Changes between Version 24 and Version 25 of ChimeraAnimationState

Timestamp:

Feb 4, 2011, 4:43:21 PM (15 years ago)

Author:

Darren Weber

Comment:

--

ChimeraAnimationState

@@ -159 +159 @@
 == Molecules ==
 
+{{{
+#!python
+# Locating the Molecule object depends a bit on what your script does.
+# If your script opened the PDB file itself with:
+
+chimera.openModels.open("/home/eortega/data.pdb")
+
+# The return value of that is a list of Molecule objects (it's a list
+# because some kinds of files cause multiple Molecules to be 
+# created [e.g. NMR ensembles]).
+
+# Similarly to get a list of all currently open Molecule objects:
+chimera.openModels.list(modelTypes=[chimera.Molecule])
+
+# Lastly, if the structure is selected, get a list of selected Molecules:
+chimera.selection.currentMolecules()
+# To get all selected atoms use: 
+chimera.selection.currentAtoms()
+a = chimera.openModels.list(modelTypes=[chimera.Molecule])[0].atoms[0]
+}}}
+
+
 Molecule models have some global attributes, like {{{display}}} and {{{color}}}, that can alter their appearance.  Note that color properties will propagate into all elements of a molecule model (residues, atoms, bonds) that do not have any specific 'component' settings.  Whenever a component (residue, atom, bond) has it's own color properties, they override the global molecule color properties.
 
@@ -190 +212 @@
 atomSelections = chimera.selection.currentAtoms()
 anAtom = chimera.openModels.list(modelTypes=[chimera.Molecule])[0].atoms[0]
+
+for atom in model.atoms:
+    if atom.color is not None:
+        atom.color.rgba()
+    atom.display
+    atom.drawMode
+    if atom.label is not None:
+        atom.label
+    atom.surfaceDisplay
+    atom.surfaceColor
+    atom.surfaceOpacity
 }}}