User:Remig/plico - Revision history

Remig: Add hydrate, utilities and plots.

2015-09-11T15:31:08Z

Add hydrate, utilities and plots.

Remig: /* The Plico Suite of Jmol Application Scripts for Modeling Protein Folding */

2015-07-24T17:57:26Z

‎The Plico Suite of Jmol Application Scripts for Modeling Protein Folding

Remig at 19:10, 13 July 2015

2015-07-13T19:10:20Z

Remig: Add fold_trna.spt

2015-07-13T17:50:09Z

Add fold_trna.spt

Remig at 13:54, 16 July 2014

2014-07-16T13:54:16Z

Remig: Add adjustNT.spt

2014-06-10T21:02:35Z

Add adjustNT.spt

Remig at 15:03, 16 May 2014

2014-05-16T15:03:10Z

Remig: /* The Plico Suite of Jmol Application Scripts for Modeling Protein Folding */

2014-05-01T14:30:13Z

‎The Plico Suite of Jmol Application Scripts for Modeling Protein Folding

Remig at 19:16, 28 March 2014

2014-03-28T19:16:19Z

Remig: /* The Plico Suite of Jmol Application Scripts for Modeling Protein Folding */

2014-03-28T19:03:13Z

‎The Plico Suite of Jmol Application Scripts for Modeling Protein Folding

@@ Line 33: / Line 33: @@
 '''AdjustNT''' - allows the user to change the inter-base spacing and twist of any portion of a single or double strand polynucleotide.  The script '''adjustNT.spt''' and its linking macro can be found [[User:Remig/plico/adjustNT|here]].
-'''ConvertResidue''' - allows the user to change a residue in a polypeptide or polynucleotide from one type to another - such as GLY to THR or DT to DA.  It also allows the user to double-bond all amino acid or nucleotide planar structures (aromatics, amides, etc. - double-bonding prevents certain minimization distortions).  The script '''convert_residue.spt''' and its linking macro can be found [[User:Remig/plico/convert|here]].
+'''ConvertResidue''' - allows the user to change a residue in a polypeptide or polynucleotide from one type to another - such as GLY to THR or DT to DA.  It also allows the user to double-bond all amino acid or nucleotide planar structures (aromatics, amides, etc. - double-bonding prevents certain minimization distortions and allows proper placement of hydrogens with the 'calculate hydrogens' command).  The script '''convert_residue.spt''' and its linking macro can be found [[User:Remig/plico/convert|here]].
 '''Fold_trna''' - allows the user to create a 3D tRNA structure from a nucleotide sequence based on templates loaded from the Protein Database. The script '''fold_trna.spt''' and its linking macro can be found [[User:Remig/plico/fold_trna|here]].
 '''TugNt''' - allows the user to pull or push by mouse actions to move or rotate one part of a polynucleotide against the rest by rotation on bonds with collision detection and restriction.   It also allows the user to pull or push by mouse actions to move or to rotate an entire chain or chains with auto-rotation to nest one chain against another.  The script is currently under development.
 '''ToBetaSheet''' - allows the user to mark a section of a polypeptide chain to form a beta sheet with another strand.  The script is currently under development.
 '''Melt''' - applies side chain rules to unfreeze sections of an alpha helix.  The script is currently under development.

← Older revision		Revision as of 17:57, 24 July 2015
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−	'''Plico''' is a suite of Jmol scripts for the visual manipulation by mouse actions of polypeptides (and polynucleotides) in a single-strand or multi-strand, multi-frame environment, accessed as Jmol application macros. It is designed to support modeling the ''de novo'' protein folding approach where folding is envisioned to occur as the polypeptide emerges from the ribosome as water and side-chain oxygens (predominantly) disrupt the h-bonds of the ~~alpha helix (likewise for RNA emerging from polymerase)~~. The following scripts are implemented or envisioned:	+	'''Plico''' is a suite of Jmol scripts for the visual manipulation by mouse actions of polypeptides (and polynucleotides) in a single-strand or multi-strand, multi-frame environment, accessed as Jmol application macros. General operation features of the suite are described [[User:Remig/plico/plicoGeneral\|here]].
		+
		+	The following scripts are implemented or envisioned:

