pwem.viewers.viewer_chimera module

class pwem.viewers.viewer_chimera.Chimera[source]

Bases: object

Helper class to execute chimera and handle its environment.

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

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()[source]

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

classmethod getHome()[source]
classmethod getProgram(progName='ChimeraX')[source]

Return the program binary that will be used.

classmethod getSymmetry(scipionSym)[source]

Return the equivalent Chimera symmetry from Scipion one.

classmethod runProgram(program=None, args='', cwd=None)[source]

Internal shortcut function to launch chimera program.

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

Bases: pyworkflow.viewer.CommandView

createAngularDistributionFile(bildFileName='/tmp/spheres.bild')[source]
initVolumeData(volfile)[source]
readAngularDistFile()[source]
class pwem.viewers.viewer_chimera.ChimeraClientView(inputFile, **kwargs)[source]

Bases: pwem.viewers.viewer_chimera.ChimeraView

View for calling an external command.

class pwem.viewers.viewer_chimera.ChimeraDataView(dataview, vol, viewParams={}, **kwargs)[source]

Bases: pwem.viewers.viewer_chimera.ChimeraView

show()[source]

This method should be overwritten to implement how this particular view will be displayed in desktop.

class pwem.viewers.viewer_chimera.ChimeraView(inputFile, **kwargs)[source]

Bases: pyworkflow.viewer.CommandView

View for calling an external command.

class pwem.viewers.viewer_chimera.ChimeraViewer(**kwargs)[source]

Bases: pyworkflow.viewer.Viewer

Wrapper to visualize PDB object with Chimera.

visualize(obj, **kwargs)[source]

Display each of the views, by default the implementation is for desktop.

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)[source]

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

pwem.viewers.viewer_chimera.printCmd(cmd)[source]

Debug function.