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\begin_body

\begin_layout Standard
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\end_layout

\begin_layout Title
The Chiropraxis tools manual
\end_layout

\begin_layout Standard
\begin_inset VSpace vfill
\end_inset


\end_layout

\begin_layout Author
Ian W.
 Davis
\end_layout

\begin_layout Chapter
The Tools
\end_layout

\begin_layout Section
BACKRUB Tool: Protein chiropraxis
\begin_inset CommandInset label
LatexCommand label
name "backrub-tool"

\end_inset


\end_layout

\begin_layout Standard
The BACKRUB tool is used to adjust short segments of protein backbone without
 disturbing the surrounding structure.
 It allows you select one residue, and rotate it around the axis between
 its neighboring C-alphas.
 Using BACKRUB requires that 
\family typewriter
chiropraxis.jar
\family default
 be present in the 
\family typewriter
plugins/
\family default
 folder.
\end_layout

\begin_layout Standard
Create a backrub by control-clicking the alpha carbon of the central residue.
 To use the dial control, click and drag the pointer to the desired value.
 For finer control you can shift-drag along an imaginary slider (this behavior
 is somewhat like the virtual dials in O).
 To reset the dial to its starting value, double click the dial face.
 The dial can also be adjusted from the graphics window using the mouse
 wheel or arrow keys; see below.
\end_layout

\begin_layout Standard
The BACKRUB panel provides feedback on the geometric quality of the current
 model, displaying residues names, deviation of the tau angle (N-CA-C) from
 ideality, and the position of the residue on the Ramachandran plot (phi,
 psi, and favored/allowed/outlier).
 Deviant geometry is highlighted in red.
\end_layout

\begin_layout Standard

\emph on
BACKRUB is described in the following publication: I.W.
 Davis, W.B.
 Arendall III, D.C.
 Richardson, and J.S.
 Richardson (2006) "The backrub motion: How protein backbone shrugs when
 a sidechain dances" Structure 14, 265-274.
\end_layout

\begin_layout Subsection
Command reference
\end_layout

\begin_layout Standard
\noindent
\align center
\begin_inset Tabular
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\begin_inset Text

\begin_layout Plain Layout
Mouse clicks
\end_layout

\end_inset
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\begin_layout Plain Layout

\end_layout

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<row>
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\begin_inset Text

\begin_layout Plain Layout
Normal
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout
Mark and identify point; make measurement (pick)
\end_layout

\end_inset
</cell>
</row>
<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout
With Shift
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout
Center on selected point (pickcenter)
\end_layout

\end_inset
</cell>
</row>
<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout
With Ctrl
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
\noun off
\color none
Select
\family default
\series default
\shape default
\emph default
\bar default
 
\size default
\noun default
\color inherit
residue for BACKRUB
\color none
 
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\shape up
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\emph off
\bar no
\noun off
(
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\noun default
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o
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\series medium
\shape up
\size normal
\emph off
\bar no
\noun off
\color none
n a C-alpha
\family default
\series default
\shape default
\size default
\emph default
\bar default
\noun default
\color inherit
); clear current selection (elsewhere)
\end_layout

\end_inset
</cell>
</row>
<row>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout
With Shift+Ctrl
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout
-
\end_layout

\end_inset
</cell>
</row>
</lyxtabular>

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\end_layout

\begin_layout Standard
\noindent
\align center
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<features tabularvalignment="middle">
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<column alignment="center" valignment="top" width="0sp">
<row>
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\begin_inset Text

\begin_layout Plain Layout
Mouse drags
\end_layout

\end_inset
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\end_layout

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Normal
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\begin_inset Text

\begin_layout Plain Layout
Rotate around X and Y axes; Z-rotate (pinwheel) near top of screen
\end_layout

\end_inset
</cell>
</row>
<row>
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\begin_inset Text

\begin_layout Plain Layout
With Shift
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout
Adjust zoom (up/down); Adjust clipping (left/right) 
\end_layout

\end_inset
</cell>
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<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout
With Ctrl
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout
Translate in X-Y plane (flatland); Z-translate near top of screen
\end_layout

\end_inset
</cell>
</row>
<row>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout
With Shift+Ctrl
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout
Rotate around Y axis only
\end_layout

\end_inset
</cell>
</row>
</lyxtabular>

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\noindent
\align center
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\begin_inset Text

