Revision: 20259
http://sourceforge.net/p/jmol/code/20259
Author: hansonr
Date: 2015-01-30 14:45:43 +0000 (Fri, 30 Jan 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.12_2015.01.30"
new feature: MUTATE command
-- operates only on last model present if multiple models are loaded
-- replaces one or more amino acids group with others
-- can read from RCSB or from user-specified file
-- examples:
mutate 33 lys // replace resno=33 with lysine
mutate @3 arg // replaces group of atom 3 with arginine
mutate @r gly // replaces groups in variable r with glycine
mutate 22 "myfile.cif" // user-defined replacement
mutate {1-3} ala // replace first three residues with alanine
mutate {1-5} GLVAG // (sequence codes) replace residues 1-5 with
gly-leu-val-ala-gly
mutate {1-3} ~LYS // (force 1-character sequence codes) replace 1-3
with leu-tyr-ser
mutate {1-3} A?L // replace 1 with ala, 3 with leu; skip 2
mutate {within(sequence, "GAT")} GYT // replace locations of GAT with GYT
(needs testing)
mutate 35 @fname // replaces resno=33 with file data (use "==ALA"
or "~A" for RCSB)
mutate {r} his // same as above; r must be an atom selection
bug fix: code fixes relating to calculate structure in 01.29
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-01-30 14:43:12 UTC
(rev 20258)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-01-30 14:45:43 UTC
(rev 20259)
@@ -2215,7 +2215,7 @@
e.checkLast(i);
if (chk)
return;
- boolean isFile = (tokAt(i) == T.string);
+ boolean isFile = (tokAt(i) == T.string && !group.startsWith("~"));
String[] list = null;
if (isFile) {
list = new String[] { group };
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-01-30 14:43:12 UTC
(rev 20258)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-01-30 14:45:43 UTC
(rev 20259)
@@ -31,7 +31,7 @@
mutate {1-3} ~LYS // (force 1-character sequence codes) replace 1-3
with leu-tyr-ser
mutate {1-3} A?L // replace 1 with ala, 3 with leu; skip 2
mutate {within(sequence, "GAT")} GYT // replace locations of GAT with
GYT (needs testing)
- mutate 35 @fname // replaces resno=33 with file data (use "==XXX"
for RCSB)
+ mutate 35 @fname // replaces resno=33 with file data (use "==ALA"
or "~A" for RCSB)
mutate {r} his // same as above; r must be an atom selection
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