The resulting coordinates are in refine_yb.inp, the electron density maps are in refine_yb_2fofc.map, refine_yb_fofc.map, refine_yb.hkl. The refine_yb.inp file is taken from the refine.inp input file, i.e., the only differences are the particular input parameter settings. Compared to the previous section, we do not perform annealing since the model has not undergone a major change (apart from adding the ytterbiums).
It is especially important toįirst obtain reasonable estimates for the ytterbium ionī-factors. Used for further refinement using the refine.inp task file. Not necessary to include a segid because the program will take any specified chainid and use it as the segid. The chain identifier has been changed to Y. This information can be obtained from the CNS topology fileĬNS_TOPPAR:ion.top. Name to YB3, these are the appropriate names for a ytterbium 3+ Note that the atom name has been changed to YB+3 and the residue The atoms name, residue name and chain idįor the ytterbium ions must be changed manually in order to give them unique resids and/or segids. We can merge the coordinates for the current model and the outstanding In order to generate a new model with the ytterbium ions included Sigma-A weighted difference map (at 7 sigma).įour large positive peaks are clearly seen. This can be seen both by visual inspection of the map but also in These areĬlearly separated from the other difference density peaks in the The Fo-Fc map shows 4 outstanding peaks (all above 20 sigma). This enables coloring of atoms by RSR, for example in PyMOL using the spectrum B option. The latter coordinate file contains the refined coordinates, but with the B-factor array set to the RSR values. Finally, the real space R (RSR) values and real space correlation coefficients (RSCC) are provide in refine_rsr.list and refine_rsr.pdb. These contain sorted lists of the positive and negative peaks in the respective electron density maps. In addition to these map files, the refine.inp task file also produces files with the extension ".peals". It can be read directly with Coot, by going to -> File -> Auto OpenMTZ (even though it is not an MTZ file). This is a CNS structure factor file that contains the Fourier coefficients of both the 2Fo-Fc and Fo-Fc maps. To convert the CNS maps to a format which can be read into O (you must have mapman installed ).įinally, the refine.inp task file produced a file with the extension ".hkl": refine.hkl Alternatively, they can be converted for to "omap" files for display with O, by using the command They can also be displayed with PyMOL when renaming the ".map" extension to ".xplor". These maps can be directly displayed with Coot. The refine.inp task file that was run in the previous section produced sigma-A weighted 2Fo-Fc and Fo-Fc maps:
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