Documentation of Channel Builder usage could be much improved. Something we need to do in the next NEURON book.
Channels specified with the Channel builder appear automatically in the appropriate GUI tool menus, just like other density mechanisms or point processes. For example, density mechanisms specified with the Channel Builder will appear in the list of mechanisms on the CellBuilder's Biophysics page, and Channel Builder specified point processes will appear in the PointProcessManager's list of mechanisms.
The basic syntax of hoc usage is identical to that of mechanisms specified in NMODL. That is, density mechanisms are inserted and their state variables, density parameters, and equilibrium potentials are referenced with suffix notation (e.g. m_abc, i_abc, g_abc, e_abc), while point processes are created as instances of a class and have state variables etc. that are referenced with dot notation.
Parameters of the rate functions that govern state transitions are not ordinarily accessible from hoc. However, they can be made accessible by clicking on
Properties / Provide transition aliases
in the main Channel Builder panel. For future use, be sure to save the Channel Builder with "Provide transition aliases" enabled.
Here's how to use a graph's Plot what? to discover the alias names. Suppose you have a Channel Builder for a potassium channel with state variable n where n' = an*(1 - n) - bn*n and the forward and backward rate constants an and bn are governed by functions of membrane potential that involve parameters A, k, and d.
(You can do this yourself right now--start NEURON, bring up a Channel Builder, click on Properties and select HH potassium channel, then click on the equation that appears in the gray field at the bottom of the Channel Builder to see the ChannelBuildGateGUI tool with the formulas for an and bn).
Code: Select all
NEURON Main Menu / Graph / Current axis (this does not require a default section)
Graph's menu box / Plot what?
Plot what? / Show / Objects
scroll down list in first column to ChannelBuild_
double click on ChannelBuild_ -->
ChannelBuild_ appears in text edit field at top of Plot what?,
If there is only one Channel Builder, Plot what?'s middle column will contain a single entry: the numeral 0.
Double click on the 0. in middle column -->
edit field changes to ChannelBuild.,
and middle column shows a list of names
double click on aliases. in middle column -->
edit field changes to ChannelBuild.aliases.,
and right column shows an. and bn.
double click on an. in right column -->
edit field changes to ChannelBuild.aliases.an.,
and right column shows A, d, k
So the "complete" hoc names of these three parameters would be ChannelBuild.aliases.an.A, ChannelBuild.aliases.an.d, and ChannelBuild.aliases.an.k
Guess what the aliases for bn's parameters would be called. Verify your prediction.