Opened 5 years ago

Closed 5 years ago

#3551 closed defect (fixed)

PromoteAtomSelection._structure is deleted

Reported by: Tristan Croll Owned by: Tom Goddard
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.13.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7bv1

7bv1 title:  
Cryo-EM structure of the apo nsp12-nsp7-nsp8 complex [more info...]  
  
Chain information for 7bv1 #1  
---  
Chain | Description  
A | SARS-CoV-2 nsp12  
B D | SARS-CoV-2 nsp8  
C | SARS-CoV-2 nsp7  
  
Non-standard residues in 7bv1 #1  
---  
ZN — zinc ion  
  

> open 7bv2

Summary of feedback from opening 7bv2 fetched from pdb  
---  
notes | Fetching CCD POP from http://ligand-
expo.rcsb.org/reports/P/POP/POP.cif  
Fetching CCD F86 from http://ligand-expo.rcsb.org/reports/F/F86/F86.cif  
  
7bv2 title:  
The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate
form of Remdesivir(RTP) [more info...]  
  
Chain information for 7bv2 #2  
---  
Chain | Description  
A | SARS-CoV-2 Nsp12  
B | SARS-CoV-2 nsp8  
C | SARS-CoV-2 nsp7  
P | Primer  
T | Templete  
  
Non-standard residues in 7bv2 #2  
---  
F86 —
[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate  
MG — magnesium ion  
POP — pyrophosphate 2-  
ZN — zinc ion  
  

> open 6m71

6m71 title:  
2019-nCoV RNA-dependent RNA polymerase in complex with cofactors [more
info...]  
  
Chain information for 6m71 #3  
---  
Chain | Description  
A | SARS-CoV-2 NSP12  
B D | SARS-CoV-2 NSP8  
C | SARS-CoV-2 NSP7  
  

> open 7bzf

Summary of feedback from opening 7bzf fetched from pdb  
---  
note | Fetching compressed mmCIF 7bzf from
http://files.rcsb.org/download/7bzf.cif  
  
7bzf title:  
COVID-19 RNA-dependent RNA polymerase post-translocated catalytic complex
[more info...]  
  
Chain information for 7bzf #4  
---  
Chain | Description  
A | RNA-directed RNA polymerase  
B D | Non-structural protein 8  
C | Non-structural protein 7  
F | RNA (31-mer)  
G | RNA (5'-R(*up*GP*up*up*CP*GP*ap*CP*GP*ap*CP*ap*CP*A)-3')  
  
Non-standard residues in 7bzf #4  
---  
ZN — zinc ion  
  

> open 7btf

7btf title:  
SARS-CoV-2 RNA-dependent RNA polymerase in complex with cofactors in reduced
condition [more info...]  
  
Chain information for 7btf #5  
---  
Chain | Description  
A | SARS-Cov-2 NSP12  
B D | SARS-Cov-2 NSP8  
C | SARS-Cov-2 NSP7  
  
Non-standard residues in 7btf #5  
---  
ZN — zinc ion  
  

> open 7c2k

Summary of feedback from opening 7c2k fetched from pdb  
---  
note | Fetching compressed mmCIF 7c2k from
http://files.rcsb.org/download/7c2k.cif  
  
7c2k title:  
COVID-19 RNA-dependent RNA polymerase pre-translocated catalytic complex [more
info...]  
  
Chain information for 7c2k #6  
---  
Chain | Description  
A | RNA-directed RNA polymerase  
B D | Non-structural protein 8  
C | Non-structural protein 7  
F | RNA (29-mer)  
G | RNA (5'-R(*up*GP*up*up*CP*GP*ap*CP*GP*ap*CP*ap*CP*ap*GP*G*(F86)P*G)-3')  
  
Non-standard residues in 7c2k #6  
---  
F86 —
[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate  
ZN — zinc ion  
  

> open 6x2g

Summary of feedback from opening 6x2g fetched from pdb  
---  
note | Fetching compressed mmCIF 6x2g from
http://files.rcsb.org/download/6x2g.cif  
  
6x2g title:  
SARS-CoV-2 RdRp/RNA complex [more info...]  
  
Chain information for 6x2g #7  
---  
Chain | Description  
A | RNA-directed RNA polymerase  
B D | Non-structural protein 8  
C | Non-structural protein 7  
E F | RNA (5'-R(P*GP*up*GP*GP*GP*CP*CP*CP*A)-3')  
  
Non-standard residues in 6x2g #7  
---  
MG — magnesium ion  
ZN — zinc ion  
  

> open 6yyt

6yyt title:  
Structure of replicating SARS-CoV-2 polymerase [more info...]  
  
