Getting Started

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Let's use, as an example, a simple small molecule (loganin) supplied with the program. To load it:





Select the input file for the test structure: loganin.sir





It is possible to visualize and to edit this file using the  button.

The file loganin.sir contains the minimal input instructions to make Sir2014 run. Only few commands and directives are mandatory: pay attention to structural info (i.e. cell parameters, space group, ...), chemical composition (i.e. chemical content in the unit cell, ...) and experimental data (i.e. reflection file, type of data - structure factors or intensities, ...).




To start the program, click on  button.


At the end of the run, Sir2014 shows the "best" model of the structure; the final Rf%  = 15.12  is quoted in the status bar (at the bottom of the program window).


To modify the style go to menu item “Settings on the main toolbar and select Plot Styleoption.



Change the plot style for the model (i.e. Bubbles) and accept it (click on Accept or OK buttons).




Add the labels (chemical species and progressive numbers) to the atoms of the model clicking on Labels button:



The new plot is the following:




Atoms C1, C4 and C15 (inside red circles) show wrong labelling, they should be oxigens.

Change the labels for C1, C4 and C15: go to menu item “Modify” on the main toolbar;  select Model option and then Change species option.





Select the atoms to change the atomic species and choose the correct chemical element (click on the related button).



Click on Intensity bar chart chemical species button to show the intensity histogram for the atoms of the model  and the associated atomic species.





Start the refining process: go to menu item “Refine” on the main toolbar and select LSQ option: the Least Square Refinement Menu will be opened.




Go to LSQ sub-menu item “General and set the LSQ options (i.e. Full Matrix,  sigma(Fo) cutoff, number of LSQ cycles, weighting scheme, ...).

Be careful to the ratio Observation / (number of refining) Parameters. For this example, the ratio value (20.69) is high enough to lead to a reliable LSQ refinement; otherwise if this value is lower than 10, the refining process could be meaningless.

Accept the choices clicking on    button; the LSQ refinement will start.

The first step (after the changes of atomic species when necessary), is an isotropic LSQ refinement for all the model atoms (only coordinates and isotropic thermal factor will be refined: four parameters per atom) plus the scale factor.




Updated Rf% value can be found in the status bar (Rf% = 12.58). The new Rf% value is lower than the previous one (Rf%  = 15.12). This mean that modified labeling is correct; otherwise the new Rf% value should be larger than the previous one.




To improve the reliability of the atomic model, we have to apply a thermal anisotropic LSQ refinement. If necessary it is possible to fix some specific atomic parameters.

Go to LSQ sub-menu item “Modify Atoms Parameters; choose the filter (i.e. All) and select the option (i.e Set Isotropic: No). Atomic coordinates and anisotropic thermal parameters will be refined: nine parameters per atom).



Change the plot style for the model:  go to menu item “Settings and select Plot Styleoption: select Radius proportional to Thermal Factor (atom thermal ellipsoids will be plotted, proportional to anisotropic thermal parameters). Updated Rf% value can be found in the status bar     (Rf% =  8.54). The Rf% value is clearly lower than the previous one




Complete the model by adding hydrogen atoms.

Go to menu item “Refine, select Hydrogens option and then Automatic option (hydrogens automatic generation).





The next step is to start a new LSQ refiniment. Updated Rf% value is shown in the status bar (Rf% =  6.74). This Rf% value is low enough to suggest that the atomic model is correct.




Using Jav, it is possible to visualize the electron density map and the related model; click on the button   in the main toolbar:



It is possible to compute some quantities (distances, angles, torsion angles, ...) trough the "Geometry" menu; access to it, clicking on the     button of the main toolbar:

 


Apply the symmetry using the   button on the toolbar; different views are possible using the    button.




Jav can be used also as an integrated interface to study the model and to modify it:






It is possible to export data and results in order to use them in another program; in particular, when the refinement is complete and the structure is ready for publication, it is possible to export data and results in CIF format.

Go to menu item “File” on the main toolbar, select Export option and then CIF option (other formats are available: i.e. PDB format, for proteins).












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