If you bundle your own mini-ccd file, you could fix the warning by copying the SO4 entry from a full compounds.cif file. The format is not that complicated, simply copy/paste the part from components.cif starting at data_SO4 until the next data_ line.despite the incomplete subset, it allows the test to pass, allowing the python-biopython build to go through. I should be able to upload a fix shortly. 🙂