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I am working through the chapter eight of the NEURON book, sec 8.4.4.2 and repeating the hoc codes in the chapter as to help me understand what is being discussed in that chapter but I am running into difficulties, please I will need some help to understand the excericses.

I created the mod file of the "capmp" wrote the hoc code for one compartment (soma), inserted hh, and capmp into it., ran the simulation and plotted the graph of the time course of Cashell (cashell) and pump current (IIcapump). Saved all in a session file for ease of retrieval

As to help me understnad how the initialization of ca_init affects the time course of the parameters (plotted above).

I wrote the hoc code (called it initiCa) you have in the book (but only defined and assigned value for ca_init )as shown below :
objref ca_init

cashell = ca_init

ca_init = 0.2

proc init() {
cashell_capmp = ca_init
finitalize(v_init)
}

When I open the saved session file described above and then load the hoc "initiCa.hoc", and ran the simulation it gives me error message :
"bad stack access: expecting (double); really (Unknown)
nrniv: interpreter stack type error
in initia1.hoc near line 3
cashell = ca_init"

I have no clue what that means and what I have done wrong, If Itry to change the value of the ca_init from the interpreter, it closes (which confirms to me that there is an error)

Though the above initilaization method was not supposed to have any effect on the time course of the cashell and pump current as explained, but I have the same result when I load this version of the initiCa.hoc:
objref ca_init
ca_init = 0.4
proc init() {
finitialize(v_init)
cashell_capmp = ca_init

// we've change a state, so the following are needed

if (cvode.active()) {

cvode.re_init()

} else {

fcurent()

}
frecod_init()
}

Please I will appreciate you help to understand what I have not done right.

Thank you

That's because cashell and ca_init have incompatible data types.tells NEURON that ca_init is an objref (a pointer to an instance of some object class)If this is the first appearance of the name cashell, NEURON will automatically treat it as a double precision floating point number (AKA a double).

The problem will go away if you delete the declarationand instead just assign a numerical value to ca_init.

The statement
cashell = ca_init
doesn't do anything useful and can be omitted. The only cashell that means anything in the example is the cashell that belongs to the capmp mechanism; this variable is known to hoc as cashell_capmp. The hoc statement
cashell = ca_init
merely creates a new double called cashell, but it isn't related to the capmp mechanism's cashell.

Though the above initilaization method was not supposed to have any effect on the time course of the cashell and pump current as explained, but I have the same result when I load this version of the initiCa.hoc:
objref ca_init
ca_init = 0.4
proc init() {
finitialize(v_init)
cashell_capmp = ca_init

// we've change a state, so the following are needed

if (cvode.active()) {

cvode.re_init()

} else {

fcurent()

}
frecod_init()
}

I'm not sure I understand "I have the same result" What result?

Please can you check the codes of cadifus (calcium diffusion) of listing 9.8 in NEURON book. Itried to compile the mod file but it gives this error message :
syntax error:
Illegal expression:
Illegal reaction syntax:
Illegal integer expression:
FROM intvar = intexpr TO intexpr BY intexpr { statements }:
Illegal block at line 100 in file Calcium_Diffusiion.mod
~ ca + Buffer <-> CaBuffer (k1buf*dsgvol, \
^

The arrow is on the "backward slash "\"" is this correct.? I have not understood how to write the kinetics very well, so I'm not sure what that is supposed to be.

I have a similar error message when I tried to compile cdp (Calcium pump) after I have made the appropriate changes
Illegal reaction syntax:
Illegal block at line 117 in file Calcium_Pump.mod
~ ca[0] + pump <-> pumpca (k1*parea*(1e10), \
^

Thank you
Irene

Thank you! It works now!

Thank you
Irene

Please I am thanking you for your explaination for Chapter 8, not for chap 9, I have not resolved that yet.
Irene

Thank you! It is taken care of.

Irene