Fe Supercell issues

[orex]

Fe Supercell issues

[orex]

Dear Debbie,
Thank you very much for using supercell. Please, specify exactly the commenad line you used for supercell launch like
./supercell -i input_Fe_222.cif -s 2x2x2 etc
and the output you get from the program to your screen.

[debbieLT]

This should be updated in the main query now but the command i use is
./supercell -i Fe_222.cif -m -q -g -o=supercell
And the output i get to my screen is attached as a file: output Fe_222.txt

[orex]

Thank you, Debbie. Sorry, I missed the file. As I can see from the output in your cif file all Fe atoms a labeled differently. Supercell program treats it as different sites (despite all of them are Fe atoms). For detailed information please check https://jcheminf.biomedcentral.com/articles/10.1186/s13321-016-0129-3#Sec5 Stage I.
Therefore you should use another input file where all atoms from one site should have the same label. In you case, probably atoms Fe2, Fe6, Fe9, Fe16 should have a label FeB, and all the rest should have a label FeA. Same label is very important not only for permutations, but for summery algorithms also. Fe1 and Fe3 will be treated as different sites for symmetry search.

Sincerely yours,
Kirill.

[debbieLT]

Thanks for your help Kirill this seems to have cleared up the problem
Many Thanks

Debbie