Opened 3 years ago

Closed 3 years ago

#7636 closed defect (fixed)

ISOLDE holding ref to deleted structure

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

Description 

The following bug report has been submitted:
Platform:        Linux-5.15.0-47-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

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

> open Working-Tutorial.cxs

Opened emdb 20205 as #1.1.1.1, grid size 98,112,104, pixel 1.07,1.07,1.07,
shown at level 0.0957, step 1, values float32  
Opened emdb 20205 gaussian as #1.1.1.2, grid size 98,112,104, pixel
1.07,1.07,1.07, shown at level 0.114, step 1, values float32  
Log from Mon Sep 19 11:34:20 2022UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> isolde demo cryo_em_intro modelOnly true startIsolde false

6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  
  
Chain information for 6out.pdb #1  
---  
Chain | Description | UniProt  
A | capsid protein VP1 | CAPSD_NVN68  
B | capsid protein VP1 | CAPSD_NVN68  
C | capsid protein VP1 | CAPSD_NVN68  
  
Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205  

> open 20205 fromDatabase emdb

Summary of feedback from opening 20205 fetched from emdb  
---  
note | Fetching compressed map 20205 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-20205/map/emd_20205.map.gz  
  
Opened emdb 20205 as #2, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at
level 0.287, step 1, values float32  

> clipper associate #2 toModel #1

Opened emdb 20205 as #1.1.1.1, grid size 98,112,104, pixel 1.07,1.07,1.07,
shown at level 0.168, step 1, values float32  
6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  
  
Chain information for 6out.pdb  
---  
Chain | Description | UniProt  
1.2/A | capsid protein VP1 | CAPSD_NVN68  
1.2/B | capsid protein VP1 | CAPSD_NVN68  
1.2/C | capsid protein VP1 | CAPSD_NVN68  
  

> ui mousemode right zoom

> ui mousemode right translate

> undo

> ui mousemode right zoom

> close

> open /srv/home/leonardo/.local/share/ChimeraX/1.4/site-
> packages/chimerax/isolde/demo_data/6out/6out.pdb format pdb

6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  
  
Chain information for 6out.pdb #1  
---  
Chain | Description | UniProt  
A | capsid protein VP1 | CAPSD_NVN68  
B | capsid protein VP1 | CAPSD_NVN68  
C | capsid protein VP1 | CAPSD_NVN68  
  

> close

> isolde demo cryo_em_intro modelOnly true startIsolde false

6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  
  
Chain information for 6out.pdb #1  
---  
Chain | Description | UniProt  
A | capsid protein VP1 | CAPSD_NVN68  
B | capsid protein VP1 | CAPSD_NVN68  
C | capsid protein VP1 | CAPSD_NVN68  
  
Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205  

> open 20205 fromDatabase emdb

Opened emdb 20205 as #2, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at
level 0.287, step 1, values float32  

> clipper associate #2 toModel #1

Opened emdb 20205 as #1.1.1.1, grid size 98,112,104, pixel 1.07,1.07,1.07,
shown at level 0.168, step 1, values float32  
6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  
  
Chain information for 6out.pdb  
---  
Chain | Description | UniProt  
1.2/A | capsid protein VP1 | CAPSD_NVN68  
1.2/B | capsid protein VP1 | CAPSD_NVN68  
1.2/C | capsid protein VP1 | CAPSD_NVN68  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 51 residues in model #1.2 to IUPAC-IUB
standards.  
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time  
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time  
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time  

> undo

[Repeated 2 time(s)]

> set bgColor white

> set bgColor #ffffff00

> addh

Summary of feedback from adding hydrogens to 6out.pdb #1.2  
---  
notes | No usable SEQRES records for 6out.pdb (#1.2) chain A; guessing termini
instead  
No usable SEQRES records for 6out.pdb (#1.2) chain B; guessing termini instead  
No usable SEQRES records for 6out.pdb (#1.2) chain C; guessing termini instead  
Chain-initial residues that are actual N termini: /A ASP 29, /B THR 9, /C ASP
29  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A SER 520, /B ALA 519, /C
ALA 519  
1438 hydrogen bonds  
/A SER 520 is not terminus, removing H atom from 'C'  
/B ALA 519 is not terminus, removing H atom from 'C'  
/C ALA 519 is not terminus, removing H atom from 'C'  
11443 hydrogens added  
  

> isolde restrain ligands #1

[Repeated 1 time(s)]

> ui tool show "Ramachandran Plot"

[Repeated 1 time(s)]

> select #1

22948 atoms, 23065 bonds, 1720 residues, 15 models selected  

> isolde sim start sel

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> isolde sim pause

> view /A57

No objects specified.  

> view /A57

No objects specified.  

> view A57

Expected an objects specifier or a view name or a keyword  

> view /A:57

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 32 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> 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: stopped sim  

> isolde sim stop

No simulation is currently running!  

