Thank you for your reply, Dale. Let me rephrase the question: Essentially I want to use COOT's Calculate-->map sharpening
but only use the backbone atoms in the process. On Thu, May 29, 2014 at 6:08 PM, Dale Tronrud <de...@daletronrud.com> wrote: > -----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----- >
