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Ted, your understanding is precisely correct about my plan for calculating the CSD. Althought I assume some symmetry about the cell distribution, so my CSD will vary along the depth of the cortex only. I am glad to know that the proc advanace() does exist and can be used. Looking forward to learning...

My model is run in parallel using python as interpreter. I need to save a vector of CSDs at every time step which results from summign currents for entire population of cells. So this vector is not a range variable and it is not associated with any particular cell. For serial implentation I used to ...

it works, thanks.

How can I access the segment area form Python? For example, I have a hoc objet L2_PC[0] and the the following does not work >>> h.L2_PC[0].dend[14](0.1).area Traceback (most recent call last): File "stdin", line 1, in <module> AttributeError: 'nrn.Segment' object has no attribute 'area' I ...

I have a python class which defines the population via a list class PL2PC: def __init__(self, morph_fname, n_cells): self.cell = [] for ic in range(0,n_cells): self.cell.append(h.L2_PC(morph_fname)) First question: Is this the proper way of defining a list of cells? Now the main question: I want to ...

thanks

I have problems with accessing a range variable defined in the custom mechanism when using python as a interpreter. However, when working directly in neuron I have no problem: I create a cell object L2_BC[0] from class where I insert a custom mechanism xtra.mod (see at the end of file for the code) ...

It looks like I was too quick to declare a victory. I am having issues with specifying the proper output format such that it would not stick adjacent elements in the vector together in the ASCII file. I have written the following 'save_results' procedure which prints each raw vector from the list at...

I am curious, what is the planned future for the NEURON? Are there new versions to be expected? Perhaps, new GUI?

Thanks

Since I did not get the reply to the last question, I figured that I must have asked for something too obvious. So I did figure out the colormap thing on my own. In case someone else needs to specify a custom colormap, you can use similar definition immediately after psh_v = new PlotShape(0) psh_v.c...

Ted, thanks for such a detailed response. I have looked at your code and used the .exec_menu("Show Diam") and .exec_menu("Shape Plot") commands to "activate" the desired Shape Plot features. It works! Perhaps, the next version of NEURON should include .exec_menu stateme...

I created the Shape plot of transmembrane voltage with specified custom variable scale and the specified "shape style". Then, I saved the session into the .ses file. However, upon reloading this .ses file the specified custom variable scale and the shape style are lost. The scale reverts b...

Ted, thanks for a quick response. This is a very nice and cleaver solution to my problem. However, I decided that since the units of distributed current and conductance cannot be easily changed throughout the NEURON, it would be best to avoid introducing custom units for some currents. Future user o...

Thanks Ted, I followed your suggestions to use List and the custom myrun() procedure. Very elegant indeed.

It seems that the NMODL allows to change some units but not the other. I have read the units tutorial http://www.neuron.yale.edu/neuron/static/docs/units/units.html but I am still confused. For instance, I was able to changed the units of conductance g to (mS/cm2), however, I cannot change the units...