The thing to do here is write a function that will take a bibtex key, and loop through your directories to find the pdf, and then return the full path to the pdf. Then customize the variable org-ref-get-pdf-filename-function to point to that function.

https://github.com/jkitchin/org-ref/blob/master/org-ref.el#L122

Out of the box, org-ref expects all the pdfs to be named key.pdf and to be in a single directory. That is partly due to this library https://github.com/jkitchin/org-ref/blob/master/doi-utils.el which downloads pdfs for you from a doi in that format.

John

-----------------------------------
Professor John Kitchin 
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803

On Wed, May 13, 2015 at 3:00 PM, Michael Giepen <mgiepen@uni-bonn.de> wrote:
Hello,

I just cannot get org-ref to accept various directories:

I tried

(setq org-ref-pdf-directory (quote (
"/home/mcg/thesis/library/folder1/"
"/home/mcg/thesis/library/folder2/"
"/home/mcg/thesis/library/folder3/"
)))


It would also suffice if I could include subdirectories of .../thesis/library/