Author Topic: CIF files help  (Read 414 times)

petersbk

  • Newbie
  • *
  • Posts: 10
    • View Profile
CIF files help
« on: April 17, 2019, 02:35:56 PM »
What software do people use to successfully manipulate .cif files and get them to work with raspa? I've tried fairly simple things (like read in the FAU_SI.cif provided with raspa, convert it to P1, and export it back to .cif) and they seem to not work; sometimes with useful error messages and sometimes not. Besides Materials Studio which I don't have access to, what software works reliably? I've tried Avogadro and VESTA without success. They usually read each other's exported files or those included with raspa, but raspa does not read theirs. Does anyone have any tricks, hints, reports of idiosyncrasies, recommendations, or things to watch out for?

As an example (but I am really looking for general help), the FAU --> P1 in VESTA exercise above yielded the .cif shown below (and attached), but gave "ERROR in cif-file: no proper space group definition found" (after reporting tons of "unknown" lines) even though it has two lines relating to the space group. (Sorry: I couldn't get attachments to work).

#======================================================================

# CRYSTAL DATA

#----------------------------------------------------------------------

data_VESTA_phase_1


_chemical_name_common                  'FAU'
_cell_length_a                         24.34500
_cell_length_b                         24.34500
_cell_length_c                         24.34500
_cell_angle_alpha                      90
_cell_angle_beta                       90
_cell_angle_gamma                      90
_space_group_name_H-M_alt              'P 1'
_space_group_IT_number                 1

loop_
_space_group_symop_operation_xyz
   'x, y, z'

loop_
   _atom_site_label
   _atom_site_occupancy
   _atom_site_fract_x
   _atom_site_fract_y
   _atom_site_fract_z
   _atom_site_adp_type
   _atom_site_B_iso_or_equiv
   _atom_site_type_symbol
   O1         1.0     0.895800      0.104200      0.000000     Biso  1.000000 O
...

Thanks for any help.

petersbk

  • Newbie
  • *
  • Posts: 10
    • View Profile
Re: CIF files help
« Reply #1 on: April 23, 2019, 01:13:06 PM »
Similar to my other post on .cif files, I'll report that I was only able to solve my .cif file problems by using the header from a working P1 .cif file (e.g. from the structures directory in the distribution), cutting out the coordinates, pasting in fractional coordinates for my system of interest, and modifying the cell parameters. I still do not know why some .cif files which work in other codes do not work in raspa, but it mentions somewhere in the manual or other documentation, that they can be tricky.


Somananda Sanyal

  • Newbie
  • *
  • Posts: 2
    • View Profile
Re: CIF files help
« Reply #2 on: May 16, 2019, 03:00:23 PM »
Hi,

I faced the same problem too, even when I used Material Studio to convert the original .cif file to P1 symmetry.
I have one query, is it necessary to always convert the input structure to P1 symmetry for RASPA or we can also provide the original symmetry?

Thanks in advance!

Warm regards,
Somananda

David Dubbeldam

  • Jr. Member
  • **
  • Posts: 79
    • View Profile
Re: CIF files help
« Reply #3 on: July 06, 2019, 03:24:19 PM »
P1 is safer. Specifying the spacegroup is not unique, unless the Hall-symbols are used. Materials Studio and other codes do not do that. So, yes you can use symmetry, but if it does not work, it is usually because the space group is not set properly.
Using P1 avoids these issues.