|
| Python-based Hierarchical ENvironment for Integrated Xtallography |
| Documentation Home |
Molecular replacement with the Phaser GUI
Although 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.
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.  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; for instance, an ensemble might be made up of two chains, each of which is defined as a separate component using sequence files. 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 parameters
The "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, click the "Partial solution" button and select the result which you want to use as input (all previous Phaser jobs for the current project will be listed).  Reference
| |