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The PHENIX Wizards are easy to use. Select the Wizards tab on the PHENIX GUI and then double-click the wizard that you want. The wizard will guide you and ask for necessary inputs. The wizard is green when running, blue when stopped, and red if an error has occurred.
The wizards are:
-AutoSol -- Structure solution by MAD/SAD/MIR
Inputs: X-ray intensities; sequence file, scattering factors
Output: experimental phases, preliminary density modification and model
-AutoMR -- Molecular replacement
Inputs: MTZ file with FP, SIGFP; one or more ensembles of aligned structures to place in cell.
Output: Ensembles placed in cell.
-AutoBuild -- Iterative model-building and refinement
Inputs: MTZ file with FP, SIGFP, optional phases/HL coeffs or model
Output: Partially-refined model and density-modified phases
-LigandFit -- Ligand fitting
- Inputs: PDB file with ligand in any stereochemically allowed conformation; MTZ file with FP;
- PDB file with partial structure without ligand; number of copies of ligand to find
Output: Copies of ligand fitted to difference density
-ImportRawData-- Importing intensity or amplitude data
Inputs: MTZ, sca, ref, or other file with amplitudes or intensities;
- Output: Data converted to sca or MTZ format and scaled so largest value
- fits in sca format
Navigating with Wizards
There is a PAUSE button on the Wizard. If you hit this button the wizard will try to stop nicely and wait for inputs. The Wizard will resume where it stoppedif you hit RUN. When the Wizard is stopped you can open the Wizard input page (the icon with 4 lines at the upper left corner of the Wizard) and set variables or navigate to other steps in the Wizard.
There are CONTROL, SET VARIABLE and NAVIGATE tabs at the bottom of the Wizard input page. When you hit RUN or SAVE AND CONTINUE the values you set in these tabs are applied.
You can navigate the steps that a Wizard carries out using the NAVIGATE tab. Any step that is currently allowed will be listed. You can go back and repeat a step (changing your choices, perhaps) and the Wizard will carry on from there.
You can use the CONTROL tab to tell a Wizard to work in Automatic mode (only ask questions if essential) or Manual mode (allow many inputs), or to change this at any time the Wizard is stopped.
The SET VARIABLE tab will tell the Wizard to put up an input window with the current value of a parameter and let you change it.
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