Changes between Version 6 and Version 7 of FAQ_MoleculeViewer

Timestamp:

Jul 6, 2014 1:28:11 PM (10 years ago)

Author:

ldelgass

Comment:

Document parallelepiped, add outline links, add link to drawing output doc.

FAQ_MoleculeViewer

@@ +1 @@
+[[PageOutline]]
+
 = Molecule Viewers In and Out =
 
-Topics discussed:
-  1. Molecule Viewer Basics
-  2. Molecule Viewers as Inputs
-  3. Molecule Viewers as Output
-  4. Sending PDB files to the Molecule Viewer
-  5. Sending LAMMPS files to the Molecule Viewer
-  6. Displaying trajectories as sequences
-
-----
+This document describes how to use the Pymol-based molecule viewer through '''<structure>''' outputs in Rappture.  For the VTK-based molecule viewer through '''<drawing>''' outputs, see [wiki:rp_xml_ele_drawing_output#Molecules drawing (output)]
 
 == Molecule Viewer Basics ==
@@ -257 +251 @@
 }}}
 
+== Creating unit cells with Parallelepiped ==
+
+You can create a wireframe parallelepiped shape to display crystal unit cells.  The shape is specified with an x,y,z '''<origin>''' position, three edge '''<vector>''' elements pointing out from the origin, and x,y,z '''<scale>''' factors to set the length of the edges.  If a single value is given for '''<scale>''', all edges will be scaled by the same amount.
+
+{{{
+  <structure>
+    <components>
+      <molecule>...</molecule>
+      <parallelepiped>
+        <origin>0.0 0.0 0.0</origin>
+        <scale>1.0 1.0 2.0</scale>
+        <vector id="1">0.5 0.5 0.0</vector>
+        <vector id="2">0.5 0.0 0.5</vector>
+        <vector id="3">0.0 0.5 0.5</vector>
+      </parallelepiped>
+    </components>
+  </structure>
+}}}
+
+See the [browser:trunk/examples/zoo/parallelepiped parallelepiped example] in the zoo of examples.
+
 [wiki:FAQ Back to Frequently Asked Questions]