Tls anisotropic refinement
WebApr 10, 2013 · Section snippets The empirical model for computing the atomic cross-correlation by using TLS parameters. Based on the TLS model (Schomaker and Trueblood, 1968), we represent the correlation between isotropic displacements of an atom as a function of the spatial coordinated and the TLS parameters, defined by Sternberg et al. … Webis described that analyses these 21 TLS rigid-body displacement parameters and their relation with the principal axes of the rigid body, from the output of the segmented anisotropic...
Tls anisotropic refinement
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WebJan 5, 1998 · Crystal structures of turkey egg lysozyme (TEL) and human lysozyme (HL) were refined by full-matrix least-squares method using anisotropic temperature factors. The refinement converged at the conventional R-values of 0.104 (TEL) and 0.115 (HL) for reflections with Fo > 0 to the resolution of 1 ... Macromolecules WebNational Center for Biotechnology Information
http://www.csb.yale.edu/userguides/datamanip/ccp4/ccp4i/help/modules/refinement.html WebAny! Resolution only affects level of detail: • Resolution < - full anisotropic refinement • Resolution ~ - marginal for full anisotropic refinement. But can do detailed TLS, e.g. Howlin et al, Ribonuclease A, , 45 side chain groups; Harris et al, papain, 1.6Å, 69 side chain groups. • Resolution -⇒model molecules/domains rather than ...
http://www.uoxray.uoregon.edu/local/manuals/ccp4-5.0.2/ccp4/html/refmac5/usage/tls_usage.html http://thelightsource.com/
WebMay 8, 2007 · Iterations of normal-mode-based anisotropic B factor refinement, TLS, positional refinement using REFMAC5 ( 34) in the CCP4 Suite ( 35 ), and manual adjustments using O ( 36) were carried out until convergence. The starting point of our refinement was an unpublished all-atom model of FTCD.
WebDec 14, 2015 · Typical procedure: Specify TLS groups (currently via TLSIN file). Use anisotropic scaling. Set B values to constant value Refine TLS parameters (and scaling parameters) against ML residual. Refine coordinates and residual B factors. Slide 17 Slide 18 Initial TLSIN file TLS Chain O NAD binding RANGE 'O 1.' 'O 137.' ALL RANGE 'O 303.' 'O … graff trucking natrona heights pahttp://my.yetnet.ch/dergutemensch/crystallography/refinement.htm china buffet avon parkhttp://my.yetnet.ch/dergutemensch/crystallography/refinement.htm china buffet beebe arWebJul 2, 2012 · >TLS and the next one without TLS then in the second run anisotropic >ADPs will be converted to isotropic automatically. This is done by >phenix.refine to prevent accidental refinement of individual >anisotropic ADPs in such cases. The keyword and threshold are: >switch_to_isotropic_high_res_limit=1.5. >>Pavel graff truck center saginaw miWebSimulated annealing (SA) is most useful early in refinement, when the model is far from convergence. Manually built models, or MR solutions involving significant local conformational changes, are common inputs where SA can improve over simple gradient-driven refinement. It is generally less helpful later in refinement, and/or at high resolution. china buffet bay city miWebJan 1, 2003 · TLS refinement is designed to provide a simple description of anisotropic displacements when the resolution is not good enough to justify refinement of atomic … graff throw up lettersWebOct 30, 1991 · The anisotropic displacements of selected rigid groups in bovine ribonuclease A have been refined from X-ray diffraction data by the application of the rigid-body TLS model. The rigid groups chosen were the side chains of tyrosine, histidine and phenylalanine and the planar side chains of aspartic acid, glutamic acid, glutamine, … graff trucking