@@ Line 33: / Line 33: @@
 '''ConvertResidue''' - allows the user to change a residue in a polypeptide or polynucleotide from one type to another - such as GLY to THR or DT to DA.  It also allows the user to double-bond all amino acid or nucleotide planar structures (aromatics, amides, etc. - double-bonding prevents certain minimization distortions).  The script '''convert_residue.spt''' and its linking macro can be found [[User:Remig/plico/convert|here]].
-'''Fold_trna''' - allows the user to
+'''Fold_trna''' - allows the user to create a 3D tRNA structure from a nucleotide sequence based on templates loaded from the Protein Database. The script '''fold_trna.spt''' and its linking macro can be found [[User:Remig/plico/fold_trna|here]].
 '''TugNt''' - allows the user to pull or push by mouse actions to move or rotate one part of a polynucleotide against the rest by rotation on bonds with collision detection and restriction.   It also allows the user to pull or push by mouse actions to move or to rotate an entire chain or chains with auto-rotation to nest one chain against another.  The script is currently under development.

@@ Line 31: / Line 31: @@
 '''AdjustNT''' - allows the user to change the inter-base spacing and twist of any portion of a single or double strand polynucleotide.  The script '''adjustNT.spt''' and its linking macro can be found [[User:Remig/plico/adjustNT|here]].
-'''ConvertResidue''' - allows the user to change a residue in a polypeptide or polynucleotide from one type to another - such as GLY to THR or DT to DA.  The script '''convert_residue.spt''' and its linking macro can be found [[User:Remig/plico/convert|here]].
+'''ConvertResidue''' - allows the user to change a residue in a polypeptide or polynucleotide from one type to another - such as GLY to THR or DT to DA.  It also allows the user to double-bond all amino acid or nucleotide planar structures (aromatics, amides, etc. - double-bonding prevents certain minimization distortions).  The script '''convert_residue.spt''' and its linking macro can be found [[User:Remig/plico/convert|here]].
 '''TugNt''' - allows the user to pull or push by mouse actions to move or rotate one part of a polynucleotide against the rest by rotation on bonds with collision detection and restriction.   It also allows the user to pull or push by mouse actions to move or to rotate an entire chain or chains with auto-rotation to nest one chain against another.  The script is currently under development.

@@ Line 2: / Line 2: @@
-'''Plico''' is a suite of Jmol scripts for the visual manipulation by mouse actions of polypeptides (and polynucleotides) in a single-strand or multi-strand environment, accessed as Jmol application macros.  It is designed to support modeling the ''de novo'' protein folding approach where folding is envisioned to occur as the polypeptide emerges from the ribosome as water and side-chain oxygens (predominantly) disrupt the h-bonds of the alpha helix (likewise for RNA emerging from polymerase).  The following scripts are implemented or envisioned:
+'''Plico''' is a suite of Jmol scripts for the visual manipulation by mouse actions of polypeptides (and polynucleotides) in a single-strand or multi-strand, multi-frame environment, accessed as Jmol application macros.  It is designed to support modeling the ''de novo'' protein folding approach where folding is envisioned to occur as the polypeptide emerges from the ribosome as water and side-chain oxygens (predominantly) disrupt the h-bonds of the alpha helix (likewise for RNA emerging from polymerase).  The following scripts are implemented or envisioned:
@@ Line 30: / Line 30: @@
 '''AdjustNT''' - allows the user to change the inter-base spacing and twist of any portion of a single or double strand polynucleotide.  The script '''adjustNT.spt''' and its linking macro can be found [[User:Remig/plico/adjustNT|here]].
 '''TugNt''' - allows the user to pull or push by mouse actions to move or rotate one part of a polynucleotide against the rest by rotation on bonds with collision detection and restriction.   It also allows the user to pull or push by mouse actions to move or to rotate an entire chain or chains with auto-rotation to nest one chain against another.  The script is currently under development.

← Older revision		Revision as of 21:02, 10 June 2014
Line 28:		Line 28:

	'''ToABnt''' - allows the user to convert a polynucleotide chain from A-form to B-form and ''vice versa''. The script '''toABnt.spt''' and its linking macro can be found [[User:Remig/plico/toABnt\|here]].		'''ToABnt''' - allows the user to convert a polynucleotide chain from A-form to B-form and ''vice versa''. The script '''toABnt.spt''' and its linking macro can be found [[User:Remig/plico/toABnt\|here]].
		+
		+	'''AdjustNT''' - allows the user to change the inter-base spacing and twist of any portion of a single or double strand polynucleotide. The script '''adjustNT.spt''' and its linking macro can be found [[User:Remig/plico/adjustNT\|here]].