Chain information for 6yyt #8  
---  
Chain | Description  
A | nsp12  
B D | nsp8  
C | nsp7  
P Q T U | RNA product  
  
Non-standard residues in 6yyt #8  
---  
ZN — zinc ion  
  

> open 7bw4

Summary of feedback from opening 7bw4 fetched from pdb  
---  
note | Fetching compressed mmCIF 7bw4 from
http://files.rcsb.org/download/7bw4.cif  
  
7bw4 title:  
Structure of the RNA-dependent RNA polymerase from SARS-CoV-2 [more info...]  
  
Chain information for 7bw4 #9  
---  
Chain | Description  
A | nsp12  
B D | nsp8  
C | nsp7  
  
Non-standard residues in 7bw4 #9  
---  
ZN — zinc ion  
  

> cartoon

> color bymodel

> hide

> matchmaker #2-9 to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7bv1, chain A (#1) with 7bv2, chain A (#2), sequence alignment
score = 4701.7  
RMSD between 819 pruned atom pairs is 0.545 angstroms; (across all 826 pairs:
0.584)  
  
Matchmaker 7bv1, chain A (#1) with 6m71, chain A (#3), sequence alignment
score = 4592.7  
RMSD between 823 pruned atom pairs is 0.556 angstroms; (across all 826 pairs:
0.578)  
  
Matchmaker 7bv1, chain A (#1) with 7bzf, chain A (#4), sequence alignment
score = 4448.7  
RMSD between 773 pruned atom pairs is 0.873 angstroms; (across all 820 pairs:
1.805)  
  
Matchmaker 7bv1, chain A (#1) with 7btf, chain A (#5), sequence alignment
score = 4584.3  
RMSD between 824 pruned atom pairs is 0.396 angstroms; (across all 826 pairs:
0.416)  
  
Matchmaker 7bv1, chain A (#1) with 7c2k, chain A (#6), sequence alignment
score = 4594.8  
RMSD between 789 pruned atom pairs is 0.537 angstroms; (across all 824 pairs:
2.004)  
  
Matchmaker 7bv1, chain A (#1) with 6x2g, chain A (#7), sequence alignment
score = 4513.4  
RMSD between 805 pruned atom pairs is 0.899 angstroms; (across all 826 pairs:
0.965)  
  
Matchmaker 7bv1, chain A (#1) with 6yyt, chain A (#8), sequence alignment
score = 4543.4  
RMSD between 793 pruned atom pairs is 0.561 angstroms; (across all 823 pairs:
2.065)  
  
Matchmaker 7bv1, chain A (#1) with 7bw4, chain A (#9), sequence alignment
score = 4472.6  
RMSD between 795 pruned atom pairs is 0.846 angstroms; (across all 808 pairs:
0.892)  
  

> select :919-928

406 atoms, 416 bonds, 9 models selected  

> cofr centerOfView

> select clear

> style stick

Changed 92960 atom styles  

> select :919-928

406 atoms, 416 bonds, 9 models selected  

> show sel

Drag select of 24 atoms, 39 residues, 21 bonds  

> select up

370 atoms, 243 bonds, 9 models selected  

> select up

414 atoms, 290 bonds, 9 models selected  

> select :910-928

1157 atoms, 1201 bonds, 9 models selected  

> ~cartoon ~sel

> cartoon

> show sel

> close #1-9

> open 7bv1

Summary of feedback from opening 7bv1 fetched from pdb  
---  
note | Fetching compressed mmCIF 7bv1 from
http://files.rcsb.org/download/7bv1.cif  
  
7bv1 title:  
Cryo-EM structure of the apo nsp12-nsp7-nsp8 complex [more info...]  
  
Chain information for 7bv1 #1  
---  
Chain | Description  
A | nsp12  
B D | nsp8  
C | nsp7  
  
Non-standard residues in 7bv1 #1  
---  
ZN — zinc ion  
  

> open 7bv2

Summary of feedback from opening 7bv2 fetched from pdb  
---  
note | Fetching compressed mmCIF 7bv2 from
http://files.rcsb.org/download/7bv2.cif  
  
7bv2 title:  
The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate
form of Remdesivir(RTP) [more info...]  
  
Chain information for 7bv2 #2  
---  
Chain | Description  
A | nsp12  
B | nsp8  
C | nsp7  
P | Primer  
T | Templete  
  
Non-standard residues in 7bv2 #2  
---  
F86 —
[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate  
MG — magnesium ion  
POP — pyrophosphate 2-  
ZN — zinc ion  
  

> open 6m71

Summary of feedback from opening 6m71 fetched from pdb  
---  
note | Fetching compressed mmCIF 6m71 from
http://files.rcsb.org/download/6m71.cif  
  
6m71 title:  
SARS-Cov-2 RNA-dependent RNA polymerase in complex with cofactors [more
info...]  
  
