General information

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Sir2014    






Sir2014 is the latest product of the Sir family


Sir2014 is available as a stand-alone program or included in the package Il Milione (Burla et al., 2007).


The SIR (SEMI-INVARIANTS REPRESENTATION) package was originally developed for ab initio crystal structures solution by Direct Methods (DM). The REPRESENTATION THEORY, proposed by Giacovazzo (1977, 1980) allowed the derivation of powerful methods for estimating structure invariants (s.i.) and structure seminvariants (s.s.). The mathematical approach makes full use of the space group symmetry. SIR uses symmetry in a quite general way allowing the estimation and use of s.i. and s.s. in all the space groups.


Sir2014 is designed for the automatic ab-initio and non ab-initio crystal structure solution of small, medium and macromolecules according to the following scheme:


Ab initio phasing approach:

Defaults:

MDM is the default choice for small (up to 80 non-hydrogen atoms in  asymmetric unit ) and medium size structures (up to 300 non-hydrogen atoms in  asymmetric unit).

SDM is the default choice for electron diffraction data.

For proteins, if heavy atoms are contained in the unit cell, the default choice is the Patterson approach.


Non ab-initio phasing approach:


It is also possible to locate the anomalous scatterers or the heavy atoms when SAD/MAD data or SIR/MIR data are available. Data can be collected with X-Ray, electron or neutron sources. There is no limit to the number of reflections and to the number of atoms in the asymmetric unit. The maximum value allowed for |h|, |k|, |l| is 512. The maximum number of different atomic species is 18.


The program has been designed to:


Expert crystallographers will have a wide range of options to solve their crystal structures.


What's new


New features have been added to Sir2014 with respect to the previous version (Sir2011). Among them we quote:




A new program named Jav has been realized. It is not only a visualizer for models and maps, but it can be a useful tool to edit the model. It can be used or as an external program started from the main toolbar of Sir2014 or as an alternative to the classical visualization of the model by Sir2014. In the first case also the electron density map is drawn, in the second case the model can be modified and updated in Sir2014.


Moreover It is now possible to start Sir2014 using a .ins file under the following conditions:

The corresponding .sir file is automatically created.


The program


The program uses some CCP4 (Collaborative Computer Project 4, Daresbury Laboratory, UK) libraries in accordance with the CCP4 License Agreement (clause 2.1.2) and it is linked to external programs to face with protein structure solution (Refmac, Buccaneer, Nautilus, ARP/wARP, Phenix). The program uses FFTw  (Frigo and Johnson, 2005) and GTK libraries which are distributed under the GPL (GNU General Public License).


The program is available for Microsoft Windows, Linux and Mac platforms (see the Installing the program section).



Authors:


M.C. Burla(1,2), R. Caliandro(1), B. Carrozzini(1), G.L. Cascarano(1), C. Cuocci(1), C. Giacovazzo(1), M. Mallamo, A. Mazzone(1), G. Polidori(1)

(1) Istituto di Cristallografia, CNR, Bari, Italy.

(2) Dipartimento di Fisica e Geologia, Università di Perugia, Perugia, Italy.



Support:


E-mail: sirmail@ic.cnr.it



References:


Please refer to:

Maria Cristina  Burla,  Rocco  Caliandro,  Benedetta  Carrozzini,  Giovanni Luca  Cascarano,  Corrado Cuocci, Carmelo  Giacovazzo,  Mariarosaria Mallamo, Annamaria  Mazzone and  Giampiero  Polidori (2014),

Crystal structure determination and refinement via Sir2014

J. App. Cryst. submitted.





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