WebPHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is a software suite for the automated determination and refinement of macromolecular structures … WebFeb 11, 2010 · Because of this, the starting B factors for further refinement are different from the ones used for motion analysis. PHENIX : Given the number of TLS groups you would like to use for each chain, TLSMD will generate a single file for input to PHENIX that describes the residues making up each group.

Tutorial: Molecular replacement, refinement, and …

Web>>> >> Yes, phenix.refine automatically does constrained occupancy refinement >> for atoms in alternative conformations. All you need for this is to have >> altloc identifiers in input PDB file. >> See slide #38 in the above link for example. >> >> Please let me know if you have any questions! >> Pavel. Web5.4 Model building and structure refinement. Molecular replacement provides the solution to the phase problem and it is now possible to calculate an electron density map, which should be inspected for secondary structure features. The quality of this electron density map depends on the quality of the initial phases, as well as the resolution ... meredith hager

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http://skuld.bmsc.washington.edu/~tlsmd/examples/1T3R/ANALYSIS/1T3R_REFINEMENT_PREP.html WebThe Phenix atom selection syntax Many of the programs in Phenix, and phenix.refine in particular, allow (or require) you to specify selections of atoms in a model. Common examples include: TLS (constrained anisotropic displacement) and rigid-body refinement groups Selections for isotropic versus anisotropic B-factor refinement WebMar 21, 2015 · For refinement in refmac or CNS or phenix; always use the original Mtz that has the original structure factor information. and use the pdb output from Molecular replacement or the heavy atom... meredith hagner gift wrapped christmas