error messages

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neilthawani

error messages

Post by neilthawani » Thu Apr 12, 2012 1:39 am

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.
Last edited by neilthawani on Fri Apr 13, 2012 9:41 am, edited 1 time in total.

ted
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Re: error messages

Post by ted » Thu Apr 12, 2012 9:37 am

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.

neilthawani

Re: error messages

Post by neilthawani » Thu Apr 12, 2012 10:17 am

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!

Code: Select all

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.
Last edited by neilthawani on Fri Apr 13, 2012 9:42 am, edited 1 time in total.

neilthawani

Re: error messages

Post by neilthawani » Thu Apr 12, 2012 4:11 pm

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!

ted
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Posts: 5572
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Location: Yale University School of Medicine
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Re: error messages

Post by ted » Thu Apr 12, 2012 9:38 pm

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.

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