How to prepare the input files for Superflip ad EDMA using Jana2000 |
Jana2000 is a crystallographic computing system for data reduction and structure refinement of periodic structures and incommensurately modulated structures. Jana2000 can produce the input file for Superflip and EDMA and it is recommended to prepare the input files through the interface of Jana2000, unless you want to use special features of Superflip or EDMA. Even in that case it is much more convenient to prepare the standard form of the input file with Jana2000 and edit the prepared file subsequently.
Superflip and EDMA can produce the output in Jana2000 Format, so that the result can be easily viewed and the structure refined using Jana2000.
To prepare the file, follow these instructions:
1) Input or import the structural information to Jana2000:
If the data has been collected on some common diffractiomenter, Jana2000 will likely be able to import the data directly via the DatRed tool.
Double click the icon DatRed and use the interface to import the crystallographic information and reflection list. Otherwise you have to enter the crystallographic data manually (see below) and import the reflection list after that (see even more below).
Click the icon EditM50 (marked green on the image above). In EditM50 define the lattice parameters and number of dimensions + q-vector, if applicable. If you imported the data by DatRed, these fields will be already filled.
On the card Symmetry give the symmetry of the structure. If you are not sure about it, you can leave P1 there, which will lead to structure solution in P1. Note however, that the symmetry is used only in avergaing the reflections and not in the structure solution. It is thus safe to input any symmetry that has the same Laue group as the true symmetry and does not induce incorrect systematic absences.
On the card Radiation define the composition. If you know the composition exactly, give the formula and the number of formula units as in the example below. If you know only the qualitative composition, fill just a list of elements expected in the structure and set the number of formula units to zero. This information will be later used in EDMA to generate a structure file.
Do not fill the hydrogen atoms, since hydrogens are too light not be detected in the density and trying to detect them leads to detection of false maxima.
Click OK and confirm saving the changes you made in EditM50.
2) If you did not do it through the DatRed interface, import the reflection list using the "Import file(s) from various resources" interface in the File menu.
3) Create a refinement reflection list
Use the appropriate item from the File menu (highlighted in the image above). Answer "yes" to the question, if you want to average the reflections. The rest of the queries during the creation of reflection file can be usually just confirmed by clicking OK. The result will be a file jobname.m91 with list of reflections averaged according to the symmetry given in EditM50. Check the file jobname.rre to make sure that the coverage in the reciprocal space is reasonable (more than 90%).
4) Open the interface for export of the files for Superflip and EDMA.
(This interface allows also to export input files for BayMEM and prior, which you will not need here.)
Click the button "structure solution" and the forms will be automatically filled with preset values suitable for structure solution by Superflip and EDMA. You might go to cards "Charge flipping" and "EDMA" to check the values, but in most cases the default values are satisfactory. Note the list of output files. The file jobname.m81 will contain the electron density, jobname.m80 will contain list of phased structure factors (both files will be produced by Superflip), file jobname.m40 will contain a structure model (will be produced by EDMA). If the file jobname.m40 contains already a structure model now, it will be overwritten when EDMA is run! So either make a backup of it before running EDMA, or change now the name of the model file on the card EDMA, field "Create m40". If you are affraid the symmetry you have specified might be wrong, switch the radio button "Symmetry" on the card "Charge flipping" from "Average over symmetry" to "Shift origin". This will make superflip search the origin of the symmetry, but the density will not be averaged, only shifted, and so you can check yourself, if the expected symmetry is present in the result.
5) Run superflip from terminal window. You can open a termminal window from Jana2000 in File/Start shell. If you have superflip installed and the system variables are set so that the system recognizes the command, run superflip by typing: superflip jobname.inflip. Watch the on-screen log of the calculation. If the program converges successfully, run EDMA by typing: EDMA jobname.inflip. This will produce a structure file jobname.m40 (if you did not redefine the name of the structure file before). After EDMA finishes, close the terminal window to return back to Jana2000.
6) Check the result. You can view the generated structure in a crystal structure viewer (Tools/graphic viewer, the path to a graphic viewer must be defined in Tools/Preferences), view the generated density map using Contour or calculate any density section you wish from the m80 file using Fourier.
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