This task allows you to run PHASER for molecular replacement, up to and including building multi-subunit complexes, each component of which is constructed from an ensemble of structures. Optionally, the model can be:
• Put through a few cycles of REFMAC refinement (option selected by default)
• Symmetry matched to a reference PDB
• Processed by running a coot script (e.g. to fill partial residues in a model that has been chainsawed).
Reflections.(1.1) Hopefully self-explanatory.
Resolution range. Based on the expected LLGs, PHASER will try to search with the best resolution. You may override the maximum resolution that PHASER will attempt here.
Spacegroups. Where there is ambiguity, you can invite PHASER to attempt MR in more than one spacegroup: data reduction generally provides insight into the likely (but not certain!) pointgroup of the crystal, with less reliable guidance as to the space group.
Free R set. Although PHASER does not take advantage of a FreeR set, the optional REFMAC cycles which run at the end of this task should be given the FreeR data object that you are using for this crystal form.
• Position multiple copies of a search molecule in the unit cell,
• Build up a macromolecular hetero-oligomeric complex, and/or
• Exploit ensembles (multiple superimposed search models for a particular component of the asymmetric unit)This will cause the expanded search model dialog to be displayed, which provides control of the search models provided and the searches to be carried out
• The search model tree (2.1), and
• The search model detail (2.2)The "search model tree" shows an overview of the search model(s) that you have provided to the gui. This is made up of "ensembles", each of which is made up of "structures". What is displayed in the "search model detail" depends on what is selected in the search model tree.
Ensembles: An ensemble corresponds to a unit of structure that can be positioned in an MR run. It generally constitutes a "rigid body" that is likely to be common between the search model(s) provided and the structure for which the data have been collected. In the simplest case, an ensemble can comprise a single structure. If this works (which it will in > 90% of solvable cases), then more power to your elbow :-). When an ensemble is selected in the search model tree, the search model detail allows you to specify 1) The number of copies of the ensemble to search for in this run, and 2) A short one word alphanumeric identifier to associate with this ensemble.
Structures: If searching with a single structure in your ensemble fails, then it may be that adding more than one (superimposed) structure into your ensemble can help. The idea is that each superimposed structure will have different strengths and weaknesses, such that the search for the composite model (i.e. ensemble) may succeed where searching for each constituent structure fails. N.B. It is currently up to the user to superimpose the structures prior to giving them to CCP4i2. When a "structure" is selected in the search model tree, the search model detail allows/requires you to specify similar properties to those described above for a simple search model.
Adding and deleting ensembles and structures. To add an ensemble to the search, click "+" and select "Add ensemble". To add a structure into an ensemble, select the ensemble in the search model tree, click "+" and select "Add structure in ensemble". To delete an ensemble or structure, select it in the search model tree and click "-"
Searching for more than one copy. To search for more than one copy of an ensemble, you will need to have clisked "Show list" to reveal the Expanded search model dialog. The number of copies to search for in this run is set be selecting the relevant ensemble in the search model tree and then specifying the number to search fo r in the search model detail panel.