<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">I am finishing the final stages of refinement with TLS at 1.7 Å and want to begin some B-factor analysis. Also, I am setting up for a series of ensemble refinements. However, I am second guessing myself and have been finding that several basic questions that are not explicitly answered by the Phenix documentation.</div><div class=""><br class=""></div><div class="">(1) Just to be sure, I looked for the definition of what is written in the ATOM records of the output PDB file after refinement with TLS: residual B or total B (residual B + TLS contribution). I always thought the latter after refinement with TLS, but nothing was explicitly stated.</div><div class=""><br class=""></div><div class="">(2) Also, I have looked for it extensively in the Phenix documentation, I have not found any information on phenix.tls, even though in several places (e.g., phenix.ensemble_refinement), there are explicit references to phenix.tls: “If TLS is used the TLS components must be present in the atom records (see phenix.tls)” The information from just doing % phenix.tls -h does not give enough insight into options and there use.</div><div class=""><br class=""></div><div class="">Can someone point me to the right place to get these answers?</div><div class=""><br class=""></div><div class="">Thanks,</div><div class=""><br class=""></div><div class="">Michael</div><div class=""><br class=""></div><div apple-content-edited="true" class="">
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