mtaddei
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
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
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
fredmarlton
Hi all,
Just wondering if there's any new updates or excellent macros for generating CIFs suitable for publication?
Thanks,
Fred
mtaddei
Hi Fred, not that I am aware of. I am currently going again thorugh the painful process of building a cif for publication and I really wish there was an easier way.
rowlesmr
Not that it helps here, but the COD is working on getting tools to help building pdCIF files. Hourly or will make it easier in the future
rowlesmr
Hi mtaddei
I'm writing up some CIF macros at the moment.
Are you able to share your data/input files? I'll see what my macros will do. They're still in development...
Matthew