no density on the anchored proteins
Hi, I am using phenix.refine to calculate the map of the 50S RNA (1FFK). It is weird that there is no density on the anchored proteins even for the Fc map. Following is the code I am using: phenix.refine ${f}.pdb ${f}.mtz main.number_of_macro_cycles=0 xray_data.high_resolution=${res} xray_data.r_free_flags.generate=True export_final_f_model=mtz Thanks for any advice! Hailiang
Hi Hailiang,
I am using phenix.refine to calculate the map of the 50S RNA (1FFK). It is weird that there is no density on the anchored proteins even for the Fc map. Following is the code I am using:
phenix.refine ${f}.pdb ${f}.mtz main.number_of_macro_cycles=0 xray_data.high_resolution=${res} xray_data.r_free_flags.generate=True export_final_f_model=mtz
using phenix.refine is possible but not the best way of calculating a map. In the example above you need to have main.number_of_macro_cycles=1 (not 0) otherwise you do not do bulk-solvent correction and anisotropic scaling and therefore the map quality you will be getting will range from poor to extremely poor. Also, export_final_f_model=mtz is not really necessary: the maps will be generated automatically and output into *.mtz file. And if you specify main.number_of_macro_cycles=1 you also need to make sure that no refinement is going to happen by using "strategy=none" A more streightforward way of computing a map is to use the tool that is specifically designed for doing this, phenix.maps: http://phenix-online.org/documentation/phenix_maps.htm Good luck! Pavel.
Hi, 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. 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? I have some limited knowledge of boost.python, and maybe thats why I didn't find the solution, but I appreciate for any quick instructions! Thanks! Best Regards, Hailiang
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
participants (3)
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Nathaniel Echols -
Pavel Afonine -
zhangh1＠umbc.edu