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Molecular Replacement Approach

 

In this section it is described how to use the Grafical User Interface to set up a new ReMo (Molecular Replacement) 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 Molecular Replacement only F and Sigma(F) are necessary; these two columns must be added from 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. It is possible also to perform a statistically based search on possible space groups.

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.
In this example Solphur and Phosphorus atoms have been added.
Some useful information is shown in the output window at the bottom of the form.


Tasks

The search models have to be provided in PDB format. It is possible to search for multiple copies of the given model by setting a number of monomers greater than one. There is the possibility to activate a procedure that uses the information on pseudotranslation eventually present in the target protein. The pseudotranslation vector is applied to search for the positions of two or more monomers with the same orientation.
The atoms not belonging to the sequence (hetero atoms) can be added to the search model (in default they are excluded from the search model). Moreover, the search model can be modified in order to be more suited for Molecular Replacement: it can be transformed in a polyalanine chain (to minimize the differences from the target protein) or portions of the sequence (those more similar to the target sequence) can be selected by the user by specifying initial and final residue number.
For the thermal factors of the atoms of the model three possibilities are allowed: to assign those contained in the PDB file, to scale them according to the overall thermal factor calculated by the Wilson procedure or to fix them to the constant value 20
Å2 for all the atoms.
The resolution range of reflections to be used in Molecular Replacement is automatically choosen by ReMo. In alternative, a user defined range can be defined.
It is possible to fix the rotation to be applied to the search model, so that only the translation and minimization step are executed by the program.

By clicking on Apply button, the Molecular Replacement process will start.


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