\begin_layout Plain Layout
Mouse wheel / Up & Down arrow keys
\end_layout

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\end_layout

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\begin_inset Text

\begin_layout Plain Layout
Normal
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout
Adjust dial (angle of rotation)
\end_layout

\end_inset
</cell>
</row>
<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout
With Shift
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout
Adjust clipping
\end_layout

\end_inset
</cell>
</row>
<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout
With Ctrl
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout
Adjust zoom
\end_layout

\end_inset
</cell>
</row>
<row>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout
With Shift+Ctrl
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout
-
\end_layout

\end_inset
</cell>
</row>
</lyxtabular>

\end_inset


\end_layout

\begin_layout Section
C-alpha Hinges
\begin_inset CommandInset label
LatexCommand label
name "hinges-tool"

\end_inset


\end_layout

\begin_layout Standard
Hinges is the generalized version of BACKRUB.
 It allows you to select any continuous region of backbone that joins two
 alpha carbons, and then rotate that segment of backbone around an axis
 drawn between those C-alphas.
 Individual peptides can also be rotated.
 Create a hinge by control-clicking the two alpha carbons that act as its
 endpoints or anchors.
\end_layout

\begin_layout Standard
Regions longer than two peptides (
\emph on
i.e.
\emph default
, what BACKRUB handles) are seldom useful in fitting structures.
 Thus, this tool has been largely superceded by BACKRUB.
\end_layout

\begin_layout Section
Shear Tool: Helical winding plus unwinding 
\begin_inset CommandInset label
LatexCommand label
name "shear-tool"

\end_inset


\end_layout

\begin_layout Standard
The shear tool can be used to modify backbone, most commonly helix, in a
 manner almost completely orthogonal to the backrub.
 A shear shifts three peptides instead of two like a backrub, and moves
 the central peptide nearly parallel to the chain direction rather than
 perpendicular to it.
 Use Ctrl+Click (a.k.a.
 middle-click) to select a residue; it, its preceding residue, and its two
 following residues will become the active 
\begin_inset Quotes eld
\end_inset

molten
\begin_inset Quotes erd
\end_inset

 state.
 Next, drag the primary shear dial for the main motion, then optionally
 drag the three peptide rotation dials to alleviate some strain.
 Functionality is generally similar to the backrub tool.
\end_layout

\begin_layout Standard

\emph on
Authored by Daniel Keedy
\emph default
 
\emph on
(daniel.keedy AT duke.edu)
\end_layout

\begin_layout Section
Tweak Phi/Psi: Visualizing possible backbone changes 
\begin_inset CommandInset label
LatexCommand label
name "phisi-tool"

\end_inset


\end_layout

\begin_layout Standard
The tweak phi/psi tool is useful for slightly altering the backbone dihedrals
 phi and psi.
 Use Ctrl+Click (a.k.a.
 middle-click) to select a residue and its adjacent region as the active
 
\begin_inset Quotes eld
\end_inset

molten
\begin_inset Quotes erd
\end_inset

 state.
 The length of the active region can be customized by entering a number
 of residues in the box and pressing enter.
 Next, drag the phi/psi dials to rotate the molten region around either
 the phi or psi axis.
 Note that this tool makes no attempt to close the resulting chain break
 or to alleviate the steric clashes it usually introduces, and thus should
 not be employed as a fitting tool.
 However, it can be useful for visualizing the local effects of small changes
 in phi/psi and simply building intuition.
\end_layout

\begin_layout Standard

\emph on
Authored by Daniel Keedy
\emph default
 
\emph on
(daniel.keedy AT duke.edu)
\end_layout

\begin_layout Section
Sidechain Rotator: Refitting protein models
\begin_inset CommandInset label
LatexCommand label
name "scrot-tool"

\end_inset


\end_layout

\begin_layout Standard
The Sidechain Rotation tool is useful for doing interactive refitting of
 protein models in conjunction with the Hinges tool and the model manager.
 Use Ctrl+Click (a.k.a.
 middle-click) to select a sidechain to rotate, then pick from a list of
 predefined rotamers or set the angles by hand using the dials.
 The rotamericity of the current sidechain and the closest named rotamer
 are monitored in the bottom right corner; it indicates how frequently (if
 ever!) the current conformation is found in well-determined structures.
 This tool was updated to use the Top8000 
\begin_inset Quotes eld
\end_inset

ultimate
\begin_inset Quotes erd
\end_inset

 version of the rotamer library in the fall of 2016.
\end_layout

\begin_layout Standard
To use the dial control, click and drag the pointer to the desired value.
 For finer control you can shift-drag along an imaginary slider (this behavior
 is somewhat like the virtual dials in O).
 To reset the dial to its starting value, double click the dial face.
\end_layout

