User:Remig/plico

The Plico Suite of Jmol Application Scripts for Modeling Protein Folding

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 here.

The following scripts are implemented or envisioned:

Generate Polypeptide - allows the user to enter a sequence string and have a corresponding alpha helix polypeptide created. The script ribozome.spt and its linking macro can be found here.

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 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 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 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 here and its manual found here.

Record - allows the user to enter the name of a file to which all Plico commands will be written. The file may be played back to reproduce the users actions. Implemented as just a macro here.

Remap - Renumbers and re-identifies residues in polypeptide chains and displays the resultant 1 char per residue string as used by the Ribozyme script. The script remap.spt and its linking macro can be found here.

RemapNT - Renumbers and re-identifies residues in polynucleotide chains and displays the resultant 1 char per NT string as used by the Polymeraze script. The script remapNT.spt and its linking macro can be found here.

Turn - allows the user to make type I and II reverse turns and beta-hairpins in polypeptides with a single mouse click as well as cis/trans rotations on proline omega bonds. The script turn.spt and its linking macro can be found here.

ToAlphaBeta - allows the user to mark a section of a polypeptide chain to fold towards an alpha helix configuration or towards a beta strand configuration. The script toAlphaBeta.spt and its linking macro can be found here and its manual found here.

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 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 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 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 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 here.

Hydrate - allows the user to add, remove and view water molecules at appropriate places. The script hydrate.spt and its linking macro can be found here.

Utilities - presents a menu of actions potentially useful for manual folding of polypeptides, such as displaying dispersion bonds, visualizing coil pairing, etc. The script utilities.spt and its linking macro can be found here.

Plots - allows the user to generate explorable plots of various interesting aspects of protein folding such as O rotations, chi values, and phi psi values. The script plots.spt and its linking macro can be found 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.

FoldRNA - matches complementary internal sections of a single stranded polynucleotide and produces a folded RNA product. The script is currently under development.

and more as I think of them...

Contributors

Remig