Check attached build log; I made sure that errors in doins will cause the ebuild to fail instead of faking proper merge, but you've got to find what is causing the build failure, most likely an automagic dep over a command that is not what they expect it to be. FYI /usr/bin/connect in the tinderbox is provided by net-misc/connect.
Created attachment 212910 [details] Build log
This version is obsolete and can be replace by sci-chemistry/pdb_extract-3.004 which includes the rcsb-data now.
*** Bug 339496 has been marked as a duplicate of this bug. ***
Already removed from tree.