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Ok, I actually had to table that question (I have a workaround for a conference next week) but will definitely readdress it after to figure out if its my code or a more general neuron issue. However, I have yet another related follow up question. Given that my spines are quite small, I have seen som...

A quick update: I tried splitting the Multi-Compartment Reaction into two separate ones so that I could use custom dynamics: ERin = rxd.MultiCompartmentReaction(ca[cyt]>ca[er],Jer_in,membrane=cyt_er_membrane,custom_dynamics=True) ERout = rxd.MultiCompartmentReaction(ca[cyt]<ca[er],Jer_out,membrane=c...

I have a follow up question to this. I am trying to initialize different calcium concentrations in different RxD regions (i.e. "cyt" and "er" as opposed to different neuron sections). I am following Neymotin et. al to do so ("Neuronal dendrite calcium wave model", 2015)...

Yes, nested shells would be awesome! I can get away with a single outer shell for now, as concentrations in that shell are what I'm most interested in, but nested shells would definitely be of interest and very useful. Thanks!

Is it possible to use the built-in RxD shells to support radial diffusion? I have only seen an RxD shell used as a membrane, and was wondering if they can also be used as segments of a section (i.e. multiple shells of a soma) as well.
Thanks!

This worked perfectly, thank you!

On a completely unrelated note (and I'm only posting this because Rob told me to post about it to keep the issue relevant...), are you closer to making RxD such that you don't have to restart Python every time you change an RxD-related parameter? That would be awesome!

What is the simplest way to allow a species to have different initial concentrations in different regions? Do I need to make two different "sub-species"? For example, I am working with a buffer "buf" that has a higher buffering capacity in the dendrites than in spines. I want to ...

Great - I just sent a toy model. Thank you!

Meanwhile I will look into your suggestions. One of the reasons I've been using python is to use the RxD module, but I'll look into making the morphology in hoc instead, and just using python for the RxD related parts.

I made an xpanel for my model so that I can demo it for my collaborators. I found the translation between Python and hoc not so smooth though so I wanted to see if I was missing something. It seemed like all I would need to do is use "h.xvalue" to update constants, and then have my own ini...

For anyone with similar questions - the issue was that I wasn't specifying the location along the section (as you would when referencing, say, the voltage). The following code does the job:

I have a follow up question. I can access the current at a given time now without a problem with: ica_car = spinehead.i_car However, I am still having trouble with the recording part. I suspect this is because the variable I reference is already specific to a section? But I am not sure. I am trying ...

Ted, thank you for your quick reply. I did mean current (from which I'm ultimately calculating concentration, hence my slip up).

This is very helpful - I will try the (safer) second method you mentioned. And thanks for the reference at the end as well.

Is there a way to record the charge* of an ion that flows through a channel defined as a mechanism? I am trying to record the calcium current that enters a spinehead through a calcium channel. I am doing the same for an NMDA channel, which is simple enough since it is a point process: ica_nmda = neu...

I have been getting numerical errors when simulating my model in RxD, and I think they are due to scaling within CVode. I've seen how to use the absolute tolerance scale multiplier for species specified in MOD files ( https://www.neuron.yale.edu/neuron/static/new_doc/simctrl/cvode.html#CVode.atolsca...