> ui tool show "Ramachandran Plot"

[Repeated 1 time(s)]

> 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  

> view /B:383

> volume gaussian #1 bfactor 150

Opened emdb 20205 gaussian as #2, grid size 98,112,104, pixel 1.07,1.07,1.07,
shown at step 1, values float32  

> clipper associate #2 toModel #1

Opened emdb 20205 gaussian as #1.1.1.2, grid size 98,112,104, pixel
1.07,1.07,1.07, shown at step 1, values float32  

> view /B:382

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 2 time(s)]

> isolde sim stop discardTo start

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

> save /srv/home/leonardo/Documents/Working-Tutorial.cxs

Taking snapshot of stepper: 6out.pdb  

——— End of log from Mon Sep 19 11:34:20 2022 ———

opened ChimeraX session  

> select /B:383@CA

1 atom, 1 residue, 1 model selected  

> isolde start

> set selectionWidth 4

> select clear

[Repeated 1 time(s)]

> isolde sim start sel

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

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

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  

> ui tool show "Ramachandran Plot"

[Repeated 1 time(s)]

> select clear

> isolde sim start sel

ISOLDE: started sim  

> isolde sim pause

> select clear

[Repeated 5 time(s)]

> ui tool show "Ramachandran Plot"

[Repeated 1 time(s)]

> isolde sim resume

> 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

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

> save /srv/home/leonardo/Documents/Analyzing-Ser-B383-after-change-tutorial-
> adapted.pdb

> select clear

[Repeated 1 time(s)]

> isolde sim start sel

ISOLDE: started sim  

> isolde cisflip sel

Performing cis<\-->trans flip for 1 residues  

> isolde cisflip sel

Performing cis<\-->trans flip 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 cisflip sel

Performing cis<\-->trans flip for 1 residues  

> isolde cisflip sel

Performing cis<\-->trans flip for 1 residues  

> isolde sim stop discardTo start

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

> close

> isolde demo cryo_em_intro modelOnly true startIsolde false

6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  
  
Chain information for 6out.pdb #1  
---  
Chain | Description | UniProt  
A | capsid protein VP1 | CAPSD_NVN68  
B | capsid protein VP1 | CAPSD_NVN68  
C | capsid protein VP1 | CAPSD_NVN68  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 51 residues in model #1 to IUPAC-IUB
standards.  
6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  
  
Chain information for 6out.pdb  
---  
Chain | Description | UniProt  
1.2/A | capsid protein VP1 | CAPSD_NVN68  
1.2/B | capsid protein VP1 | CAPSD_NVN68  
1.2/C | capsid protein VP1 | CAPSD_NVN68  
  
Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205  

> select clear

> open 20205 fromDatabase emdb

Opened emdb 20205 as #2, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at
level 0.287, step 1, values float32  

> clipper associate #2 toModel #1

Opened emdb 20205 as #1.1.1.1, grid size 98,112,104, pixel 1.07,1.07,1.07,
shown at step 1, values float32  

> isolde start

> ui tool show "Ramachandran Plot"

> set bgColor white

> addh

Summary of feedback from adding hydrogens to 6out.pdb #1.2  
---  
notes | No usable SEQRES records for 6out.pdb (#1.2) chain A; guessing termini
instead  
No usable SEQRES records for 6out.pdb (#1.2) chain B; guessing termini instead  
No usable SEQRES records for 6out.pdb (#1.2) chain C; guessing termini instead  
Chain-initial residues that are actual N termini: /A ASP 29, /B THR 9, /C ASP
29  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A SER 520, /B ALA 519, /C
ALA 519  
1438 hydrogen bonds  
/A SER 520 is not terminus, removing H atom from 'C'  
/B ALA 519 is not terminus, removing H atom from 'C'  
/C ALA 519 is not terminus, removing H atom from 'C'  
11443 hydrogens added  
  

> isolde restrain ligands #1

> ui tool show "Ramachandran Plot"

> select #1

22948 atoms, 23065 bonds, 1720 residues, 15 models selected  

> isolde sim start sel

ISOLDE: started sim  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process  
func(*args, **kwargs)  
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize  
c.draw()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw  
self.figure.draw(self.renderer)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper  
result = draw(artist, renderer, *args, **kwargs)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper  
return draw(artist, renderer)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw  
artists = self._get_draw_artists(renderer)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists  
ax.apply_aspect()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect  
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect  
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")  
ValueError: 'box_aspect' and 'fig_aspect' must be positive  

> ui tool show "Ramachandran Plot"

[Repeated 2 time(s)]

> isolde sim pause

> ui tool show "Ramachandran Plot"

[Repeated 1 time(s)]

> view /A:57

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 19 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> 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  

> isolde sim stop

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

> ui tool show "Ramachandran Plot"

> view /B:383

> volume gaussian #1 bfactor 150

Opened emdb 20205 gaussian as #2, grid size 98,112,104, pixel 1.07,1.07,1.07,
shown at step 1, values float32  