	'''TugNt''' - allows the user to pull or push by mouse actions to move or rotate one part of a polynucleotide against the rest by rotation on bonds with collision detection and restriction. It also allows the user to pull or push by mouse actions to move or to rotate an entire chain or chains with auto-rotation to nest one chain against another. The script is currently under development.		'''TugNt''' - allows the user to pull or push by mouse actions to move or rotate one part of a polynucleotide against the rest by rotation on bonds with collision detection and restriction. It also allows the user to pull or push by mouse actions to move or to rotate an entire chain or chains with auto-rotation to nest one chain against another. The script is currently under development.

@@ Line 11: / Line 11: @@
 '''PlicoCommon''' - contains routines common to the following scripts. It must be in the same directory as the scripts that use these routines.  The script '''plicoCommon.spt''' can be found [[User:Remig/plico/plicoCommon|here]].
-'''PlicoCommonNT''' - contains routines common to the following NT scripts for polynucleotide manipulation. It must be in the same directory as the scripts that use these routines.  The script '''plicoCommonNT.spt''' can be found [[User:Remig/plico/plicoCommonNT|here]].
+'''PlicoCommonNT''' - contains routines common to the following NT scripts for polynucleotide manipulation. It must be in the same directory as the scripts that use these routines.  The script '''plicoNTcommon.spt''' can be found [[User:Remig/plico/plicoCommonNT|here]].
 '''Tug''' - allows the user to pull or push by mouse actions to move or rotate one part of a polypeptide against the rest by rotation on its psi and phi bonds with collision detection and restriction.   It also allows the user to pull or push by mouse actions to move or to rotate an entire chain or chains with auto-rotation to nest one chain against another.  The script '''tug.spt''' and its linking macro can be found [[User:Remig/plico/tug|here]] and its manual found [[User:Remig/plico/tugManual|here]].

@@ Line 9: / Line 9: @@
 '''Generate Polynucleotide''' - allows the user to enter a sequence string and have a corresponding single-stranded or double-stranded RNA or DNA polynucleotide created.  The script '''polymeraze.spt''' and its linking macro can be found [[Recycling_Corner/DNA_Generator|here]].
-'''PlicoCommon''' - contains routines common to the following scripts. It must be in the same directory as the scripts that use these routines.  The script '''plicoCommon.spt''' can be found [[User:Remig/plico/plicoCommon|here]]
+'''PlicoCommon''' - contains routines common to the following scripts. It must be in the same directory as the scripts that use these routines.  The script '''plicoCommon.spt''' can be found [[User:Remig/plico/plicoCommon|here]].
 '''Tug''' - allows the user to pull or push by mouse actions to move or rotate one part of a polypeptide against the rest by rotation on its psi and phi bonds with collision detection and restriction.   It also allows the user to pull or push by mouse actions to move or to rotate an entire chain or chains with auto-rotation to nest one chain against another.  The script '''tug.spt''' and its linking macro can be found [[User:Remig/plico/tug|here]] and its manual found [[User:Remig/plico/tugManual|here]].
@@ Line 25: / Line 25: @@
 '''Modify''' - generates the common polypeptide and polynucleotide modifications: methylation of purines and pyrimidines, hydroxylation of proline, phosphorylation of serine, etc.  The script '''modify.spt''' and its linking macro can be found [[User:Remig/plico/modify|here]].
-'''ToABnt''' - allows the user to convert a polynucleotide chain from A-form to B-form and vice versa.  The script '''toABnt.spt''' and its linking macro can be found [[User:Remig/plico/toABnt|here]].
+'''ToABnt''' - allows the user to convert a polynucleotide chain from A-form to B-form and ''vice versa''.  The script '''toABnt.spt''' and its linking macro can be found [[User:Remig/plico/toABnt|here]].
 '''TugNt''' - allows the user to pull or push by mouse actions to move or rotate one part of a polynucleotide against the rest by rotation on bonds with collision detection and restriction.   It also allows the user to pull or push by mouse actions to move or to rotate an entire chain or chains with auto-rotation to nest one chain against another.  The script is currently under development.