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EDM/FreeLunch Approach

 

In this section it is described how to use the Grafical User Interface to set up a new EDM project. The user has to fill the following forms named:

 

The following buttons are used to set the default values or to apply the changes to the fields of the form. By clicking on quit button the project will be abandoned and the main window will be displayed. To access the next form, if some changes have been introduced, it is necessary to click on Apply.


General

In this form some information are displayed such as the Configuration directory, the User working directory and the Project name.
The user can supply a Job title for this project.


MTZ File

This form is used to get all the information  from an MTZ file. Once browsed, it is possible to view a short summary of the MTZ file.
For EDM or FreeLunch tasks F and Sigma(F) are necessary and also a phase-weight pair (P and W colums type); these columns must be added from available columns (using the Add pair button or Add button from the list of the available columns).

If necessary it is possible to specify a different space group. The user can just write the new symbol or to select it from a list.

On the bottom of this form information about symmetry and reflections is diplayed.
 


Cell Content

This form is used to supply the cell content. It is possible to specify the number of molecules in asymmetric unit.
The chemical content can be specified trough the weight or the number of residues or the sequence (in FASTA format);
the sequence can be stored in a file or pasted directly in the right part of the form.
Atoms external to the residues (ligands, heavy atoms, ...) should be added to make the structure solution simpler.
Some useful information is shown in the output window at the bottom of the form.


Tasks

The strategy to improve an initial map by EDM and FreeLunch. The recommended procedure is the default one. ILMILIONE has two possibilities for the EDM procedure. For the first option, it's possible to decide to use or not the Histogram matching, to select the Convergence Criteria to stop the procedure(the default criteria is Real-Rfree) and also how to extend the phase information(in the case when the observed reflections are not all phased) The second option, use an EDM procedure called FLEX (probably obsolete, but same time can bee useful...). This option can be run only in default way.
It is also possible to use extrapolated reflections (The FreeLunch procedure) for final map improving only. The extrapolated resolution is chose automatically by the program (the default) but it is possible to chose another value. The FreeLunch procedure can be run with or without the EDM procedure.

By clicking on Apply button, the EDM/FreeLunch procedures will start.


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