Opened 4 years ago

Closed 4 years ago

#6598 closed defect (fixed)

Can't show sequence

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: critical Milestone:
Component: Sequence Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.14-x86_64-i386-64bit
ChimeraX Version: 1.4.dev202204120245 (2022-04-12 02:45:15 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.4.dev202204120245 (2022-04-12)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/admin/Desktop/coot_modeling/D135_04012022_SP_AK.pdb

Summary of feedback from opening
/Users/admin/Desktop/coot_modeling/D135_04012022_SP_AK.pdb  
---  
warnings | Cannot find LINK/SSBOND residue MG (741 )  
Cannot find LINK/SSBOND residue MG (743 )  
Cannot find LINK/SSBOND residue A (341 )  
Cannot find LINK/SSBOND residue MG (743 )  
Cannot find LINK/SSBOND residue A (6 )  
4 messages similar to the above omitted  
  
D135_04012022_SP_AK.pdb title:  
Crystal structure of A eukaryotic group II intron lariat [more info...]  
  
Chain information for D135_04012022_SP_AK.pdb #1  
---  
Chain | Description  
A | group iib intron lariat  
  
Non-standard residues in D135_04012022_SP_AK.pdb #1  
---  
IRI — iridium hexammine ion  
MG — magnesium ion  
NA — sodium ion  
  

> open /Users/admin/Desktop/coot_modeling/postprocess-2.mrc

Opened postprocess-2.mrc as #2, grid size 356,356,356, pixel 0.844, shown at
level 0.00516, step 2, values float32  

> set bgColor white

> lighting simple

> lighting soft

> lighting full

> lighting soft

> hide cartoons

> show atoms

> hide atoms

> show cartoons

> set bgColor gray

[Repeated 1 time(s)]

> set bgColor white

> lighting simple

> lighting soft

> lighting full

> lighting shadows false

> graphics silhouettes true

> lighting soft

> volume style mesh

> volume style surface

> volume #2 color #b2b2b24c

> volume #2 color #b2b2b24d

> volume style surface

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> undo

[Repeated 1 time(s)]

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume #2 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 150.2 tiltedSlabSpacing 0.844 tiltedSlabPlaneCount 10

> mousemode rightMode "rotate slab"

> volume #2 orthoplanes xyz positionPlanes 178,178,178 style image region all

> mousemode rightMode "move planes"

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume zone #2 nearAtoms #1 range 5.06

> volume #2 region 0,0,0,355,355,355

[Repeated 1 time(s)]

> undo

> volume #2 region 0,0,0,355,355,355

[Repeated 1 time(s)]

> volume step 1

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume #2 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 150.2 tiltedSlabSpacing 0.844 tiltedSlabPlaneCount 10

> mousemode rightMode "rotate slab"

> volume #2 orthoplanes xyz positionPlanes 178,178,178 style image region all

> mousemode rightMode "move planes"

> volume #2 orthoplanes xyz positionPlanes 178,178,121

> volume #2 orthoplanes xyz positionPlanes 178,178,12

> volume #2 orthoplanes xyz positionPlanes 178,178,214

> volume #2 orthoplanes xyz positionPlanes 178,178,182

> volume #2 orthoplanes xyz positionPlanes 178,178,217

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume zone #2 nearAtoms #1 range 5.06

> volume style surface

> volume #2 region 0,0,0,355,355,271

> nucleotides fill

> style nucleic stick

Changed 9723 atom styles  

> hide cartoons

[Repeated 1 time(s)]

> hide atoms

> show atoms

> color bynucleotide

> volume showOutlineBox false

> volume #2 region 0,0,0,355,355,265

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  
Traceback (most recent call last):  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/show_sequences/tool.py", line 64, in show_seqs  
run(self.session, "seq chain %s" % " ".join([chain.atomspec for chain in
chains]))  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.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
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.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
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/cmd.py", line 211, in seqalign_chain  
alignment = session.alignments.new_alignment([chain], ident, seq_viewer="sv",  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/manager.py", line 243, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 99, in __init__  
self.associate(None, keep_intrinsic=True)  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 186, in associate  
self.associate([], seq=seq, reassoc=reassoc, keep_intrinsic=keep_intrinsic)  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 205, in associate  
self.prematched_assoc_structure(match_map, 0, reassoc)  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 576, in
prematched_assoc_structure  
aseq.match_maps[chain] = match_map  
AttributeError: 'Chain' object has no attribute 'match_maps'  
  

Populating font family aliases took 718 ms. Replace uses of missing font
family ".SF NS Text" with one that exists to avoid this cost.  

AttributeError: 'Chain' object has no attribute 'match_maps'  
  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 576, in
prematched_assoc_structure  
aseq.match_maps[chain] = match_map  
  
See log for complete Python traceback.  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  
Traceback (most recent call last):  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/show_sequences/tool.py", line 64, in show_seqs  
run(self.session, "seq chain %s" % " ".join([chain.atomspec for chain in
chains]))  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.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
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.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
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/cmd.py", line 211, in seqalign_chain  
alignment = session.alignments.new_alignment([chain], ident, seq_viewer="sv",  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/manager.py", line 243, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 99, in __init__  
self.associate(None, keep_intrinsic=True)  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 186, in associate  
self.associate([], seq=seq, reassoc=reassoc, keep_intrinsic=keep_intrinsic)  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 205, in associate  
self.prematched_assoc_structure(match_map, 0, reassoc)  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 576, in
prematched_assoc_structure  
aseq.match_maps[chain] = match_map  
AttributeError: 'Chain' object has no attribute 'match_maps'  
  
AttributeError: 'Chain' object has no attribute 'match_maps'  
  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 576, in
prematched_assoc_structure  
aseq.match_maps[chain] = match_map  
  
See log for complete Python traceback.  
  

