Stoicheiometric Consistency

[AnnyMais03]

Question

Hello, I have made a model of a pseudomonas strain using carve me, I have balanced out the reactions and fixed the fluxes but I have 0% in stoicheiometric consistency. Can you help me fix this?

[Midnighter]

Hi,

First of all, the stoichiometric consistency is a binary measure, so it's either 0 or 100%.

What are your mass and charge balance test results looking like?

[AnnyMais03]

Hello, sorry for the late reply, all my reactions except from sink and exchange reactions are balanced.

[Midnighter]

In that case, I would think that the one of you exchange, sink, or other artificial reactions is not recognized as such. If you are comfortable doing so, you can look at the code for the test case and try out the utility function for detecting such unbalanced reactions on your model directly.

[AnnyMais03]

my growth reaction also seems very unbalanced, should I fix this one? although I am not sure how to balance this one.
also I am not familiar with how to do what you say with the utility function

[Midnighter]

Biomass reactions are unbalanced by design, and so are non-growth associated maintenance reactions (NGAM). It's just a matter of identifying and ignoring them correctly.

Do you have someone in your lab or environment familiar with Python who can help you?