Hi Shivesh, this is what I usually do: manipulate the structure in Coot and make publishable pictures in Pymol. To do this, just take the output from Autosol and run phenix.refine - it will produce the Xplor formatted maps that you can use in Pymol: % phenix.refine overall_best.pdb data.mtz where data.mtz is you data file containing Fobs, freeR flags (please do not confuse it with map coefficients file overall_best_refine_map_coeffs.mtz). By default it will produce two files (with .map extensions) one containing 2mFo-DFc and another mFo-DFc. You can also ask phenix.refine to produce any number of maps with other coefficients, for example 3Fo-2Fc, 3.3Fo-2.2Fc, etc. (for this you will need the latest version of phenix.refine currently available from CCI Apps). Cheers, Pavel. shivesh kumar wrote:
Dear all, I have an overall_best.pdb and overall_best_refine_map_coeffs.mtz file as an output file from Autosol.When I open this in coot I see the nice density.How can make a figure with density using pymol.Thanx in advance for the suggestions. Shivesh
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