I have updated tcl/tk to version 8.4.x (currently both ebuild are masked in
Looking at you ebuild, I suspect, that it can stop working.
Please test it with new tcl/tk, and fix it or close bug, if it works.
Steps to Reproduce:
For examples of tcl/tk version detection see:
see /usr/lib/tclConfig.sh, net-analyzer/rrdtool or media-sound/waif
pymol-0.86.ebuild works for me, even if "export TCL_LIBRARY=/usr/lib/tcl8.3" is set.
On my opinion this line is obsolete, especially for tcl8.4.