Opened 3 years ago

Closed 3 years ago

Last modified 3 years ago

#7714 closed defect (duplicate)

Morph: 'set' object has no attribute 'items'

Reported by: feixia.chu@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Comparison Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.5.dev202209270114 (2022-09-27 01:14:36 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5.dev202209270114 (2022-09-27)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

QOpenGLShader::compile(Fragment): ERROR: 4:1: 'textureSampler' : syntax error
syntax error  
  
  

*** Problematic Fragment shader source code ***  
#version 110  
#ifdef GL_KHR_blend_equation_advanced  
#extension GL_ARB_fragment_coord_conventions : enable  
#extension GL_KHR_blend_equation_advanced : enable  
#endif  
#define lowp  
#define mediump  
#define highp  
#line 1  
varying highp vec2 uv;uniform sampler2DRect textureSampler;uniform bool
swizzle;uniform highp float opacity;void main() { highp vec4 tmpFragColor =
texture2DRect(textureSampler,uv); tmpFragColor.a *= opacity; gl_FragColor =
swizzle ? tmpFragColor.bgra : tmpFragColor;}  
***  

> open "C:\Users\Feixia\Feixia2022\Teaching\BMCB 794\Structure\2H59 clean.pdb"
> format pdb

Chain information for 2H59 clean.pdb #1  
---  
Chain | Description  
A | No description available  
D | No description available  
  

> open "C:/Users/Feixia/Feixia2022/Teaching/BMCB 794/Structure/2h4f.pdb"

2h4f.pdb title:  
SIR2-P53 peptide-nad+ [more info...]  
  
Chain information for 2h4f.pdb #2  
---  
Chain | Description | UniProt  
A | regulatory protein SIR2 homolog | NPD_THEMA  
D | cellular tumor antigen P53 | P53_HUMAN  
  
Non-standard residues in 2h4f.pdb #2  
---  
NAD — nicotinamide-adenine-dinucleotide  
ZN — zinc ion  
  

> matchmaker #2 to #1

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 2H59 clean.pdb, chain A (#1) with 2h4f.pdb, chain A (#2), sequence
alignment score = 1169.7  
RMSD between 232 pruned atom pairs is 0.699 angstroms; (across all 240 pairs:
1.150)  
  

> morph #1,2 frames 40

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\motion.py", line 111, in segment_and_pair_atoms  
results = segmentHingeExact(sm, m, cf, mhs, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\segment.py", line 109, in segmentHingeExact  
raise AtomPairingError('%s chain %s (%d) and %s chain %s (%d) have different
number of residues'  
chimerax.morph.segment.AtomPairingError: Morph - 2H59 clean.pdb chain A (352)
and 2h4f.pdb chain A (309) have different number of residues  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\morph.py", line 73, in morph  
traj = compute_morph(structures, session.logger, method=method, rate=rate,
frames=frames,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\motion.py", line 24, in compute_morph  
res_groups, atom_map, trimmed = motion.segment_and_pair_atoms(mol)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\motion.py", line 114, in segment_and_pair_atoms  
results = segmentHingeApproximate(sm, m, cf, mhs, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\segment.py", line 190, in segmentHingeApproximate  
score, gapped0, gapped1 = align(session, seq0, seq1,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 181, in align  
for s, ss_info in dssp_cache.items():  
AttributeError: 'set' object has no attribute 'items'  
  
AttributeError: 'set' object has no attribute 'items'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 181, in align  
for s, ss_info in dssp_cache.items():  
  
See log for complete Python traceback.  
  

> close session

> open "C:/Users/Feixia/Feixia2022/Teaching/BMCB 794/Structure/2KDM-clean.pdb"
> "C:/Users/Feixia/Feixia2022/Teaching/BMCB 794/Structure/2KDL-clean.pdb"

Chain information for 2KDM-clean.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for 2KDL-clean.pdb #2  
---  
Chain | Description  
A | No description available  
  

> matchmaker #2 to #1

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 2KDM-clean.pdb, chain A (#1) with 2KDL-clean.pdb, chain A (#2),
sequence alignment score = 115.3  
RMSD between 5 pruned atom pairs is 1.065 angstroms; (across all 56 pairs:
15.446)  
  

