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I have a problem with making unavailable document classes available for LyX on Mac OS X. I have installed LyX and MacTeX (latest versions). I can see the nature class in TeX information of LyX, but when I go to

LyX > Document Setting > Local Layout > Library > TeX > Root > texmf-dist > TeX > LaTeX > nature

I can see the nature.cls there but it looks like hidden files and cannot select it to make it active. I have checked this for available classes also, those are hidden too but they are working. I am confused now. May someone guide me on this please?

Thank you.

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It seems to me that you are confusing LyX layout files and LaTeX class files. nature.cls is a LaTeX class file, but LyX may not necessarily understand it out-of-the-box. LyX needs a layout file which acts as a bridge between LyX and the LaTeX class file. If LyX has a nature.layout (I'm not sure that it does), then all you need to do is install nature.cls for your LaTeX distribution, then in LyX do Tools > Reconfigure and restart LyX. Now LyX will be aware of the new LaTeX class.

If LyX has no nature.layout (I would suggest that you post this query on lyx-users), then it might be straightforward to come up with a layout file yourself. See LyX > Help > Customization > Sections 5.1 and 5.2.

Lastly, check the following question for simple step-by-step instructions to coming up with a new layout for LyX:

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