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.
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.
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.
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.
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.
By clicking on Apply button, the Molecular Replacement process
will start.
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
20Å2 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.