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There is some discussion about how segment areas and volumes are calculated at: https://www.neuron.yale.edu/neuron/static/py_doc/modelspec/programmatic/topology/geometry.html#d-specification-of-geometry To say what hines said another way: in your first case, you're defining a tapered shape while the...

Most likely that means that either Python is not installed, or it is installed but NEURON can't connect to it (likely a path issue). You're free to program NEURON models in HOC or Python, but to use the rxd module, Python must be installed and loadable by NEURON To check for this, check the return v...

Are you using a fixed time step or variable? I assume variable step will choose time points at the beginning and end of each current change... And thus you would see the current injection having an effect. If fixed, what is dt? Note that for fixed step, the default timestep (0.025 ms) is longer than...

Doesn't solve the mystery, but...

Assuming the morphology is not changing with successive runs, you could load it once before entering the loop, and see this particular issue entirely

You can probably do what you want by using Vector.play . In brief, Vector.play allows you to use two Vectors (one listing time points and one with the values) to control an arbitrary memory location (e.g. a current, or in your case a variable in a MOD file). Example that plays a stimulus into the in...

Currents of the same type from different mechanisms add.

You can test this yourself by creating two trivial mod files that generate a constant current, and measuring the current when one vs both are inserted.

If you're working on a HOC kernel, I also encourage this... But: (1) Consider teaching in Python instead of HOC. That's what we do for the official NEURON courses. The Python programmer's reference is not only the default version, but it's also more up-to-date and has more examples. (2) As long as y...

Upgrade to NEURON 7.6.1 (the current release version) to use Python 3.7.

Older versions of NEURON are not compatible with Python 3.7.

My mistake, sorry. I made that post on my phone without checking it.

You're right. diam3d is ready only. Use pt3dchange to set the diameter: the

Use diam3d instead of diam, and forall sections adjust indices from 0 to n3d -1, inclusive. EDIT: The idea is right but this code is wrong. diam3d is read only and diameters most he changed with pt3dchange. See my next post. forall { for (j = 0; j < n3d(); j+=1) { diam3d(j) = diam3d(j)*1.0 } } There...

Not exactly what you're looking for, but check out Rempe and Chopp 2006, A Predictor‐Corrector Algorithm for Reaction‐Diffusion Equations Associated with Neural Activity on Branched Structures. In particular, section 8 is entitled "spatial adaptivity." They demonstrate this on a morphologically deta...

Every segment corresponds to a location where membrane potential is computed. In particular, this is a distinct concept from the 3D shape of the cell. Segments can contain arbitrarily many 3D points and the surface area, etc for that segment will be computed correctly. In Python with NEURON 7.5+, yo...

In addition to the text editors that ted mentioned, consider Visual Studio Code. It's free and runs on all platforms. More importantly for NEURON: the first time you open a HOC or MOD file, it will prompt you to install an extension that provides NEURON syntax highlighting.

Ion channel genealogy lists 524 NEURON calcium channel models, not all distinct. If you click that link, you'll see them grouped by similarity. Clicking on an individual model (dot) in the figure will load it in the channel details pane on the bottom right. The info tab (opened by default) contains ...

Note that Hodgkin and Huxley considered only the role of sodium, potassium, and leak currents. In particular, it follows that the hh mechanism does not generate a calcium current.