> color bynucleotide

> color byhetero

> color bychain

> color #1 #524b8d transparency 0

> color #1 #282545 transparency 0

> color #1 #544d91 transparency 0

> color #1 #4c9162 transparency 0

> color #1 #489136 transparency 0

> color #1 #913f2c transparency 0

> color #1 #914a33 transparency 0

> color #1 #912323 transparency 0

> color #1 #579138 transparency 0

> color #1 #915e2e transparency 0

> color #1 #914120 transparency 0

> color #1 #914911 transparency 0

> color #1 #915d68 transparency 0

> color #1 #915f58 transparency 0

> color #1 #917758 transparency 0

> color #1 #91403d transparency 0

> color #1 #912c2f transparency 0

> color #1 #91181d transparency 0

> color #1 #910605 transparency 0

> color #1 #910002 transparency 0

> color #1 #911943 transparency 0

> color #1 #411f91 transparency 0

> color #1 #638591 transparency 0

> volume #2 region 19,0,0,355,355,265

> volume #2 change image level -0.001395,0 level 0.01043,0.8 level 0.05195,1

> volume #2 level 0.005157

> volume #2 level 0.006073

> hide atoms

> show cartoons

> volume #2 region 19,0,0,355,355,265

> style ball

Changed 9779 atom styles  

> style ball

Changed 9779 atom styles  

> volume #2 region 19,0,0,355,355,265

[Repeated 1 time(s)]

> volume #2 level 0.006759

> volume #2 level 0.00859

> color /A 570-571 hot pink atoms

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  
Traceback (most recent call last):  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/show_sequences/tool.py", line 64, in show_seqs  
run(self.session, "seq chain %s" % " ".join([chain.atomspec for chain in
chains]))  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.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
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.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
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/cmd.py", line 211, in seqalign_chain  
alignment = session.alignments.new_alignment([chain], ident, seq_viewer="sv",  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/manager.py", line 243, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 99, in __init__  
self.associate(None, keep_intrinsic=True)  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 186, in associate  
self.associate([], seq=seq, reassoc=reassoc, keep_intrinsic=keep_intrinsic)  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 205, in associate  
self.prematched_assoc_structure(match_map, 0, reassoc)  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 576, in
prematched_assoc_structure  
aseq.match_maps[chain] = match_map  
AttributeError: 'Chain' object has no attribute 'match_maps'  
  
AttributeError: 'Chain' object has no attribute 'match_maps'  
  
File
"/private/var/folders/pl/kxg51t8140l69br12sxln62c0000gp/T/AppTranslocation/4842604E-1AB4-48DA-A748-7D949325F883/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 576, in
prematched_assoc_structure  
aseq.match_maps[chain] = match_map  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.0.36
OpenGL renderer: AMD Radeon R9 M290X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.2.3, Qt 6.2.3
Qt runtime version: 6.2.4
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac15,1
      Processor Name: Intel Core i7
      Processor Speed: 4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Memory: 32 GB
      Boot ROM Version: IM151.0217.B00
      SMC Version (system): 2.22f16

Software:

    System Software Overview:

      System Version: macOS 10.14 (18A391)
      Kernel Version: Darwin 18.0.0
      Time since boot: 119 days 22:52

Graphics/Displays:

    AMD Radeon R9 M290X:

      Chipset Model: AMD Radeon R9 M290X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Dynamic, Max): 2048 MB
      Vendor: AMD (0x1002)
      Device ID: 0x6810
      Revision ID: 0x0000
      ROM Revision: 113-C408A0-730
      VBIOS Version: 113-C408A0-017
      EFI Driver Version: 01.00.730
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 5120 x 2880 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    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: 2.4.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.37.1
    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
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.2
    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: 2.2.3
    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.dev202204120245
    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: 1.1
    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-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    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
    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
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16.4
    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: 1.0.1
    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
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.32.0
    funcparserlib: 1.0.0a0
    grako: 3.16.5
    h5py: 3.6.0
    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: 4.9.2
    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: 21.0
    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: 3.0.8
    PyQt6-commercial: 6.2.3
    PyQt6-Qt6: 6.2.4
    PyQt6-sip: 13.2.1
    PyQt6-WebEngine-commercial: 6.2.1
    PyQt6-WebEngine-Qt6: 6.2.4
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 22.3.0
    qtconsole: 5.3.0
    QtPy: 2.0.1
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.1
    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 (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Sequence
Owner: set to Eric Pettersen
Platform: → all
Priority: normal → critical
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Can't show sequence

comment:2 by Eric Pettersen, 4 years ago

Resolution: → fixed
Status: accepted → closed
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