Model Properties

From QuB

Jump to: navigation, search
Prev: New Model Outline Next: State Properties


The Model Properties dialog lets you edit display settings, rate constants, and constraints. To see the Properties of a model, double-click its name in the Model window, or right-click in the background of the Model window and choose "Properties."

Colors and display settings are saved with new QMF files. New models, and models saved without display info, inherit the display settings of the last open model. Use the Presets menu (lower right) to save colors and display info as a preset, or set them from an existing preset.

Contents

Colors

Background
the space behind the picture
Rates lines
the lines connecting two states
Rates captions
the text of rate constants
Selected rate
the lines and text of the selected rate constant (in the Rates tab)
Frame
the dashed line around the border
the margin outside the dashed line

Display

States panel size
width and height of a state
Rates line width
weight of the lines between states
Margins
space between the window's edge and the model picture
Align states panels to grid
snap states to the nearest position on a grid, for easier positioning
Use global conditions
calculate the displayed value of a stimulus-dependent rate constant from Global Conditions instead of the current point of the current data file
Edit rates with mouse wheel
lets you change a rate constant by pointing at it and spinning the mouse wheel. Hold down Control or Shift to get smaller or larger increments. You may have to click in the model first.
Write rates along arrows
write text diagonally instead of all horizontally
Show K1
writes k0 and k1 separately, instead of the calculated k=k0*C*e^(k1*V)
only available with "Write rates along arrows"

Model

Channel count
The number of ion channels in the patch (same as Channel count in the Model window)
Vrev

Rates

See Model Theory#Rates. This tab is also shown when you double-click a rate constant in the Model window. Click any rate constant in the picture to edit it. These fields change the highlighted rate:

k0
The pre-exponential rate constant
P
whether the rate is concentration-dependent
Ligand (or whatever)
the name of the concentration variable
k1
the exponential rate constant, used only with voltage (or pressure) dependence
set to 0 to disable k1 in optimizers such as MIL
Q
whether the rate is voltage-dependent
Voltage (or whatever)
the name of the voltage variable

The value of experimental variables is set in

Set as default
use this rate's k0, P, k1, Q for new connections from now on
Enforce constraints
whenever a rate is changed (including by scroll wheel, updates other rates to preserve any #Kinetic Constraints

Kinetic Constraints

MIL and other algorithms honor constraints on the rate constants. Each constraint reduces the number of free parameters by 1.

A kinetic constraint is described by a type (e.g. "Fix rates"), a list of state numbers, and an optional Value. You can add and delete them by hand, or use shortcut buttons for common tasks.

(someone please explain the Value)

Types

Fix rates s1 s2
Holds k0 from s1 to s2 at its present value
Scale rates s1 s2 s3 s4
Maintains the ratio between (k0 from s1 to s2) and (k0 from s3 to s4)
Fix exp
Holds k1 from s1 to s2 at its present value
Scale exp s1 s2 s3 s4
Maintains the ratio between (k1 from s1 to s2) and (k1 from s3 to s4)
Loop balance s1 s2 ... sN
Requires the product of rate constants going forward around a cycle to equal the product of rate constants going backward
s1ks2 * s2ks3 * ...sNks1 = s1ksN * ... * s3ks2 * s2ks1
Loop imbalance
Preserves the ratio between the forward and backward products

Shortcuts

Fix all rates
Adds a "Fix rates" constraint for each rate in the model
Balance loops
Finds a minimal set of cycles using a minimum spanning tree 1 and adds "Loop balance" constraints
Delete extras
removes any constraints that can be expressed as linear combinations of preceding constraints, e.g. if a loop balance constraint is duplicated by scale constraints.
this may be necessary for MIL. It can take a while for large models

Amplitude Constraints

exc Amp is the excess amplitude, of a given class vs the black. In other words, the difference. 

 exc Amp is the excess amplitude, of a given class vs the black.
 In other words, the difference.
 Fix Amp constraints the absolute amp value of a given class.
 Fix exc Amp constraints the difference (excess) in amp between a given class and the black.
 Fix diff exc Amp constraints the difference in excess amp between
 any two classes. Since the excess is defined relative to the same
 class (black), it is identical to the absolute difference.
 Scale ... has the usual meaning.

Note that the amplitude constraints are implemented only in the IdlBase algorithm, for singles.


Prev: New Model Outline Next: State Properties
Retrieved from "http://www.qub.buffalo.edu/wiki/index.php/Model_Properties"
Personal tools