Chemtool always segfaults upon startup in Fedora 16. According to upstream http://ruby.chemie.uni-freiburg.de/~martin/chemtool/chemtool.html "chemtool-1.6.13 (December 24, 2011) This release consists mainly of fixes for bugs that were exposed by recent versions of the gcc compiler, linker and X11 libraries - failures to build the program or to enable translations with the generated Makefile, and most importantly a bug that led to an immediate crash at startup on at least Fedora 16."
chemtool-1.6.13-1.fc16 has been submitted as an update for Fedora 16. https://admin.fedoraproject.org/updates/chemtool-1.6.13-1.fc16
Package chemtool-1.6.13-1.fc16: * should fix your issue, * was pushed to the Fedora 16 testing repository, * should be available at your local mirror within two days. Update it with: # su -c 'yum update --enablerepo=updates-testing chemtool-1.6.13-1.fc16' as soon as you are able to. Please go to the following url: https://admin.fedoraproject.org/updates/FEDORA-2012-3721/chemtool-1.6.13-1.fc16 then log in and leave karma (feedback).
chemtool-1.6.13-1.fc16 has been pushed to the Fedora 16 stable repository. If problems still persist, please make note of it in this bug report.