Molecular Replacement (MR) is the most popular method for solving protein crystal structures. Sir2014 uses REMO09 (Caliandro et al., 2009) for orienting and locating in the unit cell of the target structure the various monomers constituting the model. REMO09 breaks the six dimensional search into 3-dimensional rotation and translation steps as follows:
a) the space group of the model structure is assumed to be the symmorphic variant of the protein space group;
b) fitting between model and target structure is searched in reciprocal space by rotating the reciprocal lattice of the protein with respect to the calculated transform of the model structure;
c) the oriented model molecule is located in the target unit cell by using correlation functions calculated by Fast Fourier Transform.
The approach is purely probabilistic: the various figures of merit are all derived by means of the method of joint probability distribution functions.
REMO09 has been integrated into a pipeline including VLD, EDM, Free Lunch algorithms and the program Refmac.
If an external Automated Model Building program is available (Buccaneer, ARP/wARP or Phenix) the program starts it in an automatic way in order to supply a refined and interpreted solution.
A graphic interface is available in Sir2014 to work with Moleculare Replacement by means of the new item of the menu File :
In this window it has been specified, among others, the working directory, the procedure to use (Molecular Replacement) and the reflection file format (MTZ). If an Automated Model Building program is installed, it is possible to use it by selecting Buccaneer or ARP/wARP or Phenix.
Once clicked on Accept, it is possible to access the MTZ section:
Using this window it has been supplied the name of the MTZ file and have been selected the necessary columns (H K L FP SIGFP).
Once clicked on Accept, it is possible to access the Cell Content section:
In this example, the sequence (in FASTA format) has been supplied.
After these data have been accepted, the Solve interface is available:
Once clicked on Accept, it is possible to access the Run section:
When the program is over, the resulting structure is plotted in a preview window by Jav. It is possible to interact with the structure using the button Best Model
The list of directives is available here. The directives for %data in case of proteins are available here
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