Hi Wolfram,
Sorry for the issue, are you using a recent build of CCTBX? Can you try these steps?
1) cd <CCTBX directory>
2) rm -fr conda_base
3) python modules/cctbx_project/libtbx/auto_build/bootstrap.py base --builder=phenix --use-conda
It basically recreates the dependencies directory. It's using conda, so it should take less than 5 minutes. If you are using conda, you will need conda version 4.4 or greater.
Let me know if that doesn't solve the problem. Thanks!
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909