-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi,
Your question is vague so I will try to guess what you want. First, an MTZ file is just a container for data in reciprocal space. It can contain intensities (merged or unmerged), amplitudes, sigmas, phases, figure-of-merits, Hendrickson-Lattman coefficients, flags, or pretty much anything that is described by hkl. It does not contain maps or coordinates because they are real space items described by xyz. One use of the MTZ format is to contain amplitudes and phases which, when Fourier Transformed, become a map. You can't just say "I have an MTZ file" and expect someone to know what that file contains. Now we come to your Q1. Since I don't know what your MTZ file contains, and MTZ files cannot contain atoms I'm not sure what you want. One possibility is that your MTZ contains the amplitudes and phases of an electron density map and you want to mask out all the density except for that close to a backbone atom. That can be done, but it is complicated and I don't want to attempt to explain it without knowing for sure that is what you want. Since you are feeding a PDB file that contains only backbone atoms into Refmac hoping for a map, perhaps you just want a calculated electron density map for your backbone atoms. This can be done with the CCP4 program SFALL. I'm looking at www.ccp4.ac.uk/html/sfall.html#files_generate_atom_map It looks like Example 6 does what you want. You only want to run REFMAC is you want a complicated map like mFo-DFc or 2mFo-DFc which are difference maps used to evaluate a model during refinement. If you just want to calculate a map from coordinates, or structure factors from either a map or coordinates SFALL does the trick. If you really want to take an existing map and mask out certain features, that's a different kettle of fish. Dale Tronrud On 5/29/2014 2:20 PM, George Devaniranjan wrote: > Hi, > > > This is really 2 questions, one related to the other coming from > someone who is just starting to learn/use CCP4/COOT so this > question might sound rather naive. > > > Q1) > > > I have a MTZ file and I want to generate a another MTZ from it but > limited to the backbone atoms only. > > (Similar to FFT with all atoms in PDB file) but I need a MTZ file > since I want to use the map sharpening tool (B factor attenuation) > in COOT. > > I tried using REFMAC with the input PDB only having the backbone > atoms but it fails due to the inconsistency between the input MTZ > and input PDB. > > Any other way I can generate a truncated MTZ? > > > Q2) > > Once I use the map sharpen tool, could I save (as MTZ ) the new > sharpened map? > > > Thank you. > > George > > > -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (MingW32) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlOHr8sACgkQU5C0gGfAG12QTwCfQVcEMCc8GlZlPLkDBGhYizQE p2sAniirY6S7RqJ0ae9PhVokAPr9XWfT =CMOz -----END PGP SIGNATURE-----