Chain information for 6m71 #3  
---  
Chain | Description  
A | SARS-Cov-2 NSP 12  
B D | SARS-Cov-2 NSP 7  
C | SARS-Cov-2 NSP 8  
  

> open 7bzf

Summary of feedback from opening 7bzf fetched from pdb  
---  
note | Fetching compressed mmCIF 7bzf from
http://files.rcsb.org/download/7bzf.cif  
  
7bzf title:  
COVID-19 RNA-dependent RNA polymerase post-translocated catalytic complex
[more info...]  
  
Chain information for 7bzf #4  
---  
Chain | Description  
A | RNA-directed RNA polymerase  
B D | Non-structural protein 8  
C | Non-structural protein 7  
F | RNA (31-mer)  
G | RNA (5'-R(*up*GP*up*up*CP*GP*ap*CP*GP*ap*CP*ap*CP*A)-3')  
  
Non-standard residues in 7bzf #4  
---  
ZN — zinc ion  
  

> open 7btf

Summary of feedback from opening 7btf fetched from pdb  
---  
note | Fetching compressed mmCIF 7btf from
http://files.rcsb.org/download/7btf.cif  
  
7btf title:  
SARS-CoV-2 RNA-dependent RNA polymerase in complex with cofactors in reduced
condition [more info...]  
  
Chain information for 7btf #5  
---  
Chain | Description  
A | NSP12  
B D | NSP8  
C | NSP7  
  
Non-standard residues in 7btf #5  
---  
ZN — zinc ion  
  

> open 7c2k

Summary of feedback from opening 7c2k fetched from pdb  
---  
note | Fetching compressed mmCIF 7c2k from
http://files.rcsb.org/download/7c2k.cif  
  
7c2k title:  
COVID-19 RNA-dependent RNA polymerase pre-translocated catalytic complex [more
info...]  
  
Chain information for 7c2k #6  
---  
Chain | Description  
A | RNA-directed RNA polymerase  
B D | Non-structural protein 8  
C | Non-structural protein 7  
F | RNA (29-mer)  
G | RNA (5'-R(*up*GP*up*up*CP*GP*ap*CP*GP*ap*CP*ap*CP*ap*GP*G*(F86)P*G)-3')  
  
Non-standard residues in 7c2k #6  
---  
F86 —
[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate  
ZN — zinc ion  
  

> open 6x2g

Summary of feedback from opening 6x2g fetched from pdb  
---  
note | Fetching compressed mmCIF 6x2g from
http://files.rcsb.org/download/6x2g.cif  
  
6x2g title:  
SARS-CoV-2 RdRp/RNA complex [more info...]  
  
Chain information for 6x2g #7  
---  
Chain | Description  
A | RNA-directed RNA polymerase  
B D | Non-structural protein 8  
C | Non-structural protein 7  
E F | RNA (5'-R(P*GP*up*GP*GP*GP*CP*CP*CP*A)-3')  
  
Non-standard residues in 6x2g #7  
---  
MG — magnesium ion  
ZN — zinc ion  
  

> open 6yyt

Summary of feedback from opening 6yyt fetched from pdb  
---  
note | Fetching compressed mmCIF 6yyt from
http://files.rcsb.org/download/6yyt.cif  
  
6yyt title:  
Structure of replicating SARS-CoV-2 polymerase [more info...]  
  
Chain information for 6yyt #8  
---  
Chain | Description  
A | nsp12  
B D | nsp8  
C | nsp7  
P Q T U | RNA product  
  
Non-standard residues in 6yyt #8  
---  
ZN — zinc ion  
  

> open 7bw4

Summary of feedback from opening 7bw4 fetched from pdb  
---  
note | Fetching compressed mmCIF 7bw4 from
http://files.rcsb.org/download/7bw4.cif  
  
7bw4 title:  
Structure of the RNA-dependent RNA polymerase from SARS-CoV-2 [more info...]  
  
Chain information for 7bw4 #9  
---  
Chain | Description  
A | nsp12  
B D | nsp8  
C | nsp7  
  
Non-standard residues in 7bw4 #9  
---  
ZN — zinc ion  
  

> select up

Nothing selected  

> select down

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/ui/gui.py", line
288, in forward_keystroke  
run(self.session, 'select down')  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/std_commands/select.py", line 162, in select_down  
session.selection.demote(session)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/selection.py", line 63, in demote  
self._promotion.demote_selection()  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/selection.py", line 191, in demote_selection  
p.demote()  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1781, in demote  
s.atoms.selected = self._prev_atom_sel_mask  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError  
  
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 450.51.05
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        7.0G         46G        268M        8.9G         55G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Core
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → PromoteAtomSelection._structure is deleted

comment:2 by Tom Goddard, 5 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Selection demotion was not checking for deleted structures.

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