The dump_pdb function consistently fails to write anything for me.
The problem presents a few different ways:
1) Blank file written. Even when I load a pdb into a pose and immediately dump it, the file is blank if written at all.
1) Segmentation fault. This happens most often, including when a blank file is created. The attendant message suggests that libstdc++.6.dylib is causing the problem, but I haven’t been able to tease anything meaningful out of that, except that the fault is caused by an attempt to access an invalid memory location.
2) Skipped entirely. I have a script which calls dump_pdb several times, and much of the time, it will finish successfully, but I’ll find two out of ten pdb files which were supposed to have been written (both blank, of course).
I haven’t been able to find any other problems–I can print residue data and fold trees, use movers, do scoring, make a pose from a sequence or a pdb, etc.