Author: bugman
Date: Wed Jun 4 10:56:18 2014
New Revision: 23632
URL: http://svn.gna.org/viewcvs/relax?rev=23632&view=rev
Log:
Expanded the capabilities of the pymol.frame_order user function.
The isotropic and pseudo-elliptic cones are now represented as they used to
be under the
pymol.cone_pdb user function. To avoid code duplication, the new
represent_cone_axis(),
represent_cone_object() and represent_rotor_object() functions have been
created to send the
commands into PyMOL.
Modified:
branches/frame_order_cleanup/pipe_control/pymol_control.py
Modified: branches/frame_order_cleanup/pipe_control/pymol_control.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/pymol_control.py?rev=23632&r1=23631&r2=23632&view=diff
==============================================================================
--- branches/frame_order_cleanup/pipe_control/pymol_control.py (original)
+++ branches/frame_order_cleanup/pipe_control/pymol_control.py Wed Jun 4
10:56:18 2014
@@ -281,56 +281,11 @@
# Read in the cone PDB file.
pymol_obj.exec_cmd("load " + file)
-
# The cone axes.
- ################
-
- # Select the AVE, AXE, and SIM residues.
- pymol_obj.exec_cmd("select (resn AVE,AXE,SIM)")
-
- # Show the vector as a stick.
- pymol_obj.exec_cmd("show stick, 'sele'")
-
- # Colour it blue.
- pymol_obj.exec_cmd("color cyan, 'sele'")
-
- # Select the atom used for labelling.
- pymol_obj.exec_cmd("select (resn AVE,AXE,SIM and symbol N)")
-
- # Hide the atom.
- pymol_obj.exec_cmd("hide ('sele')")
-
- # Label using the atom name.
- pymol_obj.exec_cmd("cmd.label(\"sele\",\"name\")")
-
+ represent_cone_axis()
# The cone object.
- ##################
-
- # Select the CON residue.
- pymol_obj.exec_cmd("select (resn CON,EDG)")
-
- # Hide everything.
- pymol_obj.exec_cmd("hide ('sele')")
-
- # Show as 'sticks'.
- pymol_obj.exec_cmd("show sticks, 'sele'")
-
- # Colour it white.
- pymol_obj.exec_cmd("color white, 'sele'")
-
- # Shorten the stick width from 0.25 to 0.15.
- pymol_obj.exec_cmd("set stick_radius,0.15000")
-
- # Set a bit of transparency.
- pymol_obj.exec_cmd("set stick_transparency, 0.3")
-
-
- # Clean up.
- ###########
-
- # Remove the selection.
- pymol_obj.exec_cmd("cmd.delete('sele')")
+ represent_cone_object()
def create_macro(data_type=None, style="classic", colour_start=None,
colour_end=None, colour_list=None):
@@ -410,7 +365,6 @@
pymol_obj.exec_cmd("load " + file)
-
def frame_order_geometric(file=None):
"""Display the frame order geometric object.
@@ -424,30 +378,14 @@
# The object ID.
id = file_root(file)
-
- # Rotor objects.
- ################
-
- # Set up the rotor axis (the residues AX and PRC).
- pymol_obj.exec_cmd("select (resn AX,PRC)")
- pymol_obj.exec_cmd("show stick, 'sele'")
- pymol_obj.exec_cmd("color red, 'sele'")
- pymol_obj.exec_cmd("cmd.delete('sele')")
-
- # Display the central point.
- pymol_obj.exec_cmd("select (name CTR)")
- pymol_obj.exec_cmd("show spheres, 'sele'")
- pymol_obj.exec_cmd("color red, 'sele'")
- pymol_obj.exec_cmd("set sphere_scale, 0.3, 'sele'")
- pymol_obj.exec_cmd("cmd.delete('sele')")
-
- # Set up the propellers.
- pymol_obj.exec_cmd("select (resn PRB)")
- pymol_obj.exec_cmd("show stick, 'sele'")
- pymol_obj.exec_cmd("set stick_radius, 0.15, 'sele'")
- pymol_obj.exec_cmd("cmd.delete('sele')")
-
-
+ # Set up the rotor objects.
+ represent_rotor_object()
+
+ # Set up the cone axis.
+ represent_cone_axis()
+
+ # Set up the cone object.
+ represent_cone_object()
def macro_apply(data_type=None, style="classic", colour_start_name=None,
colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None,
colour_list=None):
@@ -611,6 +549,79 @@
add_result_file(type='pymol', label='PyMOL', file=file_path)
+def represent_cone_axis():
+ """Set up the PyMOL cone axis representation."""
+
+ # Select the AVE, AXE, and SIM residues.
+ pymol_obj.exec_cmd("select (resn AVE,AXE,SIM)")
+
+ # Show the vector as a stick.
+ pymol_obj.exec_cmd("show stick, 'sele'")
+
+ # Colour it blue.
+ pymol_obj.exec_cmd("color cyan, 'sele'")
+
+ # Select the atom used for labelling.
+ pymol_obj.exec_cmd("select (resn AVE,AXE,SIM and symbol N)")
+
+ # Hide the atom.
+ pymol_obj.exec_cmd("hide ('sele')")
+
+ # Label using the atom name.
+ pymol_obj.exec_cmd("cmd.label(\"sele\",\"name\")")
+
+ # Remove the selection.
+ pymol_obj.exec_cmd("cmd.delete('sele')")
+
+
+def represent_cone_object():
+ """Set up the PyMOL cone object representation."""
+
+ # Select the CON and EDG residues.
+ pymol_obj.exec_cmd("select (resn CON,EDG)")
+
+ # Hide everything.
+ pymol_obj.exec_cmd("hide ('sele')")
+
+ # Show as 'sticks'.
+ pymol_obj.exec_cmd("show sticks, 'sele'")
+
+ # Colour it white.
+ pymol_obj.exec_cmd("color white, 'sele'")
+
+ # Shorten the stick width from 0.25 to 0.15.
+ pymol_obj.exec_cmd("set stick_radius, 0.15, 'sele'")
+
+ # Set a bit of transparency.
+ pymol_obj.exec_cmd("set stick_transparency, 0.3, 'sele'")
+
+ # Remove the selection.
+ pymol_obj.exec_cmd("cmd.delete('sele')")
+
+
+def represent_rotor_object():
+ """Set up the PyMOL rotor object representation."""
+
+ # Rotor objects: Set up the rotor axis (the residues AX and PRC).
+ pymol_obj.exec_cmd("select (resn AX,PRC)")
+ pymol_obj.exec_cmd("show stick, 'sele'")
+ pymol_obj.exec_cmd("color red, 'sele'")
+ pymol_obj.exec_cmd("cmd.delete('sele')")
+
+ # Rotor objects: Display the central point.
+ pymol_obj.exec_cmd("select (name CTR)")
+ pymol_obj.exec_cmd("show spheres, 'sele'")
+ pymol_obj.exec_cmd("color red, 'sele'")
+ pymol_obj.exec_cmd("set sphere_scale, 0.3, 'sele'")
+ pymol_obj.exec_cmd("cmd.delete('sele')")
+
+ # Rotor objects: Set up the propellers.
+ pymol_obj.exec_cmd("select (resn PRB)")
+ pymol_obj.exec_cmd("show stick, 'sele'")
+ pymol_obj.exec_cmd("set stick_radius, 0.15, 'sele'")
+ pymol_obj.exec_cmd("cmd.delete('sele')")
+
+
def tensor_pdb(file=None):
"""Display the diffusion tensor geometric structure.
r23632 - /branches/frame_order_cleanup/pipe_control/pymol_control.py