> morph #1,2

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\motion.py", line 111, in segment_and_pair_atoms  
results = segmentHingeExact(sm, m, cf, mhs, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\segment.py", line 116, in segmentHingeExact  
raise AtomPairingError("residues have different number atoms")  
chimerax.morph.segment.AtomPairingError: residues have different number atoms  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\morph.py", line 73, in morph  
traj = compute_morph(structures, session.logger, method=method, rate=rate,
frames=frames,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\motion.py", line 24, in compute_morph  
res_groups, atom_map, trimmed = motion.segment_and_pair_atoms(mol)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\motion.py", line 114, in segment_and_pair_atoms  
results = segmentHingeApproximate(sm, m, cf, mhs, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\segment.py", line 190, in segmentHingeApproximate  
score, gapped0, gapped1 = align(session, seq0, seq1,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 181, in align  
for s, ss_info in dssp_cache.items():  
AttributeError: 'set' object has no attribute 'items'  
  
AttributeError: 'set' object has no attribute 'items'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 181, in align  
for s, ss_info in dssp_cache.items():  
  
See log for complete Python traceback.  
  

> morph #1,2

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\motion.py", line 111, in segment_and_pair_atoms  
results = segmentHingeExact(sm, m, cf, mhs, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\segment.py", line 116, in segmentHingeExact  
raise AtomPairingError("residues have different number atoms")  
chimerax.morph.segment.AtomPairingError: residues have different number atoms  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\morph.py", line 73, in morph  
traj = compute_morph(structures, session.logger, method=method, rate=rate,
frames=frames,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\motion.py", line 24, in compute_morph  
res_groups, atom_map, trimmed = motion.segment_and_pair_atoms(mol)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\motion.py", line 114, in segment_and_pair_atoms  
results = segmentHingeApproximate(sm, m, cf, mhs, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\segment.py", line 190, in segmentHingeApproximate  
score, gapped0, gapped1 = align(session, seq0, seq1,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 181, in align  
for s, ss_info in dssp_cache.items():  
AttributeError: 'set' object has no attribute 'items'  
  
AttributeError: 'set' object has no attribute 'items'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 181, in align  
for s, ss_info in dssp_cache.items():  
  
See log for complete Python traceback.  
  

> open 3gbp

Summary of feedback from opening 3gbp fetched from pdb  
---  
notes | Fetching compressed mmCIF 3gbp from
http://files.rcsb.org/download/3gbp.cif  
Fetching CCD BGC from http://ligand-expo.rcsb.org/reports/B/BGC/BGC.cif  
  
3gbp title:  
Structure of the periplasmic glucose/galactose receptor of salmonella
typhimurium [more info...]  
  
Chain information for 3gbp #3  
---  
Chain | Description | UniProt  
A | GALACTOSE-BINDING PROTEIN | DGAL_SALTY  
  
Non-standard residues in 3gbp #3  
---  
BGC — beta-D-glucopyranose  
CA — calcium ion  
  

> close session

> open 3gbp

3gbp title:  
Structure of the periplasmic glucose/galactose receptor of salmonella
typhimurium [more info...]  
  
Chain information for 3gbp #1  
---  
Chain | Description | UniProt  
A | GALACTOSE-BINDING PROTEIN | DGAL_SALTY  
  
Non-standard residues in 3gbp #1  
---  
BGC — beta-D-glucopyranose  
CA — calcium ion  
  

> open 2fwo

Summary of feedback from opening 2fwo fetched from pdb  
---  
note | Fetching compressed mmCIF 2fwo from
http://files.rcsb.org/download/2fwo.cif  
  
2fwo title:  
MHC Class I H-2Kd heavy chain in complex with beta-2microglobulin and peptide
derived from influenza nucleoprotein [more info...]  
  
