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And here is the problem. Coot sharpens maps. The process has nothing to do with atoms. I still don't understand the question. Dale On 5/29/2014 3:17 PM, George Devaniranjan wrote: > 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 > <[email protected] <mailto:[email protected]>> wrote: > > 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 > <http://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/ iEYEARECAAYFAlOHszoACgkQU5C0gGfAG10olACdGxDCDaDI6jbaFXwCnYtc9xnO XkgAnjuoRavrGJW3FQHYfDrDuhp+qAwR =NRFM -----END PGP SIGNATURE-----
