www.neuron.yale.edu

To follow up on the questions: I have a M1 Mac running Monterey (12.6.5 at the time) I installed NEURON using the dmg installer. Next time I'll use pip. I've had trouble with python environments in which I used pip to install things, so I've been trying to stick with using mamba to install python pa...

OK, I found the right documentation page.

Setting NRN_PYTHONEXE in the shell script that gets called when activating the python environment used for NEURON resolves the problem.

Apologies for all the posts.

Maybe I'm being dense. I was starting NEURON from the command line:
If I run
and then load file.hoc from the gui, I don't get the error.

Was it incorrect of me to try to start NEURON from the command line?

Well, I think I answered some of my question. This site https://docs.conda.io/projects/conda/en/latest/dev-guide/deep-dives/activation.html explains about per-environment activation and deactivation scripts. I have implemented that and have tried adding additional paths to PYTHONPATH when activating...

OK, here's another question. I have used mamba to set up a python environment for NEURON. If I activate this environment, start python, and import neuron all seems OK. If, however, I start nrngui and load an old (pre-python) NEURON model and start a ModelView, I get this error: oc>Traceback (most re...

Thanks for confirming. I recently needed to reinstall python and I thought that maybe I was still having issues.

Hi all! Does anyone have an idea why (https://www.neuron.yale.edu/neuron/static/py_doc/visualization/plotshapeclass.html) from neuron import h from matplotlib import pyplot h.load_file('c91662.ses') for sec in h.allsec(): if 'apic' in str(sec): sec.v = 0 ps = h.PlotShape(False) ps.plot(pyplot) pyplo...

I found the source for the install_name_tool suggestion, in case it helps someone sort this out further:

Ewen McNeill/ blog/ entry/ OS X dylib: care and feeding, http://ewen.mcneill.gen.nz/blog/entry/2 ... d-feeding/

Regards,

- Bill Kath

I recently got a new computer (Macbook Pro) and re-compiled NEURON with Anaconda python present. I ran into the problem of the missing libreadline.6.2.dylib when trying to "import neuron" in python, and came across this thread while searching for solutions to the issue. As previously repor...

The question is, what formats can Import3d handle properly despite the best attempts of those who create morphometric data files to screw things up. The chief problem with swc format is that it is not a completely specified file format. The most serious issue is lack of a uniform policy for how the...

Hi, What format should a swc soma have to convert properly to hoc using Import3D? The single point soma example at http://research.mssm.edu/cnic/swc.html gives a single point warning upon loading, and another upon exporting to the CellBuilder. The example at http://neuromorpho.org/neuroMorpho/dableF...

I'm not having any problem writing PostScript files at all. MPC TransPort T3100--laptop with 1.73 GHz Intel Pentium M, 1 GB RAM WinXP Pro version 2002 SP2 NEURON 6.2.1024 2008-06-13 launched neurondemo selected Pyramidal used PFWM to select the Shape plot (window in the lower left corner of the GUI...

Here's some additional information: It turns out that this problem only occurs if one clicks on the hoc file in the windows file manager (i.e., Windows Explorer) in order to run it. If one opens the nrngui first, moves to the proper directory, and then loads the hoc file that everything is OK. Mayb...

I even get the error if I type system("ls") So it seems that the problem is that the "system" command is broken, at least for this version (again, NEURON -- Release 6.1.2 (1927) 2007-12-30) on my machine (an IBM/Lenovo Thinkpad running Windows XP SP2). - Bill Kath Here's some ad...

It's Windows XP SP2, and the latest version of NEURON -- 6.1.2 (1927) 2007-12-30. The problem didn't go away by itself, but since it looked like a permission problem, I reinstalled from an administrator account (I don't normally work from an administrator account, only as a poweruser; since the NEU...