Changes between Initial Version and Version 1 of FlipZ

Timestamp:

Sep 3, 2020, 4:25:27 PM (6 years ago)

Author:

goddard

Comment:

--

FlipZ

@@ +1 @@
+= Flip Atom Z Coordinates =
+
+Here is Python code defining a command flip that changes atom z coordinates z -> -z.   This changes the hand of the atomic structure, for instance changing all L amino acids to D amino acids.  Open flip.py in ChimeraX 1.0 to define the flip command
+
+{{{
+open flip.py
+}}}
+
+then use the command on the atomic model.
+
+{{{
+flip #1
+}}}
+
+[[Image(flip.png, 500px)]]
+
+Here is the [attachment:flip.py flip.py] code:
+
+{{{
+# Create command to change atom coordiates z -> -z.
+# Opening this file in ChimeraX 1.0 defines the flip command.
+#
+#  flip #1
+
+def flip(session, atoms):
+    xyz = atoms.coords
+    xyz[:,2] *= -1
+    atoms.coords = xyz
+
+def register_command(session):
+    from chimerax.core.commands import CmdDesc, register
+    from chimerax.atomic import AtomsArg
+    desc = CmdDesc(required=[('atoms', AtomsArg)],
+                   synopsis='flip atom z coordinates')
+    register('flip', desc, flip, logger=session.logger)
+
+register_command(session)
+}}}