Hi Adiphol, > electron density map. First, I only have .mtz file at a hand so could > anyone suggest me how can I convert this .mtz-file to the map or any file > that support to PyMol. Second, this is quite not so involve with the PyMol > program - sorry, if I would like to have an electron density map from > reported PDB structure, where can I get it from? I only know that I can > get the .mtz-file from EDS. Thank you very very much for any of your > suggestion.
1. An mtz file stores reflection data, so you'll need to pick which amplitudes and phases to use to calculate a map (which will depend on which type of map you'd like to calculate). Assuming you're using ccp4 programs, then fft will calculate a map from an mtz file; you will probably also want to use mapmask to extract a region of the map covering your model. Just a side note, this isn't really a conversion; there's different information stored in reflection data vs a map. 2. If the authors deposited their amplitudes along with their structure, then you can download them from the pdb in cif format (which can be converted to mtz). You'll have to calculate model phases (and possibly deal with weighting) before calculating a map (most likely you'll want Fo alpha_c or 2Fo-Fc alpha_c, but this'll depend on what you're trying to do). Their migh be an easier way with EDS, but somebody else'll have to chime in there (I haven't used it). Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
