<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Dave,<div class=""><br class=""></div><div class=""> I’d suggest using the Phenix program phenix.map_to_structure_factors to convert a map to an MTZ file. This will generate HLs with reasonable FOMs. I suspect the problem with what you did before is that the FOMs are all 1, and this isn’t handled well by the MLHL target (this is a guess on my part). </div><div class=""><br class=""></div><div class=""> We don’t have a vector LS target in phenix.refine - we encourage people to use real space refinement for cryo-EM data.</div><div class=""><br class=""></div><div class=""> Cheers,</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Paul<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On May 15, 2021, at 10:29 AM, David A Case <<a href="mailto:david.case@rutgers.edu" class="">david.case@rutgers.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">I'm trying to use experimental phases derived from an cryoEM density map do<br class="">carry out reciprocal space refinement in phenix.refine.<br class=""><br class="">I used phenix.map_box to get the map coefficients, and then the CCP4<br class="">program chltofom (with the -colin-phifom flag) to create the HL coefficients<br class="">from F/PHI computed from the electron density map.<br class=""><br class="">1. If I ask for the mlhl target, I get quite odd target values, e.g. for a 2.9 Å data set:<br class=""><br class="">| normalized target function (mlhl) (work): -5862.311069 |<br class="">| target function (mlhl) not normalized (work): -6438670043.811632<br class=""><br class="">and attempted refinements more or less destroy my protein and increases<br class="">both the mlhl target value and the R-factors. Is there an example data set<br class="">I could access to help me find out what I'm doing wrong? (Using the ml<br class="">target, as suggested in DeMaio et al, Nature Methods 10:1102, 2013, seems to<br class="">work well, and has a postive target function, but seems sub-optimal if phase<br class="">information is available.)<br class=""><br class="">2. Is there a way to do a "simple" least-squares refinement, minimizing<br class="">sum( w_i * |Fobs_i - Fcalc_i|**2 ) where both Fobs and Fcalc are treated as<br class="">vectors? Does the ls target perhaps do this if use_experimental_phases=True?<br class=""><br class="">Usual apologies if there is some great tutorial on this that I've not found.<br class=""><br class="">...thanks...dave case<br class=""><br class="">_______________________________________________<br class="">phenixbb mailing list<br class=""><a href="mailto:phenixbb@phenix-online.org" class="">phenixbb@phenix-online.org</a><br class="">http://phenix-online.org/mailman/listinfo/phenixbb<br class="">Unsubscribe: phenixbb-leave@phenix-online.org<br class=""></div></div></blockquote></div><br class=""><div class="">
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