Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#6184 closed defect (fixed)

color byattribute failure

Reported by: r.m.vandenbos@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Analysis Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19042
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Running the command: color byattr seq_conservation 
PDB open
ClustalW alignment.aln

Log:
Startup Messages  
---  
warning | Your computer has Intel graphics driver 7157 with a known bug that
causes all Qt user interface panels to be blank. ChimeraX can partially fix
this but may make some panel titlebars and edges black. Hopefully newer Intel
graphics drivers will fix this.  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "\\\soliscom.uu.nl\users\4114914\My
> Documents\Desktop\Proteome_Unpolished\Models_homologues\Natamycinase_modeller.pdb"
> format pdb

Chain information for Natamycinase_modeller.pdb #1  
---  
Chain | Description  
X | No description available  
  

> open "//soliscom.uu.nl/users/4114914/My
> Documents/Desktop/Alignment_Aspergillus.aln"

Summary of feedback from opening //soliscom.uu.nl/users/4114914/My
Documents/Desktop/Alignment_Aspergillus.aln  
---  
notes | Alignment identifier is Alignment_Aspergillus.aln  
Associated Natamycinase_modeller.pdb chain X to Natamycinase with 0 mismatches  
Showing consensus header ("seq_consensus" residue attribute) for alignment
Alignment_Aspergillus.aln  
Showing conservation header ("seq_conservation" residue attribute) for
alignment Alignment_Aspergillus.aln  
  
Opened 8 sequences from Alignment_Aspergillus.aln  

> color byattribute seq_conservation

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1194, in color_by_attr  
acolors = _value_colors(palette, range, attr_vals)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1287, in _value_colors  
cmap = _colormap_with_range(palette, r, default = 'blue-white-red')  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\surface\colorvol.py", line 164, in _colormap_with_range  
cm = cmap.linear_range(vmin, vmax)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\colors.py", line 334, in linear_range  
v = numpy.linspace(min_value, max_value, len(self.colors))  
File "<__array_function__ internals>", line 5, in linspace  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\numpy\core\function_base.py", line 127, in linspace  
start = asanyarray(start) * 1.0  
numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a
loop with signature matching types (dtype('<U1'), dtype('float64')) -> None  
  
numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a
loop with signature matching types (dtype(' None  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\numpy\core\function_base.py", line 127, in linspace  
start = asanyarray(start) * 1.0  
  
See log for complete Python traceback.  
  

> color byattribute seq_conservation protein palette cyanmaroon range -1.4,1.4
> noValueColor yellow

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1194, in color_by_attr  
acolors = _value_colors(palette, range, attr_vals)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1290, in _value_colors  
colors = cmap.interpolated_rgba8(values)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\colors.py", line 322, in interpolated_rgba8  
c = self.interpolated_rgba(values)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\colors.py", line 316, in interpolated_rgba  
colors = map.interpolate_colormap(values, self.data_values, self.colors,  
TypeError: Array argument has non-numeric values  
  
TypeError: Array argument has non-numeric values  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\colors.py", line 316, in interpolated_rgba  
colors = map.interpolate_colormap(values, self.data_values, self.colors,  
  
See log for complete Python traceback.  
  

> color byattribute seq_conservation

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1194, in color_by_attr  
acolors = _value_colors(palette, range, attr_vals)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1287, in _value_colors  
cmap = _colormap_with_range(palette, r, default = 'blue-white-red')  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\surface\colorvol.py", line 164, in _colormap_with_range  
cm = cmap.linear_range(vmin, vmax)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\colors.py", line 334, in linear_range  
v = numpy.linspace(min_value, max_value, len(self.colors))  
File "<__array_function__ internals>", line 5, in linspace  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\numpy\core\function_base.py", line 127, in linspace  
start = asanyarray(start) * 1.0  
numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a
loop with signature matching types (dtype('<U1'), dtype('float64')) -> None  
  
numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a
loop with signature matching types (dtype(' None  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\numpy\core\function_base.py", line 127, in linspace  
start = asanyarray(start) * 1.0  
  
See log for complete Python traceback.  
  

> select /X:46-47

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select /X:46-48

21 atoms, 20 bonds, 3 residues, 1 model selected  

> color byattribute seq_conservation

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1194, in color_by_attr  
acolors = _value_colors(palette, range, attr_vals)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1287, in _value_colors  
cmap = _colormap_with_range(palette, r, default = 'blue-white-red')  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\surface\colorvol.py", line 164, in _colormap_with_range  
cm = cmap.linear_range(vmin, vmax)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\colors.py", line 334, in linear_range  
v = numpy.linspace(min_value, max_value, len(self.colors))  
File "<__array_function__ internals>", line 5, in linspace  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\numpy\core\function_base.py", line 127, in linspace  
start = asanyarray(start) * 1.0  
numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a
loop with signature matching types (dtype('<U1'), dtype('float64')) -> None  
  
numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a
loop with signature matching types (dtype(' None  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\numpy\core\function_base.py", line 127, in linspace  
start = asanyarray(start) * 1.0  
  
See log for complete Python traceback.  
  

