Re: [Avogadro-Discuss] Problem reading a .cif file (Unknown spacegroup)

[Jean B. <jea...@no...>]

Hi all,

We have two options:
1. Add all variants to the database (who volunteers?)
2. Accept unkonwn groups.

Of course it's easy to add just this group to the database.
I can't work on that at the monment, may be next month.

Regards,
Jean

Le dimanche 11 mars 2012 à 10:06 -0400, David Lonie a écrit :
> Hi Fabienne,
> 
> The problem here is that the space group database Avogadro uses
> doesn't recognize spacegroup C-1 -- the closest I could find was:
> 
> 13
> -P 2ab
> P 1 1 2/n
> x,y,z
> 1/2-x,1/2-y,z
> -x,-y,-z
> 1/2+x,1/2+y,-z
> 
> Which is what you want, except for the sign of the z component of the
> 2nd and 4th transforms. I've cc'd this to the OpenBabel mailing list
> -- maybe Jean Brefort (maintainer of the OpenBabel space group code)
> or someone else will have an idea for a work-around.
> 
> Hope this helps,
> 
> Dave
> 
> On Mon, Mar 5, 2012 at 12:37 PM,  <be...@ir...> wrote:
> > Hello,
> >
> >   I want to read the following file .cif. Apparently Avogadro has
> > problems to read "_symmetry_space_group_name_H-M 'C -1'". I do not
> > know how to fix the problem. Could you help me?
> >
> > Thanks, best regards,
> >
> > Fabienne.
> >
> > data_global
> > _chemical_name_mineral 'Pyrophyllite'
> > loop_
> > _publ_author_name
> > 'Wardle R'
> > 'Brindley G W'
> > _journal_name_full 'American Mineralogist'
> > _journal_volume 57
> > _journal_year 1972
> > _journal_page_first 732
> > _journal_page_last 750
> > _publ_section_title
> > ;
> >  The crystal structures of pyrophyllite, 1Tc, and of its dehydroxylate
> > ;
> > _database_code_amcsd 0000285
> > _chemical_formula_sum 'Al Si2 O6 H'
> > _cell_length_a 5.1614
> > _cell_length_b 8.9576
> > _cell_length_c 9.3511
> > _cell_angle_alpha 91.03
> > _cell_angle_beta 100.37
> > _cell_angle_gamma 89.75
> > _cell_volume 425.206
> > _exptl_crystal_density_diffrn      2.814
> > _symmetry_space_group_name_H-M 'C -1'
> > loop_
> > _space_group_symop_operation_xyz
> >   'x,y,z'
> >   '1/2+x,1/2+y,z'
> >   '-x,-y,-z'
> >   '1/2-x,1/2-y,-z'
> > loop_
> > _atom_site_label
> > _atom_site_fract_x
> > _atom_site_fract_y
> > _atom_site_fract_z
> > Al   0.50000   0.16700   0.00000
> > Si1   0.74800   0.00000   0.28900
> > Si2   0.75900   0.33100   0.28900
> > O1   0.67100   0.00400   0.11300
> > O2   0.72100   0.31900   0.11300
> > O-H   0.22100   0.18600   0.11300
> > Ob1   0.05500   0.38700   0.35300
> > Ob2   0.72400   0.16700   0.35300
> > Ob3   0.55000   0.44800   0.33600
> >
> >
> >
> > -----
> > Pièces jointes
> > https://webmail.irsamc.ups-tlse.fr/imp/attachment.php?u=bessac&t=1330969048&f=AMS_DATA.cif
> >
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