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error messages

Posted: Thu Apr 12, 2012 1:39 am
by neilthawani
Thank you for your help so far.

I am running some tests on the conductances across the apical branch and am starting by removing the non-passive channels from all the dendrites except apical[0]. Here is the resulting code for the model:

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*** Removed ***
And here is the rather odd error I am getting:
*** Removed ***
What could be the reason for these two odd errors? Thank you again.

Re: error messages

Posted: Thu Apr 12, 2012 9:37 am
by ted
neilthawani wrote:I am running some tests on the conductances across the apical branch and am starting by removing the non-passive channels from all the dendrites except apical[0].
OK. How are you doing this? There are still lots of "insert" statements in your hoc code.
And here is the rather odd error I am getting:

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na_ion mechanism not inserted in section apical[1]
nrniv: 
 in C:/Users/Neil/Desktop/Minimized Power Model/BLA AHP model current clamp revised 10micorn segs.hoc near line 320
 }
  ^
oc>nrniv: runcIV undefined function
 near line 320
 {runcIV()}
           ^
runcIV(        )
What could be the reason for these two odd errors?
At last! Useful error messages from hoc!

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na_ion mechanism not inserted in section apical[1]
If a mechanism is inserted into a section that contains a USEION x statement that WRITEs or READs the ionic current ix or the intra- or extracellular concentrations xi or xo of that ion, NEURON automatically inserts a "helper" mechanism called x_ion. The particular error message you're getting means that some statement is trying to access nai or nao in a section called apical[1] but that section no longer has such a mechanism because you removed some other mechanism that WRITEs or READs nai or nao in that section.

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oc>nrniv: runcIV undefined function
This error message means your code has a statement that refers to a procedure or function called runcIV, but you haven't provided code to define runcIV.

Re: error messages

Posted: Thu Apr 12, 2012 10:17 am
by neilthawani
ted wrote:OK. How are you doing this? There are still lots of "insert" statements in your hoc code.
From lines 235-284:

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*** Removed ***
I commented out the "for" loop so that when I move past one dendrite (apical[0]), I can loop it from 0 to 1, 0 to 2, etc.
At last! Useful error messages from hoc!

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na_ion mechanism not inserted in section apical[1]
If a mechanism is inserted into a section that contains a USEION x statement that WRITEs or READs the ionic current ix or the intra- or extracellular concentrations xi or xo of that ion, NEURON automatically inserts a "helper" mechanism called x_ion. The particular error message you're getting means that some statement is trying to access nai or nao in a section called apical[1] but that section no longer has such a mechanism because you removed some other mechanism that WRITEs or READs nai or nao in that section.
The strange thing is, though, that I don't address apical[1] at all in my code apart from lines 243-249:

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*** Removed ***
I thought it might be lines 309-319 (line 311 in particular):

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*** Removed ***
but after commenting it out, I found that such was not the case.

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oc>nrniv: runcIV undefined function
This error message means your code has a statement that refers to a procedure or function called runcIV, but you haven't provided code to define runcIV.
I defined runcIV() at the end of my code in lines 346-360, though:

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*** Removed ***
It seems like NEURON is ignoring the init() proc, as line 320 is where that, advance() and runcIV() are defined in the code.

Re: error messages

Posted: Thu Apr 12, 2012 4:11 pm
by neilthawani
Aha! I got it. I changed

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ena=70
to

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if (ismembrane("na3") || ismembrane("nax")) {ena=70}
Thank you!

Re: error messages

Posted: Thu Apr 12, 2012 9:38 pm
by ted
So it wasn't nai or nao, but ena. Could have been ina for that matter. Kudos for sticking with it and finding the source of the problem.