Today I have uninstalled completely my NEURON 7.1 version and installed fresh copy. This is just to ensure that the "bug" is really there and not because I customized my NEURON (as you suggested in your previous reply to my post). I have found manual solution to the bug that I am reporting, maybe you can fix this or explain why the bug occurred.
The problem is as follows: so far I was using the Cell Builder to input channels into a reconstructed 3D neuron. Also I was setting the reversal potentials E_Na and E_K through the Tools Menu > Distributed mechanisms > Na and K ion (Global), as well as Celsius menu for temperature. Unfortunately when the Cell Builder exports .hoc file it does not input code for reversal potentials E_Na and E_K and also if I load .hoc that does not contain information about reversal potentials E_Na and E_K even if I set these through the Tools menu (as i explained above), and try to perform current clamp, the values for reversal potentials E_Na and E_K that NEURON uses to compute action potentials are the default for mollusk neurons, not the values inputted by me.
In summary: setting intracellular and extracellular concentrations of Na+ and K+ ions through the Tools menu does not work. Also exporting fresh .hoc file from the Cell Builder does not take into account the settings for intracellular and extracellular concentrations of Na+ and K+ ions and does not create the appropriate .hoc code.
I performed manual fix for this. After exporting the .hoc file, I followed advice from "A NEURON Programming Tutorial" by Andrew Gillies and David Sterratt - http://www.anc.ed.ac.uk/school/neuron/t ... /tutD.html - who said that the reversal potentials for E_Na and E_K .."should be set after the channel mechanisms are inserted into a section, and must be set for each section that has channels using that ionic species inserted."
Thus I added in my .hoc file the following code at the end of each section after the channel mechanisms were inserted:
Code: Select all
forsec somatic {
insert channel
gmax_channel = 0.045
ena = 71.5
ek = -89.1
}
forsec axonal {
insert channel
gmax_channel = 0.045
ena = 71.5
ek = -89.1
}
forsec basal {
insert channel
gmax_channel = 0.045
ena = 71.5
ek = -89.1
}
This manual fix ensured that the reversal potentials are set properly after all channel mechanisms.
(Note: I tried to insert in my .hoc file with the command forsec all, however NEURON complained that in some section there are no K+ or Na+ channels.)
After I run the current clamp with the fixed .hoc file everything was nice, and I was able to see clearly effects by manipulating the reversal potentials.
I am wondering why the Tools menu did not work, and why setting the ion concentrations and temperature had no effect on the current clamp performed through the Tools > Point Process Manager.
I am not aware whether this problem is available only under Windows XP OS, etc. For now I will input the missing code on reversal potentials in my .hoc files manually.