pwem.viewers.viewer_chimera module

class pwem.viewers.viewer_chimera.Chimera

Bases: object

Helper class to execute chimera and handle its environment.

classmethod createCoordinateAxisFile(dim, bildFileName='/tmp/axis.bild', sampling=1, r1=0.1)

Create a coordinate system, Along each dimension we place a small sphere in the negative axis. In this way chimera shows the system of coordinates origin in the window center

classmethod getEnviron()

Return the proper environ to launch chimera. CHIMERA_HOME variable is read from the ~/.config/scipion.conf file.

classmethod getHome()

Returns chimera home, trying first to take it from chimera plugin. If it fails it will return, the default value in the config

classmethod getProgram(progName='ChimeraX')

Return the program binary that will be used.

classmethod getSymmetry(scipionSym)

Return the equivalent Chimera symmetry from Scipion one.

classmethod isOnWindows()

classmethod runProgram(program=None, args='', cwd=None)

Internal shortcut function to launch chimera program.

class pwem.viewers.viewer_chimera.ChimeraAngDist(volFile, tmpFilesPath, **kwargs)

Bases: CommandView

createAngularDistributionFile(bildFileName='/tmp/spheres.bild')

initVolumeData(volfile)

readAngularDistFile()

class pwem.viewers.viewer_chimera.ChimeraOldView(inputFiles, **kwargs)

Bases: ChimeraView

View for calling an external command.

getEnviron()

getProgram()

class pwem.viewers.viewer_chimera.ChimeraOldViewer(**kwargs)

Bases: ChimeraViewer

Wrapper to visualize Chimera OLD (1.10 , 1.13, ..) compatible objects .

class pwem.viewers.viewer_chimera.ChimeraView(inputFiles, **kwargs)

Bases: CommandView

View for calling an external command.

getEnviron()

getProgram()

class pwem.viewers.viewer_chimera.ChimeraViewer(**kwargs)

Bases: Viewer

Wrapper to visualize PDB object with Chimera.

pwem.viewers.viewer_chimera.generateColorLegend(stepColors, colorList, threeLabelsOnly=True)

Return a string to write in a chimera script file a color legend - key command

Parameters

• stepColors – list with the values for the colors

• colorList – list with the colors

• threeLabelsOnly – True, with ignore stepColors and show just 3 values: min, max and medium.

pwem.viewers.viewer_chimera.mapVolsWithColorkey(displayVolFileName, mapVolFileName, stepColors, colorList, voldim, volOrigin=None, step=-1, sampling=1.0, scriptFileName='/tmp/chimeraColor.py', bgColorImage='white', showAxis=True, fontSize=12)

colors surface of volume ‘displayVolFileName’ using values from ‘mapVolFikeName’. A colorkey is created using the values in stepColors and the color in colorList.