> clipper associate #2 toModel #1

Opened emdb 20205 gaussian as #1.1.1.2, grid size 98,112,104, pixel
1.07,1.07,1.07, shown at step 1, values float32  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim pause

> select clear

[Repeated 10 time(s)]

> isolde sim resume

> select clear

> isolde sim pause

> isolde sim resume

> 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 sim pause

> select clear

> ui mousemode right "isolde tug atom"

> isolde sim resume

> ui mousemode right "isolde tug atom"

> ui mousemode right "isolde tug residue"

> ui mousemode right "isolde tug selection"

> ui mousemode right "isolde tug residue"

> isolde sim pause

> ui mousemode right "isolde tug atom"

> isolde sim resume

> isolde sim pause

> select clear

> isolde sim resume

> 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 sim pause

> isolde sim resume

> isolde sim stop discardTo start

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

> select clear

[Repeated 7 time(s)]

> isolde sim start sel

ISOLDE: started sim  

> isolde sim pause

> isolde sim resume

> isolde sim pause

> select clear

[Repeated 1 time(s)]

> ui tool show "Ramachandran Plot"

> isolde sim resume

> isolde cisflip sel

Performing cis<\-->trans flip for 1 residues  

> isolde cisflip sel

Performing cis<\-->trans flip for 1 residues  

> select clear

[Repeated 3 time(s)]

> isolde sim pause

> isolde sim resume

> 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 sim pause

> isolde sim resume

> isolde sim pause

> select clear

[Repeated 1 time(s)]

> isolde sim resume

> isolde sim pause

> isolde sim resume

> isolde sim pause

> isolde sim resume

> isolde cisflip sel

Performing cis<\-->trans flip 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  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select clear

[Repeated 1 time(s)]

> isolde sim pause

> select clear

[Repeated 4 time(s)]

> isolde sim resume

> isolde sim pause

> ui tool show "Ramachandran Plot"

[Repeated 1 time(s)]

> stepTo first

Unknown command: isolde stepTo first  

> stepTo first

Unknown command: isolde stepTo first  

> stepTo first

Unknown command: isolde stepTo first  

> stepTo first

Unknown command: isolde stepTo first  

> help step

No help found for 'step'  

> help stepTo

No help found for 'stepTo'  

> help stepto

No help found for 'stepto'  

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  

> help help:user

> st first

> st second

Unrecognised residue argument! If specified, must be either a residue,
"first", "last", "next" or "prev"  

> st next

> st

> isolde sim resume

> isolde sim pause

> close

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/position.py", line 118, in
_selection_changed_cb  
sel = self.isolde.selected_atoms  
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms  
return m.atoms[m.atoms.selecteds]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop  
vcount = getattr(self, value_count)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "selection changed":  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/distance.py", line 150, in
_selection_changed_cb  
sel = self.isolde.selected_atoms  
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms  
return m.atoms[m.atoms.selecteds]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop  
vcount = getattr(self, value_count)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "selection changed":  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/secondary_structure.py", line 79,
in _selection_changed_cb  
sel = self.isolde.selected_atoms.unique_residues  
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms  
return m.atoms[m.atoms.selecteds]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop  
vcount = getattr(self, value_count)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "selection changed":  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/register_shift.py", line 105, in
_selection_changed_cb  
sel = self.isolde.selected_atoms  
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms  
return m.atoms[m.atoms.selecteds]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop  
vcount = getattr(self, value_count)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "selection changed":  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 470.141.03
OpenGL renderer: Quadro K4200/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision Tower 5810
OS: Ubuntu 22.04 jammy
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Xeon(R) CPU E5-1650 v3 @ 3.50GHz
Cache Size: 15360 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi       3.6Gi        20Gi       149Mi       7.6Gi        27Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK104GL [Quadro K4200] [10de:11b4] (rev a1)	
	Subsystem: NVIDIA Corporation GK104GL [Quadro K4200] [10de:1096]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.4
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    distro: 1.6.0
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (3)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE holding ref to deleted structure

Reported by Leonardo Lima

in reply to:  2 ; comment:2 by Tristan Croll, 3 years ago 

There's an error hiding away near the top that is new to me:

Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive


Can reproduce that by using the mouse to resize the Ramachandran plot
window down to nothing - looks like I just need to enforce a minimum size.

As for the string of errors at the bottom: a current limitation of ISOLDE
is that it *really* doesn't like it if you close the working model while a
simulation is running - simulations involve a whole host of callbacks that
would need to be carefully unwound to handle that scenario, and I haven't
had the resources to take that on to date. Hopefully I'll be able to
improve on that in future, but for now... don't do that. :)


On Tue, Sep 20, 2022 at 5:07 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

comment:3 by Tristan Croll, 3 years ago

Resolution: → fixed
Status: assigned → closed
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