<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="">Hi,<div class=""><br class=""></div><div class="">I can see that this could be slightly confusing! It's explained if you give the command "phenix.phaser --help", which returns the following:</div><div class=""><br class=""></div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><div style="margin: 0px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">Usage: </span></div></div><div class=""><div style="margin: 0px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">phenix.phaser is a multi-function command: it can launch either the binary</span></div></div><div class=""><div style="margin: 0px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">version, which accepts CCP4-style keyword input, or the Python version, which</span></div></div><div class=""><div style="margin: 0px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">uses the standard Phenix configuration file syntax. If called with no</span></div></div><div class=""><div style="margin: 0px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">arguments or the recognized command-line flags, the binary will be launched;</span></div></div><div class=""><div style="margin: 0px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">if a valid Phenix configuration file is provided on the command line, it</span></div></div><div class=""><div style="margin: 0px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">will run the Python version.</span></div></div><div class=""><div style="margin: 0px; line-height: normal; font-family: Menlo; min-height: 14px;" class=""><br class=""></div></div><div class=""><div style="margin: 0px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">CCP4 style:</span></div></div><div class=""><div style="margin: 0px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> phenix.phaser</span></div></div><div class=""><div style="margin: 0px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> phenix.phaser [--version]</span></div></div><div class=""><div style="margin: 0px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> phenix.phaser [--changelog]</span></div></div><div class=""><div style="margin: 0px; line-height: normal; font-family: Menlo; min-height: 14px;" class=""><br class=""></div></div><div class=""><div style="margin: 0px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">Phenix style:</span></div></div><div class=""><div style="margin: 0px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> phenix.phaser [params.eff] [<param_name>=<param_value> ...]</span></div></div><div class=""><div style="margin: 0px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> phenix.phaser —show_defaults</span></div></div></blockquote><div class=""><div style="margin: 0px; line-height: normal; font-family: Menlo; min-height: 14px;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""><br class=""></span></div></div><div class=""><div>So, "phenix.phaser" is a launcher that behaves differently depending on how you run it! The way you've run it, it is being run as a Python script that reads the input through Python and passes it, in the form of Python objects, to the Phaser routines. So, in fact, by the time the data gets to Phaser through the command-line flags, it's not being passed in the form of an MTZ file. That's why the log file doesn't record the name of the MTZ file either.</div><div><br class=""></div><div>I don't usually run Phaser this way myself, so I was actually surprised to see that this works! For molecular replacement, Phaser requires the mean F (or preferably the mean intensity), not the Friedel pairs. The script is using the phenix reflection file reader, which can do things like take F+ and F- and merge them to give Fmean, which is what is actually passed to Phaser.</div><div><br class=""></div><div>I hope that helps!</div><div><br class=""></div><div>Best wishes,</div><div><br class=""></div><div>Randy Read</div><div><br class=""><blockquote type="cite" class=""><div class="">On 19 Jan 2017, at 03:40, Murpholino Peligro <<a href="mailto:murpholinox@gmail.com" class="">murpholinox@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class="">When I do in the terminal:<br class="">phenix.phaser phaser.hklin="out.mtz" phaser.labin="F(+),SIGF(+),F(-),SIGF(-),merged" phaser.model="prot.pdb" phaser.mol_weight=14400 phaser.model_rmsd=0.3<br class=""><br class=""></div>my log file says it is using F and SIGF:<br class="">LABIN F = F SIGF = SIGF<br class=""><br class=""></div>Why it does not respect the labels provided? or..Am I doing something wrong.<br class=""><br class=""><br class=""></div>PS MR is successful <br class=""><br class=""></div>Thanks<br class=""></div>
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<span class="Apple-style-span" style="border-collapse: separate; font-variant-ligatures: normal; font-variant-position: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; line-height: normal; border-spacing: 0px;"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; 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; "><div class="">------</div><div class="">Randy J. Read</div><div class="">Department of Haematology, University of Cambridge</div><div class="">Cambridge Institute for Medical Research Tel: + 44 1223 336500</div><div class="">Wellcome Trust/MRC Building Fax: + 44 1223 336827</div><div class="">Hills Road E-mail: <a href="mailto:rjr27@cam.ac.uk" class="">rjr27@cam.ac.uk</a></div><div class="">Cambridge CB2 0XY, U.K. <a href="http://www-structmed.cimr.cam.ac.uk" class="">www-structmed.cimr.cam.ac.uk</a></div></span></span>
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