<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Nath,<div>Happy 2013!</div><div>Is it possible to use anomalous automatism also under GUI?</div><div>Will be the event of refinement of anomalous dispersion parameters f' and f" recorded in PDB file?</div><div>FF<br><div apple-content-edited="true">
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; ">Dr Felix Frolow <br>Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology<br>Tel Aviv University 69978, Israel<br><br>Acta Crystallographica F, co-editor<br><br>e-mail: <a href="mailto:mbfrolow@post.tau.ac.il">mbfrolow@post.tau.ac.il</a><br>Tel: ++972-3640-8723<br>Fax: ++972-3640-9407<br>Cellular: 0547 459 608</span>
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<br><div><div>On Jan 9, 2013, at 22:38 , Nathaniel Echols <<a href="mailto:NEchols@lbl.gov">NEchols@lbl.gov</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">On Wed, Jan 9, 2013 at 12:26 PM, Brennan Bonnet<br><<a href="mailto:Brennan.Bonnet@lightsource.ca">Brennan.Bonnet@lightsource.ca</a>> wrote:<br><blockquote type="cite">I hope everyone had relaxing holidays to begin the new year. I am back to work trying to refine anomalous groups using phenix.refine.<br><br>I have managed to merge my files so that my exptl_fobs_phases_flags_1_with_hl_anom.mtz now contains F(+), SIGF(+), F(-), SIGF(-).<br><br>Now I have a new problem which was not occurring before the break. Usually I check the box for "Anomalous groups", then select "Modify selections for: Anomalous groups" which brings up a screen for atom selection and definition of f' and f''. In the past, clicking on the View/pick button launches Coot for selection of the atoms. Sadly, now clicking on the View/pick doesn't launch Coot and instead crashes Phenix.<br></blockquote><br>What OS (including version) are you using, which Phenix installer did<br>you use (including the exact package name), and could you please send<br>me any error messages printed to the console? The built-in graphics<br>is spectacularly difficult to get working on some Linux systems, for<br>reasons I still don't understand. However, I don't think those<br>buttons ever launched Coot - maybe something that looks superficially<br>similar, perhaps, but it's obviously stopped working on your computer.<br><br>I do have a suggestion for working around this, but it's a pain to<br>use: a few weeks ago I added an option to set up the anomalous groups<br>automatically. You have to choose the "Edit parameters and run"<br>option when starting phenix.refine, then look for this parameter<br>(heavily condensed):<br><br>refinement {<br> group_anomalous {<br> find_automatically = False<br> }<br>}<br><br>Change that to True, and every atom heavier than P will be treated as<br>a separate anomalous group. (This is not necessarily the optimal way<br>to do it, which is why it's hidden right now, but it worked well for<br>the tests I've done so far.)<br><br>-Nat<br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://phenix-online.org/mailman/listinfo/phenixbb<br></blockquote></div><br></div></body></html>