On Thu, Jun 16, 2011 at 12:27 PM,
phenix.install provide an option of --source which will force the source code installation. However, I can't find the source directory in the downloaded package.
That flag isn't really relevant, since all of the installers are either binary or source, never both. It's probably a holdover from earlier versions. There is a full source installer available, but it's less obvious on the download page because it's much easier to support binary installation. (Also, compiling from source takes forever unless you have a lot of processors.) That said, we stopped removing source code from the binary installers a while ago, so they should still have everything you need to recompile the sources in-place.
More specifically, I was looking for the "extract_bond_params" subroutine under "cctbx_project/cctbx/geometry_restraints/". It was defined in "bond.h", and looks like its already been pre-compiled into the binary. So, is there any way I can recompile this C/C++ code?
Something like this would probably work: cd $PHENIX/build/$PHENIX_MTYPE libtbx.configure phenix libtbx.scons (And if you have, say, 8 processors, add the argument "-j8" when running libtbx.scons to speed it up.) -Nat