\begin_layout Standard
Sidechain Rotator and the Hinges tool play well together: you can use both
 on the same residue(s) at the same time.
 It's often easiest to establish which sidechains will be rotatable before
 beginning to move the backbone, but it's possible to establish the moving
 parts in any order.
\end_layout

\begin_layout Section
Sidechain Mutator: Redesigning protein models
\begin_inset CommandInset label
LatexCommand label
name "scmut-tool"

\end_inset


\end_layout

\begin_layout Standard
The Sidechain Mutation tool is useful for doing interactive refitting of
 protein models in conjunction with the Hinges and Rotator tools and the
 model manager.
 Use Ctrl+Click (a.k.a.
 middle-click) to select a sidechain to mutate, then pick from a list of
 known amino acid types.
 If you select histidine, you will also be prompted to choose a protonation
 state.
\end_layout

\begin_layout Standard
Sidechain Mutator plays well with the other tools, but you cannot mutate
 the model while any part of it is mobile (
\begin_inset Quotes eld
\end_inset

molten
\begin_inset Quotes erd
\end_inset

).
 Thus, it's often easiest to make mutations first, and then refit the new
 sequence.
\end_layout

\begin_layout Section
Model Manager: Editing a macromolecular model
\begin_inset CommandInset label
LatexCommand label
name "modelman-plugin"

\end_inset


\end_layout

\begin_layout Standard
This facility is for doing molecular modeling based on some starting model,
 usually a PDB file.
 The Model Manager handles opening and saving these files, and is required
 for the operation of the following tools:
\end_layout

\begin_layout Itemize
Backrub
\end_layout

\begin_layout Itemize
C-alpha hinges
\end_layout

\begin_layout Itemize
Shear
\end_layout

\begin_layout Itemize
Tweak phi/psi
\end_layout

\begin_layout Itemize
Sidechain rotator
\end_layout

\begin_layout Itemize
Sidechain mutator
\end_layout

\begin_layout Standard
The model manager also tracks the changes made to the model and allows near-unli
mited undo.
 In addition, it provides access to dynamic visualizations, like Probe dots
 and NOE constraints.
 Using this feature requires that your OS can find Probe – 
\emph on
i.e.
\emph default
, that either Probe resides in the same directory as 
\family typewriter
king.jar
\family default
 and is named either 
\family typewriter
probe
\family default
 or 
\family typewriter
probe.exe
\family default
; or that Probe is somewhere on your PATH and is named 
\family typewriter
probe
\family default
 or 
\family typewriter
probe.exe
\family default
.
 The same is true of 
\family typewriter
noe-display
\family default
.
\end_layout

\begin_layout Standard
There are several special symbols that can be inserted into the Probe and
 NOE command lines.
 Their meanings are as follows:
\end_layout

\begin_layout Description
{pdbfile} The fully-qualified name of the 
\begin_inset Quotes eld
\end_inset

base
\begin_inset Quotes erd
\end_inset

 PDB file; 
\emph on
i.e.

\emph default
 the one with all changes except the currently molten ones.
 (Those are piped in via standard input.)
\end_layout

\begin_layout Description
{molten} The list of molten residues, separated by commas: 1, 2, 3, ...
\end_layout

\begin_layout Description
{center} The coordinates of the current center of view, in real space: x,
 y, z.
 This can be used for the 
\family typewriter
within
\family default
 
\emph on
distance
\emph default
 
\family typewriter
of
\family default
 
\emph on
x, y, z
\emph default
 selection statement.
 Note that visualizations aren't automatically updated when the center of
 view changes.
\end_layout

\begin_layout Chapter
Copyright & acknowledgments
\end_layout

\begin_layout Section
Copyright
\end_layout

\begin_layout Standard
The Chiropraxis code and all its associated original resources and documentation
 are copyright (C) 2002-2010 by Ian W.
 Davis, Daniel A.
 Keedy, and Vincent B.
 Chen.
\end_layout

\begin_layout Section
Revision status
\end_layout

\begin_layout Standard
This manual was last updated 28 September 2016 by VBC for Chiropraxis version
 1.11.
\end_layout

\end_body
\end_document