Chain information for 2fwo #2  
---  
Chain | Description | UniProt  
A | H-2 class I histocompatibility antigen, K-D alpha chain | HA1D_MOUSE  
B | Beta-2-microglobulin | B2MG_MOUSE  
P | TYQRTRALV peptide from Nucleoprotein | Q701N7_9INFA  
  

> matchmaker #2 to #1

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 3gbp, chain A (#1) with 2fwo, chain P (#2), sequence alignment
score = 9.4  
RMSD between 6 pruned atom pairs is 1.219 angstroms; (across all 9 pairs:
7.101)  
  

> close session

> open 2fw0

Summary of feedback from opening 2fw0 fetched from pdb  
---  
notes | Fetching compressed mmCIF 2fw0 from
http://files.rcsb.org/download/2fw0.cif  
Fetching CCD NA from http://ligand-expo.rcsb.org/reports/N/NA/NA.cif  
Fetching CCD CIT from http://ligand-expo.rcsb.org/reports/C/CIT/CIT.cif  
Fetching CCD MLA from http://ligand-expo.rcsb.org/reports/M/MLA/MLA.cif  
  
2fw0 title:  
Apo Open Form of Glucose/Galactose Binding Protein [more info...]  
  
Chain information for 2fw0 #1  
---  
Chain | Description | UniProt  
A | D-galactose-binding periplasmic protein | DGAL_ECOLI  
  
Non-standard residues in 2fw0 #1  
---  
CA — calcium ion  
CIT — citric acid  
MLA — malonic acid (dicarboxylic acid C3; propanediolic acid;
methanedicarboxylic acid)  
NA — sodium ion  
  

> save "C:/Users/Feixia/Feixia2022/Teaching/BMCB 794/Structure/2fw0.pdb"
> relModel #1

> open 3gbp

3gbp title:  
Structure of the periplasmic glucose/galactose receptor of salmonella
typhimurium [more info...]  
  
Chain information for 3gbp #2  
---  
Chain | Description | UniProt  
A | GALACTOSE-BINDING PROTEIN | DGAL_SALTY  
  
Non-standard residues in 3gbp #2  
---  
BGC — beta-D-glucopyranose  
CA — calcium ion  
  

> matchmaker #2 to #1

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 2fw0, chain A (#1) with 3gbp, chain A (#2), sequence alignment
score = 1483.7  
RMSD between 150 pruned atom pairs is 0.439 angstroms; (across all 304 pairs:
6.811)  
  

> ui tool show "Color Actions"

> set bgColor white

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> morph #1,2

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\motion.py", line 111, in segment_and_pair_atoms  
results = segmentHingeExact(sm, m, cf, mhs, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\segment.py", line 109, in segmentHingeExact  
raise AtomPairingError('%s chain %s (%d) and %s chain %s (%d) have different
number of residues'  
chimerax.morph.segment.AtomPairingError: Morph - 2fw0 chain A (661) and 3gbp
chain A (413) have different number of residues  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\morph.py", line 73, in morph  
traj = compute_morph(structures, session.logger, method=method, rate=rate,
frames=frames,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\motion.py", line 24, in compute_morph  
res_groups, atom_map, trimmed = motion.segment_and_pair_atoms(mol)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\motion.py", line 114, in segment_and_pair_atoms  
results = segmentHingeApproximate(sm, m, cf, mhs, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\segment.py", line 190, in segmentHingeApproximate  
score, gapped0, gapped1 = align(session, seq0, seq1,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 181, in align  
for s, ss_info in dssp_cache.items():  
AttributeError: 'set' object has no attribute 'items'  
  
AttributeError: 'set' object has no attribute 'items'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 181, in align  
for s, ss_info in dssp_cache.items():  
  
See log for complete Python traceback.  
  

> matchmaker #2 to #1

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 2fw0, chain A (#1) with 3gbp, chain A (#2), sequence alignment
score = 1483.7  
RMSD between 150 pruned atom pairs is 0.439 angstroms; (across all 304 pairs:
6.811)  
  

> close session

> open "C:\Users\Feixia\Feixia2022\Teaching\BMCB 794\Structure\2H59 clean.pdb"
> format pdb

Chain information for 2H59 clean.pdb #1  
---  
Chain | Description  
A | No description available  
D | No description available  
  

> ui tool show "Color Actions"

> set bgColor white

> select clear

> open "C:/Users/Feixia/Feixia2022/Teaching/BMCB 794/Structure/2h4f.pdb"

2h4f.pdb title:  
SIR2-P53 peptide-nad+ [more info...]  
  
