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The new code still uses a conditional statement. The INITIAL block sets both i_1 and i_2 to 0, so both of these variables will stay equal to 0 forever. This mechanism will deliver 30 nA for the first 30 ms, after which it will deliver 15 nA forever. That's definitely not what you want. Maybe I don't...

Thanks for following up with your solution.

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I needed (okay, wanted) to implement a version of interp_zyx.hoc and calc_rxc.hoc functions in Python Have you verified that your Python code properly calculates the locations of segment centers? One way to demonstrate this is graphically. For example, treat the x3d data from a real neurite as samp...

measure the ca++ concentration in the spine_neck during synaptic transmissions from the spine_head Then you need an "ion accumulation mechanism" for calcium. The simplest mechanisms consider only transmembrane flux through ion channels, might include buffering (most intracellular Ca is bo...

If you want to add the calcium current described by the code in cachan.mod to your model, put a copy of cachan.mod in the same directory as your hoc and ses files and then compile it (at nrn.readthedocs.io click on the item Guides in the left column, and in the page that pops up search for How do I ...

in this mod file, what should I write in Python code to give a value to weight Nothing. Do not change the NMODL code. The weight associated with an event is specified by the weight parameter of the NetCon that (1) detected the presynaptic spike and (2) delivers the event to the synaptic target mech...

While I’m making sure I’m using accurate algorithms for current in the spine_neck, I thought I might play around with creating an electric field from an electrode adjacent to the neck. So I added electrode point processor. Sorry, that's not something that can be used for extracellular stimulation. ...

Taking a peek at spine_neck current flow. Only two graphs show the time course of any current: right upper quadrant, which shows the ionic current through the neck's "pas" channels, and left lower quadrant, which shows capacitive current through the neck's membrane capacitance. There is n...

it should represent a current that is injected into the cell through an electrode So this really is to be similar to an IClamp. The name I chose for this particular mechanism is ExpIClamp because it delivers a current that decays monoexponentially with time. Its source code is in a file called expi...

One more comment: the purpose of some of these graphs is to verify that the extracellular stimulus is actually happening, and reaching the external surface of the model cell--and that it makes sense.

I am still learning how to describe mechanisms with NMODL. Then it will save your time and mine if I just implement something that matches your needs. As bad as most user-written hoc or Python code may be, the sad truth is that most user-written NMODL code is even worse because of NMODL's peculiari...

A lot of your code is good, but you're having to wrestle with many different, unfamiliar pieces. Also, not all documentation is as clear or complete as it should be. And, unfortunately debugging is complicated by the fact that, while matplotlib + NEURON is a powerful combination, it doesn't enable i...