Problem reading a .cif file (Unknown spacegroup)

General Discussion
1

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, bessac@irsamc.ups-tlse.fr 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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2

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, bessac@irsamc.ups-tlse.fr 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

Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/

Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
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3

Dear all,

Thank you very much. I will wait until next month :slight_smile:

Fabienne.

Jean Bréfort jean.brefort@normalesup.org a écrit :

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, bessac@irsamc.ups-tlse.fr 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

Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/

Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
avogadro-discuss List Signup and Options

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Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/

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4
  1. Add all variants to the database (who volunteers?)
  2. Accept unkonwn groups.

I think we’d want a combination of both. Over time, we have been adding more variants. I’m not sure there’s a complete list of all variants – several times, I’ve looked.

But we could also add code which accepts an unknown group and parses the symmetry operations from the CIF, correct?

-Geoff

5

Hi,

Can someone test attached patch? It fixes the space groups list (adding
variants for groups #1 and #2, accepts unknown groups, and understand
the symmetry operations from the CIF file (they changed the field name).

Regards,
Jean

Le lundi 12 mars 2012 à 11:56 -0400, Geoffrey Hutchison a écrit :

  1. Add all variants to the database (who volunteers?)
  2. Accept unkonwn groups.

I think we’d want a combination of both. Over time, we have been adding more variants. I’m not sure there’s a complete list of all variants – several times, I’ve looked.

But we could also add code which accepts an unknown group and parses the symmetry operations from the CIF, correct?

-Geoff

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6

Hi Jean,

On Tue, Mar 27, 2012 at 2:58 PM, Jean Brefort
jean.brefort@normalesup.org wrote:

Can someone test attached patch? It fixes the space groups list (adding
variants for groups #1 and #2, accepts unknown groups, and understand
the symmetry operations from the CIF file (they changed the field name).

I can confirm that this will open the problematic cif file that
Fabienne submitted. I had to make a small change to get it to compile
(m_SpaceGroup → mSpaceGroup in cifformat.cpp).

Also, was this chunk intentional?

— a/src/formats/cifformat.cpp
+++ b/src/formats/cifformat.cpp
@@ -270,6 +270,7 @@ namespace OpenBabel
void Parse(std::istream &in);
/// The data blocks, after parsing. The key is the name of the data block
std::mapstd::string,CIFData mvData;

  • /// The current iterator r
    /// Global comments, outside and data block
    std::liststd::string mvComment;
    };

Other than those two questions it should be ready to submit – thanks
for fixing this!

Dave

7

Le mardi 27 mars 2012 à 15:15 -0400, David Lonie a écrit :

Hi Jean,

On Tue, Mar 27, 2012 at 2:58 PM, Jean Brefort
jean.brefort@normalesup.org wrote:

Can someone test attached patch? It fixes the space groups list (adding
variants for groups #1 and #2, accepts unknown groups, and understand
the symmetry operations from the CIF file (they changed the field name).

I can confirm that this will open the problematic cif file that
Fabienne submitted. I had to make a small change to get it to compile
(m_SpaceGroup → mSpaceGroup in cifformat.cpp).

Also, was this chunk intentional?

No, I should have run svn diff before starting. Thanks for the revue.

— a/src/formats/cifformat.cpp
+++ b/src/formats/cifformat.cpp
@@ -270,6 +270,7 @@ namespace OpenBabel
void Parse(std::istream &in);
/// The data blocks, after parsing. The key is the name of the data block
std::mapstd::string,CIFData mvData;

  • /// The current iterator r
    /// Global comments, outside and data block
    std::liststd::string mvComment;
    };

Other than those two questions it should be ready to submit – thanks
for fixing this!

Dave

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