color comparison: numpy stupidity

[Tristan Croll]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-11-15)
Description
Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-11-15)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed
'ChimeraX_ISOLDE-1.0b3.dev7-cp37-cp37m-macosx_10_9_x86_64.whl'  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
/Users/tic20/Library/Caches/ChimeraX/0.91/installers/ChimeraX_ISOLDE-1.0b3.dev7-cp37-cp37m-macosx_10_9_x86_64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in
/Applications/ChimeraX_Daily.app/Contents/lib/python3.7/site-packages (from
ChimeraX-ISOLDE==1.0b3.dev7) (1.0)  
Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.91 in
/Applications/ChimeraX_Daily.app/Contents/lib/python3.7/site-packages (from
ChimeraX-ISOLDE==1.0b3.dev7) (0.91)  
Requirement already satisfied, skipping upgrade: ChimeraX-Clipper>=0.9.11 in
/Users/tic20/Library/Application Support/ChimeraX/0.91/site-packages (from
ChimeraX-ISOLDE==1.0b3.dev7) (0.9.11)  
Installing collected packages: ChimeraX-ISOLDE  
Found existing installation: ChimeraX-ISOLDE 1.0b3.dev6  
Uninstalling ChimeraX-ISOLDE-1.0b3.dev6:  
Successfully uninstalled ChimeraX-ISOLDE-1.0b3.dev6  
Successfully installed ChimeraX-ISOLDE-1.0b3.dev7  
Lock 4506110736 acquired on
/Users/tic20/Library/Caches/ChimeraX/0.91/toolshed/bundle_info.cache.lock  
Lock 4506110736 released on
/Users/tic20/Library/Caches/ChimeraX/0.91/toolshed/bundle_info.cache.lock  
  

WARNING: You are using pip version 19.2.3, however version 19.3.1 is
available.  
You should consider upgrading via the 'pip install --upgrade pip' command.  
  

> open 3io0 format mmCIF fromDatabase pdb

3io0 title:  
Crystal structure of EtuB from Clostridium kluyveri [more info...]  
  
Chain information for 3io0 #1  
---  
Chain | Description  
A | EtuB protein  
  
3io0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
  

> close

> open 3io0 structureFactors true

Summary of feedback from opening 3io0 fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma,  
pdbx_anom_difference, pdbx_anom_difference_sigma,  
intensity_meas, intensity_sigma,  
pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma  
Automatically choosing "intensity_meas, intensity_sigma".  
notes | Fetching compressed 3io0 structure factors from
http://files.rcsb.org/download/3io0-sf.cif  
Resolution: 3.003  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
3io0 title:  
Crystal structure of EtuB from Clostridium kluyveri [more info...]  
  
Chain information for 3io0  
---  
Chain | Description  
1.3/A | EtuB protein  
  
3io0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
  

> addh

Summary of feedback from adding hydrogens to 3io0 #1.3  
---  
notes | Termini for 3io0 (#1.3) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A PRO 76  
Chain-final residues that are actual C termini: /A PHE 304  
Chain-final residues that are not actual C termini:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 62, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 167, in hbond_add_hydrogens  
_prep_add(session, structures, unknowns_info, template, **prot_schemes)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 423, in _prep_add  
complete_terminal_carboxylate(session, rc)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/util.py", line 27, in
complete_terminal_carboxylate  
if c.color == element_colors(c.element.number):  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/util.py", line 27, in
complete_terminal_carboxylate  
if c.color == element_colors(c.element.number):  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.12
OpenGL renderer: Intel(R) HD Graphics 6000
OpenGL vendor: Intel Inc.

[Eric Pettersen]

atom.color until recently returned a tinyarray. Those don't support slicing (which is frequently used to drop the alpha component), so it was changed to return a tuple. Whereas a tinyarray can be compared to a numpy array without complaint, a tuple can't...