Revision: 20805
http://sourceforge.net/p/jmol/code/20805
Author: hansonr
Date: 2015-10-02 02:19:13 +0000 (Fri, 02 Oct 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.16_2015.10.01"
bug fix: hydrogens added to backbone should be part of "backbone" definition
-- no-hydrogen definition is _bb, but that is
new feature: calculate hydrogens TRUE
-- calculates hydrogens and multiple bonding
-- same as
calculate hydrogens
connect aromatic modify
calculate aromatic
-- similar to, but not identical to set pdbAddHydrogens
-- allows reasonable addition of multiple bonds to proteins after loading
bug fix: connect aromatic should not touch H atoms or atoms with 4 or more
covalent bonds
bug fix: calculate hydrogen should consider backbone N sp2
bug fix: {backbone} should include attached H atoms
bug fix: calculate hydrogens should not place H atoms on water
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2015-10-01 13:11:38 UTC (rev
20804)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2015-10-02 02:19:13 UTC (rev
20805)
@@ -620,8 +620,8 @@
// structure related
//
"@alpha _a=2", // rasmol doc says "approximately *.CA" - whatever?
- "@bbone0 protein&(_a>=1&_a<6|_a>=64&_a<72)|nucleic&(_a>=6&_a<14|_a>=72)",
// may or may not include H
- "@backbone back_bone | _H && connected(single, bbone0)",
+ "@_bb protein&_a>=1&_a<6 | nucleic& _a>=6&_a<14", // no H atoms
+ "@backbone _bb | _H && connected(single, _bb)",
"@spine protein&_a>=1&_a<4|nucleic&_a>=6&_a<14&_a!=12",
"@sidechain (protein,nucleic) & !backbone",
"@base nucleic & !backbone",
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-01 13:11:38 UTC
(rev 20804)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-02 02:19:13 UTC
(rev 20805)
@@ -61,12 +61,11 @@
TODO: consider if models with no atoms will cause issues in relation to
model.firstAtomIndex
-Jmol.___JmolVersion="14.3.16_2015.09.28b"
+Jmol.___JmolVersion="14.3.16_2015.10.01"
+
+bug fix: hydrogens added to backbone should be part of "backbone" definition
+ -- no-hydrogen definition is _bb, but that is
-bug fix: draw ramachandran broken
-
-JmolVersion="14.3.16_2015.09.30"
-
new feature: calculate hydrogens TRUE
-- calculates hydrogens and multiple bonding
-- same as
@@ -99,6 +98,10 @@
-- reversed by another .array(k)
-- causes a script exception if arrayOfMaps is not an array of maps or key k
is not present in all maps
+JmolVersion="14.3.16_2015.09.28b"
+
+bug fix: draw ramachandran broken
+
JmolVersion="14.3.16_2015.09.28"
new feature: array.sort("key")
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
------------------------------------------------------------------------------
_______________________________________________
Jmol-commits mailing list
Jmol-commits@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-commits
