMD Radeon Pro 5300:

      Chipset Model: AMD Radeon Pro 5300
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0047
      ROM Revision: 113-D3220I-231
      VBIOS Version: 113-D322A1XL-012
      Option ROM Version: 113-D322A1XL-012
      EFI Driver Version: 01.01.231
      Metal Support: Metal 3
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.19.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.5
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    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: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.3.1
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    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: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc: Eric Pettersen Greg Couch added
Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → isolde residue stepper referencing dead structure

comment:2 by Tristan Croll, 19 months ago

Resolution: → fixed
Status: assigned → closed

See #14894.

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