Chain information for 2h4f.pdb #2  
---  
Chain | Description | UniProt  
A | regulatory protein SIR2 homolog | NPD_THEMA  
D | cellular tumor antigen P53 | P53_HUMAN  
  
Non-standard residues in 2h4f.pdb #2  
---  
NAD — nicotinamide-adenine-dinucleotide  
ZN — zinc ion  
  

> matchmaker #2 to #1

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 2H59 clean.pdb, chain A (#1) with 2h4f.pdb, chain A (#2), sequence
alignment score = 1169.7  
RMSD between 232 pruned atom pairs is 0.699 angstroms; (across all 240 pairs:
1.150)  
  

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> morph #1,2

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\motion.py", line 111, in segment_and_pair_atoms  
results = segmentHingeExact(sm, m, cf, mhs, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\segment.py", line 109, in segmentHingeExact  
raise AtomPairingError('%s chain %s (%d) and %s chain %s (%d) have different
number of residues'  
chimerax.morph.segment.AtomPairingError: Morph - 2H59 clean.pdb chain A (352)
and 2h4f.pdb chain A (309) have different number of residues  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\morph.py", line 73, in morph  
traj = compute_morph(structures, session.logger, method=method, rate=rate,
frames=frames,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\motion.py", line 24, in compute_morph  
res_groups, atom_map, trimmed = motion.segment_and_pair_atoms(mol)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\motion.py", line 114, in segment_and_pair_atoms  
results = segmentHingeApproximate(sm, m, cf, mhs, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\segment.py", line 190, in segmentHingeApproximate  
score, gapped0, gapped1 = align(session, seq0, seq1,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 181, in align  
for s, ss_info in dssp_cache.items():  
AttributeError: 'set' object has no attribute 'items'  
  
AttributeError: 'set' object has no attribute 'items'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 181, in align  
for s, ss_info in dssp_cache.items():  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 20.19.15.4835
OpenGL renderer: Intel(R) HD Graphics 5500
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: LENOVO
Model: 20BXCTO1WW
OS: Microsoft Windows 10 Education (Build 19044)
Memory: 12,566,208,512
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i7-5600U CPU @ 2.60GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.0.8
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2
    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: 1.41.3
    ChimeraX-AtomicLibrary: 8.0.1
    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-ColorActions: 1.0.2
    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.dev202209270114
    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-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: 1.8.1
    ChimeraX-Map: 1.1.1
    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: 2.1
    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
    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: 2.6.7
    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: 1.24.1
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.3
    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
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.1.0
    filelock: 3.7.1
    fonttools: 4.37.3
    funcparserlib: 1.0.0
    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: 4.12.0
    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: 4.11.1
    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: 1.5.5
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.3
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    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: 2022.2.1
    pywin32: 303
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.2.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    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: 0.5.1
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.8.1

Change History (3)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Structure Comparison
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Morph: 'set' object has no attribute 'items'

comment:2 by Eric Pettersen, 3 years ago

Resolution: → duplicate
Status: accepted → closed

Hi Feixia,

This bug was fixed on Thursday, so get a new daily build to fix it. Sorry for the inconvenience.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  3 ; comment:3 by Feixia.Chu@…, 3 years ago 

Thank you so much, Eric!
Best,
Feixia

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Monday, October 03, 2022 12:40 PM
Cc: Feixia Chu <feixia.chu@unh.edu>; pett@cgl.ucsf.edu
Subject: Re: [ChimeraX] #7714: Morph: 'set' object has no attribute 'items'

CAUTION: This email originated from outside of the University System. Do not click links or open attachments unless you recognize the sender and know the content is safe.


#7714: Morph: 'set' object has no attribute 'items'
-------------------------------------------+--------------------
          Reporter:  feixia.chu@...          |      Owner:  pett
              Type:  defect                |     Status:  closed
          Priority:  normal                |  Milestone:
         Component:  Structure Comparison  |    Version:
        Resolution:  duplicate             |   Keywords:
        Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
           Project:  ChimeraX              |
-------------------------------------------+--------------------
Changes (by pett):

 * status:  accepted => closed
 * resolution:   => duplicate


Comment:

 Hi Feixia,
         This bug was fixed on Thursday, so get a new daily build to fix  it.  Sorry for the inconvenience.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

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