The only form of end-user PyMOL compilation we support on Windows is via Python's distutils facility.
Assuming that your system paths are set up correctly, distutils compilations will work fine with msvc6 -- no Makefile is required.
Your own c/c++ code should be built as a standalone DLL -- separate from _cmd.*, and you should use the Python interpreter to bring all of the native components together at runtime.
Warren L. DeLano, Ph.D.
. DeLano Scientific LLC
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. South San Francisco, CA 94080 USA
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