createMultipleSpeciesModel() conflicts with thylakoids

[Elisabeth Bubna-Litic]

Hi,

I'm trying to build a multiple species model for a consortium of a photoautotroph (Synechocystis 6803,  SynCJ816) and heterotroph. However the added compartment 'lumen' conflicts with the thylakoids included in the photoautotrophic model, as both are labelled 'u'.

I have tried changing the thylakoid abbreviation by S_edit.comps(5) = {'t'}; but this ends up giving me a model without the thylakoid reactions entirely.

Any advice how to get past this? 

Thanks!

Elisabeth

PS: I'm using Matlab R2019a, Cobra Toolbox 3.0