www.neuron.yale.edu

Hi there, Noticed that "https://neuron.yale.edu/neuron/nrnpubs" is a Page Not Found... should point to-> https://www.neuron.yale.edu/neuron/publications/biblio Also, unless you have a way to automate this or "Crowd source it" this may be a fantastical idea, but I wondered if you ...

Hi so in a previous post I mentioned that I had been defining a no go zone in the middle of my cells by creating a region with zero diffusion. I can't get that to work, so next I have tried using h.pt3dremove() to "bite" a nucleus out of the cell. That doesn't work for me: h.pt3dremove(int...

Sorry for the delay in my reply to your reply! Firstly, the nthreads thing; I am just wrong. There seems to be an optimal number of threads. Might work out to be the cores or something I don't know, but I was wrong to say it slowed it down of course. Must of been changing several things at the same ...

Hi there, is this my understanding or an issue.. If I create my mode in 1D, my species.nodes have a diffusion value node.d that I can either read or write to... ...but if I do the same with 3D models, I find that node.d is unread or writable? Well it seems to be a string not a float value anyway. I ...

Sorry, my RXD models use pointers to gate channelbuilder channels with temperature not Ca[er]. So that approach may work with your problem, using Ca[er] instead of temperature... but look I am just a regular NEURON user, not an expert, so lets see what the experts say :-) If "your" method ...

...Interesting, I didn't realise that was a feature of RxD, my Markov channel models are built with Channel Builder and then imported into my code (that includes RxD). I will interested to hear the answer to this enquiry also.
Regards

Ah ha!!
so now I loaded python with simply successfully brings up the menus!!

In fact still no go through spyder, but I am sure I can work it out from here!
Thanks!
..,.and so to bed (UK)...
R.

I am sorry, I don't know the ldd `which python3` instruction, but it returned this linux-vdso.so.1 (0x00007ffdbc3fb000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007ff4e8c09000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007ff4e8818000) libdl.so.2 => /lib/x86_64-linux-gnu/...

Thanks, cp hoc.cpython-37m-x86_64-linux-gnu.so hoc.so # be sure to make a copy of hoc.so first!!! cp hoc.cpython-37m-x86_64-linux-gnu.so hoc37.so so copying that file to those two alternative hoc.so and hoc37.made no difference that I can see. However: ldd /usr/local/nrn/lib/python/neuron/hoc.cpytho...

Thank you, so yes tried these: firstly python3 -v Gives: import _frozen_importlib # frozen import _imp # builtin import '_thread' # <class '_frozen_importlib.BuiltinImporter'> import '_warnings' # <class '_frozen_importlib.BuiltinImporter'> import '_weakref' # <class '_frozen_importlib.BuiltinImport...

Thank you for your reply, So firstly, no NEURON does not work from a regular python prompt. In fact it gets less far, failing to find neuron at all, because I only set PYTHONPATH within the PYTHONPATH preferences of Spyder. Same as I do on my mac. Secondly, the PYTHONPATH I am using on these UBUNTU ...

I have Neuron successful installed on OSX and Windows 7/10... but I have failed with two separate linux (Ubuntu) machines now and so I think it is time to call for help. I don't have much experience with linux, so it is highly probably I am being an idiot. I have been trying off and on for days, tho...

Yes, sorry I realise this. That is the only way I know to turn it on and off. The post says "Instead of using... an argument of 1 or 0 to turn ..., it is better to call cvode_active() with the appropriate argument....". I thought I might be missing the alternative arguments to 1 and 0. Sor...

Sorry Ted, I am doubtless being really slow here; but I keep reading the first line of this post over and over and don’t follow. If one should not use cvode.active(1) etc., please can you give an explicit example of the “appropriate argument” one would use? Thanks, sorry... just want to be sure I am...

Thank you yes that nails it!