plot conductances through different channels

Using the graphical user interface to build and exercise models. Includes customizing the GUI by writing a little bit of hoc.
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monkeybusiness

plot conductances through different channels

Post by monkeybusiness » Wed Apr 29, 2015 4:27 am

I try to plot different currents through the different ion channels. I have the model from (Hemond et al., 2008) http://senselab.med.yale.edu/ModelDB/Sh ... del=101629

I tried current axis, and plot the soma ina(0.5) and ik(0.5). This works. But if I try to plot ica(0.5) nothing appears. Also not all currents are listed for every ion channel, but the conductances are. Below are the symbols one can choose to plot. For example Kdr,is not in the form i..(0.5). But it is in the form of gkdr_kdr(0.5). So I thought it is better to plot conductances instead of currents. I would like to plot this, and tried also grapher and state axis via the NEURON main menu --> Tools. But this did not succeed. I guess this is really a noob question, but I would really appreciate some help. Thank you in advance

g_pas(0.5)
gbar_KahpM95(0.5)
gbar_cagk(0.5)
gbar_km(0.5)
gbar_na3(0.5)
gcal_cal(0.5)
gcalbar_cal(0.5)
gcanbar_can(0.5)
gat_cat(0.5)
gcatbar_cat(0.5)
ggk_cal(0.5)
ghdbar_hd(0.5)
gka_kap(0.5)
gkabar_kap(0.5)
gkahp¬_kahpM95(0.5)
gkca_cagk(0.5)
gkd_kd(0.5)
gkdbar_kd(0.5)
gkdr_kdr(0.5)
gkdrbar¬¬_kdr(0.5)
h¬_can(0.5)
h_cat(0.5)
h_na3(0.5)
i_cacum(0.5)
i_cap(0.5)
i_hd(0.5)
i_pas(0.5)
ica(0.5)
ica¬_cal(0.5)
ica_can(0.5)
ica_cat(0.5)
ik(0.5)
ik_KahpM95(0.5)
ik_cagk(0.5)
ik_km(0.5)
ina(0.5[/size])

ted
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Re: plot conductances through different channels

Post by ted » Wed Apr 29, 2015 10:46 am

Variables used in NMODL code may or may not be visible to hoc or Python.
The rules are simple.

1. Any variable that is mentioned in the NEURON block is visible from hoc or Python.
2. All STATEs and PARAMETERs are visible from hoc or Python.
3. Any variable whose value comes from outside of an NMODL file is visible from hoc or Python. Examples include celsius, t, v, segment surface area or diameter, concentration or equilibrium potential or net current density for a known ionic species.

Intermediate variables, such as ionic conductances, are often not visible to hoc or Python because they are declared in the ASSIGNED block but not mentioned in the NEURON block. That's easy to fix--for example, suppose
gk = gbar*n^4
appears in the BREAKPOINT block and you want to see the value of gk. Add this statement
RANGE gk
to the NEURON block, recompile the mod files, and presto! your variable of interest is now visible.

Let me know if you have questions about a particular variable that belongs to a particular mod file.

monkeybusiness

Re: plot conductances through different channels

Post by monkeybusiness » Wed May 06, 2015 1:22 pm

Thank you very much, this helped me a lot!

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