[Chimera-users] Ringer/Chimera/IDLE

[Alejandro Virrueta]

Hello,

I am modifying some Ringer files for my own needs, but I am running into a
weird issue. If I run Ringer via typical means:

$RINGER/ringer/ringer -i ringer_in_${pdb_ID}.txt -o ringer_out_${pdb_ID}.txt

it works fine. However, when I step through it in what I think is my
version of IDLE ("$CHIMERA_HOME/bin/chimera --nogui --nostatus --script
`which idle2.7`
/usr/bin/idle2.7", with `which idle2.7` returning "/usr/bin/idle2.7"), I
run into this error:

Traceback (most recent call last):
  File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 233, in <module>
    main()
  File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 161, in main
    move_set, pdb = structureFile(parameters, path)
  File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 65, in
structureFile
    pdb = chimera.openModels.open(parameters.pdbfileName)
  File
"/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py",
line 1817, in open
    checkForChanges=False, noprefs=noprefs)
  File
"/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py",
line 1644, in add
    makePseudoBondsToMetals(realMolecules)
  File
"/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py",
line 1961, in makePseudoBondsToMetals
    cmPBG = mol.metalComplexGroup(issueHint=True)
  File
"/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py",
line 119, in _getMetalPbg
    am.color = preferences.get(MOLECULE_DEFAULT, MOL_COMPLEX_COLOR)
  File
"/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py",
line 608, in get
    forPrefSave=forPrefSave)
  File
"/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py",
line 179, in get
    return self._options[name].get(forPrefSave=forPrefSave)
  File
"/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py",
line 80, in get
    return self.prefToVal(self.value)
  File
"/Applications/Chimera.app/Contents/Resources/share/chimera/tkoptions.py",
line 1229, in _prefToColor
    return getColorByName(pref)
  File
"/Applications/Chimera.app/Contents/Resources/share/chimera/colorTable.py",
line 87, in getColorByName
    color = chimera.MaterialColor(r/255.0, g/255.0, b/255.0)
ValueError: missing default material

Any suggestions?

Cheers,
Alex
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