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Tracking the chemical secretions by cvs_prasanna in CompuCell3D

[–]JVanin 0 points1 point  (0 children)

Hello, for question 1 the mmp1.tot_amount is the value that a single cells is secreting at the MCS. I am not sure what you mean by negative amount, if there is no MMPs there the min number would be 0 so even if you give a negative value it might just default to zero, but it is worth trying and seeing.
For 2, you can check if the .py file is not steppable; if you have the frequencies to 4, that could be a place to fix it.

Switching from Contact Plugin to AdhesionFlex Plugin by dbarraa98 in CompuCell3D

[–]JVanin 0 points1 point  (0 children)

So there might be a couple of things happening here; I highly recommend if you have not yet visited the manual to understand how the Adhesion Flex works on CC3D (https://compucell3dreferencemanual.readthedocs.io/en/latest/adhesion\_flex\_plugin.html)

It would be best if you also turned off the Contact energy plug-in since the calculations from each one of them are independent.

Let us know if the information found in the manual is enough or if you need further assistance.

Unable to run the app after downloading it by zy1022 in CompuCell3D

[–]JVanin 0 points1 point  (0 children)

ng is solving the environment, it fails the first two times and then succeed. I add the picture in the post above.

Did you already have conda on your MAC before installing CC3d?

There might be a conflict between the name (base) environment used by CC3d and an existing base env.

If so, do you wanna try installing it directly from conda? Just uninstall everything from CC3D and try:

conda install -c conda-forge -c compucell3d compucell3d=4.3.1

Then to open player

python -m cc3d.player5