User:Remig - Revision history

Remig: Add links

2014-02-04T21:52:30Z

Add links

Remig: Move script to another page

2013-11-05T20:23:13Z

Move script to another page

Show changes

Remig at 00:42, 5 November 2013

2013-11-05T00:42:51Z

Remig: Revision of Polymeraze

2013-11-04T18:48:12Z

Revision of Polymeraze

Show changes

Remig at 21:36, 31 October 2013

2013-10-31T21:36:19Z

Remig: DNA helix generator script

2013-10-31T21:34:44Z

DNA helix generator script

Remig: DNA helix generator script

2013-10-31T21:31:25Z

DNA helix generator script

Show changes

Remig: Protein Folding Utility Scripts

2013-10-31T18:55:38Z

Protein Folding Utility Scripts

New page

My interest is in protein folding for which I have written software tools in Java over the years. I had always displayed in JMol and only now realize I could have written in JMol script directly and have folded and viewed in the same application. I am now doing so and will present scripts of possible interest to others in the discussion tab for the general amusement.

← Older revision		Revision as of 21:52, 4 February 2014
Line 1:		Line 1:
−	My interest is in protein folding for which I have written software tools in Java over the years. I had always displayed in JMol and only now realize I could have written in JMol script directly and have folded and viewed in the same application. I am now doing so and will present scripts of possible interest to others for the general amusement.	+	My interest is in protein folding for which I have written software tools in Java over the years. I had always displayed in JMol and only now realize I could have written in JMol script directly and have folded and viewed in the same application. I am now doing so and will present scripts of possible interest to others for the general amusement. Some are now available here [[User:Remig/plico]].
−
−	~~The script shown here before that generates polypeptide helices is~~ now available ~~in the Recycling Corner:~~ [[~~Recycling_Corner/Alpha_Helix_Generator]] so I have removed it from here.~~
−
−	~~The script shown here before that generates DNA and RNA helices is now available in the Recycling Corner~~: ~~[[Recycling_Corner~~/~~DNA_Generator~~]] ~~so I have removed it from here as well~~.

@@ Line 1: / Line 1: @@
 My interest is in protein folding for which I have written software tools in Java over the years. I had always displayed in JMol and only now realize I could have written in JMol script directly and have folded and viewed in the same application. I am now doing so and will present scripts of possible interest to others for the general amusement.
-The script shown here before that generates polypeptide helices is now available in the Recycling Corner: [[Recycling_Corner/Alpha_Helix_Generator]] so I have removed it from here. In its place is a similar script (now revised) I wrote that accepts a nucleotide sequence (1 letter encoding: "TACGAAC...GCT" for example) and generates a DNA or RNA single or double helix using the Model Kit:
+The script shown here before that generates polypeptide helices is now available in the Recycling Corner: [[Recycling_Corner/Alpha_Helix_Generator]] so I have removed it from here. In its place is a similar script (now revised) that I wrote that accepts a nucleotide sequence (1 letter encoding: "TACGAAC...GCT" for example) and generates a DNA or RNA single or double helix using the Model Kit:
 <pre>#   POLYMERAZE - Jmol script by Ron Mignery
@@ Line 16: / Line 16: @@
 #   If prepended with 'S' then a single strand helix is produced
 #   If prepended with 'M' then a mixed helix is produced where the first
-#   strand is DNA and the second RNA
+#   strand is DNA and the second RNA - multiple prepends are allowed
+#
 #   The IUPAC/IUBMB 1 letter code is used:

@@ Line 1: / Line 1: @@
 My interest is in protein folding for which I have written software tools in Java over the years. I had always displayed in JMol and only now realize I could have written in JMol script directly and have folded and viewed in the same application. I am now doing so and will present scripts of possible interest to others in the discussion tab for the general amusement.
-The script shown here before that generates polypeptide helices is now available in the Recycling Corner: Recycling_Corner/Alpha_Helix_Generator so I have removed it from here. In its place is a similar script I wrote that accepts a nucleotide sequence (1 letter encoding: "TACGAAC...GCT" for example) and generates a DNA or RNA single or double helix using the Model Kit:
+The script shown here before that generates polypeptide helices is now available in the Recycling Corner: [[Recycling_Corner/Alpha_Helix_Generator]] so I have removed it from here. In its place is a similar script I wrote that accepts a nucleotide sequence (1 letter encoding: "TACGAAC...GCT" for example) and generates a DNA or RNA single or double helix using the Model Kit:
 <pre>#   POLYMERAZE - Jmol script by Ron Mignery

@@ Line 3: / Line 3: @@
 The script shown here before that generates polypeptide helices is now available in the Recycling Corner: Recycling_Corner/Alpha_Helix_Generator so I have removed it from here. In its place is a similar script I wrote that accepts a nucleotide sequence (1 letter encoding: "TACGAAC...GCT" for example) and generates a DNA or RNA single or double helix using the Model Kit:
-#   POLYMERAZE - Jmol script by Ron Mignery
+<pre>#   POLYMERAZE - Jmol script by Ron Mignery
 #   v1.0 beta    10/31/2013
+#
@@ Line 360: / Line 360: @@
      genHelix(gSeq)
+}
 I thought adapting the Ribozome script to polynucleotides would be easy since there are only four types rather than 20. I was not easy and this script has its problems. With five rotors in a row for each nucleotide, finding correct values for the bond angles was beyond me. If anyone can tweak them better, please do and let me know. Regardless I plan to develop some more utility scripts to make that process easier and hope to update this script in the hopefully not too distant future.