[Jmol-commits] SF.net SVN: jmol:[15496] trunk/Jmol/src/org/jmol/viewer

[<ahe...@us...>]

Revision: 15496
          http://jmol.svn.sourceforge.net/jmol/?rev=15496&view=rev
Author:   aherraez
Date:     2011-05-21 16:10:40 +0000 (Sat, 21 May 2011)

Log Message:
-----------
bug fix: third oxygen atom in 5'-terminal phosphate (OP3) was not assigned to backbone (e.g. 4tna.pdb)

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties
    trunk/Jmol/src/org/jmol/viewer/JmolConstants.java

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2011-05-21 16:09:50 UTC (rev 15495)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2011-05-21 16:10:40 UTC (rev 15496)
@@ -6,6 +6,7 @@
 # bug fix: cartoons with hermite level do not reposition for atom position changes or trajectories
 # bug fix: isosurface plane x=-1 (with no spaces) not accepted 
 # bug fix: x = write("VRML") should give VRML contents and not write to disk
+# bug fix: third oxygen atom in 5'-terminal phosphate was not assigned to backbone (e.g. 4tna.pdb)
 
 # new feature: MO POINTS / AO POINTS mapping onto a plane
 #   for (var i = -5;i < 5;i += 0.2) {isosurface color range -1.0 1.0 plane x= @i map atomicorbital 4 3 1 points 1000;refresh}

Modified: trunk/Jmol/src/org/jmol/viewer/JmolConstants.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JmolConstants.java	2011-05-21 16:09:50 UTC (rev 15495)
+++ trunk/Jmol/src/org/jmol/viewer/JmolConstants.java	2011-05-21 16:10:40 UTC (rev 15496)
@@ -1879,7 +1879,10 @@
     "H2'",
     "H2''",
     "HO2'",
-    
+
+    "O3P", //    - third equivalent oxygen on phosphorus of phosphate    
+    "OP3", //    - third equivalent oxygen on phosphorus of phosphate -- new designation
+        
   };
 
   public final static String getSpecialAtomName(int atomID) {


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