<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear Prof. Dr. Nathaniel Echols<br><br>thank you very much for this comprhensive explanation.<br><br>you payed my attention to something i did<br><br>in first round of refinment after molecular replacment<br><br>i used <br>1- output.sca<br>2- MR.1.pdb<br>3- MR.1.mtz<br><br>as input files<br><br>then i proceded with the output of this round of refinment to other<br><br>because you sayed ((do not use MR.mtz for refinement!*))<br><br>1- in this case should i start agian from the begining or it does not matter because .sca was included.<br><br>2- how can i know form the output files of this first run, if both .sca and MR.1.mtz were used or only one was used in refinment<br><br>thank you for your time...<br><br>Haytham<br>UdeM<br>Canada<br><br><br><br>Message: 10<br>Date: Mon, 13 Jun 2011 07:26:04 -0700<br>From: Nathaniel Echols <<a
href="compose?to=nechols@lbl.gov"><span class="yshortcuts" id="lw_1307979999_32">nechols@lbl.gov</span></a>><br>To: PHENIX user mailing list <<a href="compose?to=phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>><br>Subject: Re: [phenixbb] sca file & anomalous difference map:<br> understanding the story from the scratch, <br>Message-ID: <<a href="compose?to=BANLkTimC7sgKXyCE5Uzocq0OPH3KwJUpKQ@mail.gmail.com"><span class="yshortcuts" id="lw_1307979999_33">BANLkTimC7sgKXyCE5Uzocq0OPH3KwJUpKQ@mail.gmail.com</span></a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>On Mon, Jun 13, 2011 at 5:28 AM, Haytham Wahba <<a href="compose?to=haytham_wahba@yahoo.com">haytham_wahba@yahoo.com</a>>wrote:<br><br>> second Q?<br>> using output.sca (with scale anomalous option on) for molecular Replacment<br>> generate MR.mtz<br>> which shows F,SIGF in data labels under phenix.refine<br>><br>>
the generated (refine_data.mtz) shows:<br>> I-obs(+),SIGI-obs(+),I-obs(-),SIGI-obs(-)<br>><br>> what is going on in first and second run?<br>><br><br>Two different things going on here:<br><br>1) in Phenix, the MR programs (AutoMR, or the Phaser GUI) will take any<br>format input (amplitudes or intensities, anomalous or non-anomalous), but<br>the output will always be non-anomalous amplitudes in MTZ format. Note: do<br>not use MR.mtz for refinement!* The data are corrected for anisotropy, and<br>thus are no longer the experimental observations.<br><br>2) When you use an anomalous Scalepack file for refinement, phenix.refine<br>will output the same data (unmodified) along with your newly generated<br>R-free flags in MTZ format, which is what you're seeing. You should hold on<br>to this file and use it for all subsequent refinements, since you have now<br>refined against that particular set of R-free flags.<br><br>(A further
note: the Phaser GUI also writes out a data file in MTZ format,<br>which contains the original data, but modified to be non-anomalous<br>amplitudes. This is a Phaser quirk and can be ignored, but the data in that<br>file [which also ends in _data.mtz] are safe to use.)<br><br>third Q?<br>> i want to generate anomalous difference map using phenix.map<br>><br>> but when i use output.sca (with scale anomalous option: ON) as reflections<br>> file<br>> the data label show ((i-obs,sigma))<br>><br>><br>Unfortunately Phenix does not always treat labels the same between different<br>reflection file formats. In MTZ files there is a strict correspondence<br>between "column labels" and what you see in the various programs in Phenix,<br>so anomalous intensities with sigmas will always appear as something like<br>"I(+),SIGI(+),I(-),SIGI(-)". Scalepack files will always appear as<br>"i_obs,sigma" whether or not they contain
anomalous data. If they are<br>genuinely unmerged (as Tom explained), they will appear as<br>"i_obs,sigma,merged", which is a signal that Phenix will merge the data<br>internally.<br><br>how to convert this SCA file (if it is merged) to unmerged sca file to creat<br>> anomalous difference map for protein contains Br, Sn and Sulpher??<br><br><br>You can use the refine_data.mtz file for this - you should use a file with<br>R-free flags anyway. Alternately, use the French&Wilson program to convert<br>the intensities to amplitudes (while preserving the anomalous signal) with<br>correction for weak and negative values; it will also add R-free flags if<br>present. However, if you have already run a round of refinement with the<br>anomalous output.sca as input, phenix.refine should have output an anomalous<br>difference map along with the other map coefficients, so there is no need to<br>make it a separate step. (The GUI may not
be automatically opening this map<br>in Coot, however - so you might need to choose the "Open MTZ..." option in<br>the first menu of Coot, and load the file manually. I'll double-check this<br>when I get in to work.)<br><br>A general recommendation: if you now have an MTZ file with your anomalous<br>data and a set of R-free flags, start using this for everything you do in<br>Phenix, and ignore output.sca from now on - it will prevent confusion and<br>ensure that you don't end up with a new set of R-free flags by accident.<br><br>-Nat</td></tr></table>