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Molecular replacement with the Phaser GUI
OverviewAlthough the AutoMR wizard presents a user-friendly and automated frontend to Phaser, especially difficult cases may require finer control over parameters. The Phaser-MR GUI exposes all options available in the standalone command-line Phaser software, and allows use of additional modes besides MR_AUTO. It can, for instance, be used to search for individual components one at a time with modified parameters, or run each stage of the search (rotation, translation, packing, phasing+refinement) separately. This document only covers configuration of the Phaser GUI; for a detailed explanation of the various terms and search procedures referenced here as well as interpretation of results, consult the overview of molecular replacement in PHENIX, the Phaser documentation, or the Phaser WIKI. Some common user questions are discussed at the end of this section, and in the MR overview page. New users looking for a step-by-step introduction should read the Phaser-MR tutorial. Input files and mandatory parametersThe input section is similar to that of AutoMR, with separate sections for reflection data, search ensembles, and ASU components. Unlike the command-line version of Phaser, the experimental data may be any file format, and both intensities and amplitudes (with or without anomalous data) are allowed. The default mode is "Automated molecular replacement" (MR_AUTO); some of the other modes require only a subset of the parameters displayed.  All modes require a description of the search ensembles, either as PDB files (singly, or superimposed as an ensemble), or map coefficients in MTZ format (e.g. for phasing using a low-resolution EM map). Adding an ensemble does not automatically include it in the search; you may, for instance, supply several alternate ensembles for a chain, and instruct Phaser to try each in turn (see below). You must also define the composition of the asymmetric unit (ASU); this is usually done by supplying information for each chain as a sequence, mass, or type and number of residues. Alternately, you may give the fractional composition of each search ensemble, if known. It is also possible to additionally specify heavy atoms that contribute to scattering, but this is rarely necessary. Note that the composition data does not necessarily have a 1:1 correspondence with the search ensembles (see FAQ list below for details). Even if you are only searching for a single ensemble out of several (e.g. the protein in a protein-DNA complex), you must still supply the expected composition of the entire crystal. Finally, the "Search procedure" tab defines the steps in the MR search, selected from each input ensemble. Enabling more than one ensemble per search will result in the single best solution being used. You do not need to search for all ensembles at once, as described below.  Additional parametersThe "Output" button at the top of the window controls basic behavior such as the resulting file names and verbosity. All other parameters are set by clicking the "Other settings" button, which will open a large dialog window with assorted controls. (Like most such windows in the Phenix GUI, only a subset of basic controls may be displayed at first, but this can be changed by selecting options in the "User level" menu at the bottom of the window.) The available parameters will be slightly different depending on which mode you have selected.  Re-using previous resultsPhaser can be instructed to start from a previous partial solution; this does not use a partial PDB file, but rather the saved results of a previous run. For example, a two-part MR solution may be obtained by running in MR_AUTO mode to place one ensemble, then modifying the parameters, selecting the previous run as the partial solution, and searching for the second ensemble. To do this, select the result which you want to use as input from the menu labeled "Use partial solution from previous job" (all previous Phaser jobs for the current project will be listed in the menu). You may also run each mode separately, e.g. the fast rotation function followed by the fast translation function using the previous result, and so on. There are some restrictions on which modes may use which results, thus you may not follow a fast rotation function with packing analysis. Frequently Asked QuestionsThese are specific to the Phaser-MR GUI, especially the MR_AUTO mode. A much longer list of questions and answers is available on the MR overview page.
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