<div dir="ltr"><div><div><div>Dear Nathaniel,<br><br>Thank you for your reply. <br><br>I am trying to run it with simulated annealing refinement. Because I am a new user I might have made some mistakes, but the error message popped up during the second cycle of twinning refinement at the beginning.<br>
<br></div>For the R-free, I agree that I could use the data generated by phenix.refine (because I generate the R-free in phenix.refine).<br><br></div>Sincerely,<br></div>Chen<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Mon, Apr 21, 2014 at 3:45 PM, Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov" target="_blank">nechols@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><div class="">On Mon, Apr 21, 2014 at 12:39 PM, Chen Zhao <span dir="ltr"><<a href="mailto:c.zhao@yale.edu" target="_blank">c.zhao@yale.edu</a>></span> wrote:<br></div><div class="gmail_extra"><div class="gmail_quote">
<div class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><div><div><div>But through the GUI, the program can run smoothly with twin refinement.</div></div></div></div></blockquote><div><br></div></div><div>It's not clear what you mean - the operation of the program should be no different on the command line versus the GUI. �All that matters is what method you use for the omit map preparation. �The default "simple" method ("iterative" might be a better name for it) is apparently incompatible with a twin law. � The "refine" or "anneal" methods will work fine with a twin law, but are far slower even if you have a big cluster. �What exactly are you trying to run?</div>
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<div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div>My only problem with the GUI is that I cannot find the the place to generate R-free flags in the highest symmetry for twinning refinement.</div>
</div></div></div></blockquote><div><br></div></div><div>The lattice symmetry option is already enabled by default. �However, if you already have R-free flags defined, it will not generate a new set; for this, you need to use the reflection file editor (GUI->Reflection tools). �However, if you're at the stage of generating a composite omit map, this usually means that you've already done refinement and have R-free flags already - in which case calculating maps or performing further refinement with a different test set is a bad idea. �If you want to change test sets in the middle of the refinement process, you should first do some simulated annealing refinement to un-bias R-free.</div>
<div><br></div><div>-Nat</div></div></div></div>
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