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> color byattribute seq_conservation

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1194, in color_by_attr  
acolors = _value_colors(palette, range, attr_vals)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1287, in _value_colors  
cmap = _colormap_with_range(palette, r, default = 'blue-white-red')  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\surface\colorvol.py", line 164, in _colormap_with_range  
cm = cmap.linear_range(vmin, vmax)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\colors.py", line 334, in linear_range  
v = numpy.linspace(min_value, max_value, len(self.colors))  
File "<__array_function__ internals>", line 5, in linspace  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\numpy\core\function_base.py", line 127, in linspace  
start = asanyarray(start) * 1.0  
numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a
loop with signature matching types (dtype('<U1'), dtype('float64')) -> None  
  
numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a
loop with signature matching types (dtype(' None  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\numpy\core\function_base.py", line 127, in linspace  
start = asanyarray(start) * 1.0  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 26.20.100.7157
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Manufacturer: HP
Model: HP EliteDesk 800 G5 TWR
OS: Microsoft Windows 10 Enterprise (Build 19042)
Memory: 16,943,194,112
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-9500 CPU @ 3.00GHz
OSLanguage: en-US
Locale: ('nl_NL', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    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: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    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: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    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: 1.1.4
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    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: 2.4.6
    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: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Attachments (2)

nonassoc.fa​ (886 bytes ) - added by Eric Pettersen 4 years ago.
Added by email2trac
5F8587F37F204696BC2A42B291C629C7.png​ (135.7 KB ) - added by Eric Pettersen 4 years ago.
screen showing same error message with test data

Download all attachments as: .zip

Change History (14)

comment:1 by Eric Pettersen, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → Structure Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → color byattribute failure

in reply to:  2 ; comment:2 by Eric Pettersen, 4 years ago 

Hi Ramon,
	I have attached an alignment file.  Open it in ChimeraX and then open 1qvc.  Then do "color byattribute seq_conservation".  Does that work, or does it fail in the same way as your alignment did?  If it works, then I will need access to your files in order to reproduce this.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

nonassoc.fa​

by Eric Pettersen, 4 years ago

Attachment: nonassoc.fa​ added

Added by email2trac

comment:3 by Eric Pettersen, 4 years ago

Status: accepted → feedback

comment:4 by Eric Pettersen, 4 years ago

Status: feedback → accepted

comment:5 by Eric Pettersen, 4 years ago

From direct email:

Hi Eric,

This fails in the same way.

Best,
Ramon

by Eric Pettersen, 4 years ago

Attachment: 5F8587F37F204696BC2A42B291C629C7.png​ added

screen showing same error message with test data

comment:6 by Eric Pettersen, 4 years ago

Cc: Eric Pettersen added; Tom Goddard removed
Owner: changed from Eric Pettersen to Tom Goddard
Status: accepted → assigned

Since this now seems to be a numpy problem rather than a "color byattribute" problem, reassigning ticket.

comment:7 by Tom Goddard, 4 years ago

The problem here is that the code is trying to multiply a numpy array of unicode 1 character strings times 1.0. Obviously the code is expecting a numpy array of numbers but is by mistake getting unicode strings.

comment:8 by Tom Goddard, 4 years ago

Cc: Tom Goddard added; Eric Pettersen removed
Owner: changed from Tom Goddard to Eric Pettersen

Then nonassoc.fa and 1qvc test case works correctly in ChimeraX 1.3 on Mac and Windows and in a Feb 13 2022 daily build on Mac and on a Feb 18 daily build on Windows. The bug is reported for ChimeraX 1.3 on Windows, although the screenshot where the reporter tested nonassoc.fa and 1qvc was with a Feb 16 2022 daily build on Windows.

This is not a numpy problem. The ChimeraX code is handing an array of unicode strings instead of numbers to the colormapping routine.

I don't have any idea what is different about the reporters test. I think they should test nonassoc.fa and 1qvc in ChimeraX 1.3 in case they happen to have a bad daily build.

I don't know if the color byattribute code behavior could be effected by an preference settings.

Sending this back to Eric since it looks like a color byattribute problem, not a numpy problem.

comment:9 by Eric Pettersen, 4 years ago

Hi Ramon,

You have set your sequence conservation header to show Clustal characters. You need to change the setting to one of the numeric conservation settings (identity histogram or AL2CO) for "color byattr seq_conservation" to work.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:10 by Eric Pettersen, 4 years ago

In case you missed by message due to all the other text in the previous update mail:

Hi Ramon,

You have set your sequence conservation header to show Clustal characters. You need to change the setting to one of the numeric conservation settings (identity histogram or AL2CO) for "color byattr seq_conservation" to work.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:11 by Eric Pettersen, 4 years ago

Resolution: → fixed
Status: assigned → closed

If the conservation header is set to show Clustal characters, it now sets a string-valued seq_clustal_conservation attribute instead of the numeric-valued seq_conservation attribute.

in reply to:  14 comment:12 by r.m.vandenbos@…, 4 years ago 

Dear all,

Changing the conservation header indeed worked. Thank you for resolving this issue.

Kind regards,

Ramon van den Bos



From: ChimeraX<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: donderdag 24 februari 2022 02:55
Cc: goddard@cgl.ucsf.edu<mailto:goddard@cgl.ucsf.edu>; pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>; Bos, R.M. van den (Ramon)<mailto:r.m.vandenbos@uu.nl>
Subject: Re: [ChimeraX] #6184: color byattribute failure

#6184: color byattribute failure
-----------------------------------------+--------------------
          Reporter:  r.m.vandenbos@…     |      Owner:  pett
              Type:  defect              |     Status:  closed
          Priority:  normal              |  Milestone:
         Component:  Structure Analysis  |    Version:
        Resolution:  fixed               |   Keywords:
        Blocked By:                      |   Blocking:
Notify when closed:                      |   Platform:  all
           Project:  ChimeraX            |
-----------------------------------------+--------------------
Changes (by pett):

 * status:  assigned => closed
 * resolution:   => fixed


Comment:

 If the conservation header is set to show Clustal characters, it now sets
 a string-valued seq_clustal_conservation attribute instead of the numeric-
 valued seq_conservation attribute.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6184#comment:11>
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