JANA 2006

[isabella]

Hi! could you help me to find something about JANA 2006? because I need to use it, but there is not a manual! thank you in advance!

[jchrist]

Hi Isabella
There is only a partial manual for JANA2000 and this is also valid for JANA2006
http://www-xray.fzu.cz/jana/doc/manual2000_part1.pdf

The problem is that JANA originally was a specialist software designed to deal with modulated structures, and it was taught in a "Master to Apprentice" system therefor there was never any need for a complete manual.

I have used JANA for several years, an would be happy to try to answer any questions you may have.

[isabella]

thank you very much for the manual!
I would like to know how I can impose the same atomic coordinates and ADP for different atoms in a site. Could you help me? I tryed with "restrictions", but when I've verified in the .m40 file the coordintes are all zero for the atoms in the same site, but I don't know why...
Isabella

[jchrist]

The .m40 file has two parts, one with the parameters and one with the standard deviations for the parameters. Before refinements and for special positions the standard deviations will be zero. It is important to look at the right part of the file to check the coordinates (I have made this mistake before ).
the two parts should be separated by a doted line as shown in the image below.

m40file.jpg

Let me know if this solves your problem or not. Otherwise it might be the way you have made your restrictions...

[Multiferroics]

hi,

I have problem with fix or refine the atom coordination position.

I use 1 to refine one parameter of atom position, but the atom does not move.

I fix all the other parameters, but always, there move....

Thanks.

[jchrist]

Per default Jana uses automatic refinement keys (symmetry constraints) this is changed in SetComands; Refinement

jana.jpg

Be careful if allowing atoms at special positions to move, and remember to correct the occupancy accordingly.

[Multiferroics]

Thanks,

I find it.

I have new problems.

profine can get quite good results.

But when go to refine, the B-factor are negative. R-factor are about 10.

It is quite difficult to improve. but the structure mode seems ok.

Thanks.

[jchrist]

Negative B factors are normally a result of poor absorption correction.
What material is it, and how were the data collected (were any corrections done by the instrument software).

[Multiferroics]

The materials is PbZrO3

Nothing was down with raw date...

I also put microabsorption parameter when do refine.

But it does not work.

[jchrist]

Depending on the sample size then PbZrO3 is effectively a beam stop.
From the refinement description it looks like a powder sample, was this transmission or reflection mode?
If transmission what was the sample thickness? Was it Cu or Mo radiation?
Any refinement or correction program will have difficulties when the absorption is more than 50%.

[Multiferroics]

It is synchrotron x-ray.

I am not sure which mode is used for measurement.

But sample is powder.

Thank you very much!

[jchrist]

Before moving on with the refinement you should check the following basic things (you probably have them right, but check anyway).

1: Check your wavelength and the polarization, JANA should ask for this when you create a new structure and load the data file. The information is stored in the header of the *.m95 file
2: make sure to enter f' and f" for the wavelength that was used, this is found under Parameters: f',f" Just enter the values, no refinement of them.
3: You need the diffraction geometry, this is needed to perform a proper absorption correction.


Is it all atoms or just the oxygen that have negative B factors?

[Multiferroics]

Thanks,
wavelength, no problem.
But, the polarization, f',f" and the diffraction geometry, i always keep default.
Because i do not the good values for different x-ray....

[jchrist]

But, the polarization, f',f" and the diffraction geometry, i always keep default.
Because i do not the good values for different x-ray....

The values of f' and f" are wavelength dependent and varies much especially around absorption edges.
If unsure about f' and f", you can find the program fprime, originally written for gsas by Robert B. von Dreele.
http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/gsas/public/gsas/windows/
It runs on most windows systems, I have tested with windows 2000, XP, Windows 7, they all work fine.

When entering a new structure in JANA2006 you are prompted to give the radiation related parameters (see picture)

selectwavelength.jpg

Select polarized beam

About the diffraction geometry, what beamline were the data collected at, did you go there your self or are you looking at
data from someone else? Best thing is to ask the person who did the experiment or the people working at the beamline.

[Sanjay]

Hii,

You can go to jana2006 website and download cookbook, here you will find several examples to do practice....