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Generating .cif file for publication
mtaddei #1
Member for 2 months · 7 posts
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Subject: Generating .cif file for publication
Hi,

I am dealing with submission of my first structure refined using TOPAS and I am having a few issues with my output .cif file.
I am trying to copy bond angles and distances in my .cif file, but it seems that TOPAS 4.2 does not support the Out_CIF_Bonds_Angles macro.
Unfortunately, I do not have access to later versions of the software.
My plan is to submit the .inp file, which contains all bond angles and distances, as supporting information, but I'd like to go smooth through the checkcif, if possible.
How can I get around this?

Thanks,
Marco
lgermann #2
Member since Nov 2015 · 11 posts · Location: MPI FKF Stuttgart
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Hey Marco,

You can use the

"append_bond_lengths" macro. It will append the bond lengths and angles in the input file, which you could copy into the .cif file:


loop_
    _geom_bond_atom_site_label_1
    _geom_bond_atom_site_label_2
    _geom_bond_distance
    _geom_bond_site_symmetry_1
    _geom_bond_site_symmetry_2

I'm not sure anymore, whether it gives the information about "_geom_bond_site_symmetry_1 & 2" or not.

Btw. to go smooth through checkcif you need just one angle and one bond length.

Cheers,
Luzia
mtaddei #3
Member for 2 months · 7 posts
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Hi Luzia,

Belated thanks for your reply.
Eventually I managed to put together a cif file that the checkcif routine could like, although it was a pretty miserable task.
We'll see if the CCDC will let me deposit it as it is or if they request modifications.

Marco
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