CIF file rendering using symmetry group application

General Discussion
1

Dear All,

I am trying to read a cif file using Avogadro, but it seems not to
apply the symmetry operators to the image (symmetry group and
operators are included in the cif file). Can anyone tell if I need to
use some different mode/option in order to do that? There’s an option
’Fill Unit Cell’ in Build --> Unit Cell Parameters, but when I inovke
it, the program seems to crash. I am using Windows7.

Regards,
Ramdas Pophale
Department of Bioengineering
Rice University, Houston, TX
cell: 713-254-0924

2

use some different mode/option in order to do that? There’s an option
‘Fill Unit Cell’ in Build → Unit Cell Parameters, but when I inovke
it, the program seems to crash. I am using Windows7.

No, this would be the correct button, so obviously you’re exposing a bug. Could you send me the CIF file to test?

Thanks very much,
-Geoff

3

Hi Geoffrey,

I have attached a sample cif file. Also, for some space groups (as in
the one in this file), the build-supercell builder-generate cell
option does not seem to apply the symmetry operators to the asymmetric
unit.

Regards,
Ramdas.

Quoting Geoffrey Hutchison geoff.hutchison@gmail.com:

use some different mode/option in order to do that? There’s an option
‘Fill Unit Cell’ in Build → Unit Cell Parameters, but when I inovke
it, the program seems to crash. I am using Windows7.

No, this would be the correct button, so obviously you’re exposing a
bug. Could you send me the CIF file to test?

Thanks very much,
-Geoff

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Ramdas Pophale
Department of Bioengineering
Rice University, Houston, TX
cell: 713-254-0924

4

Also, for some space groups (as in the one in this file), the build-supercell builder-generate cell option does not seem to apply the symmetry operators to the asymmetric unit.

If you have other examples of this behavior, please send them as well. While CIF is supposed to be a standard, I can confirm from discussions with other software authors, that there are many non-standard CIFs which need careful testing.

So to anyone who finds problems with CIF support, please send us the files for debugging.

Thanks and best regards,
-Geoff

5

On Saturday 25 September 2010 16:32:16 Ramdas Sunil Pophale wrote:

Dear All,

I am trying to read a cif file using Avogadro, but it seems not to
apply the symmetry operators to the image (symmetry group and
operators are included in the cif file). Can anyone tell if I need to
use some different mode/option in order to do that? There’s an option
‘Fill Unit Cell’ in Build → Unit Cell Parameters, but when I inovke
it, the program seems to crash. I am using Windows7.

For the list, Ramdas also emailed me off list where I provided some answers
about how I previously produced images for a paper that came out of their
group. As Geoff has stated - not all CIFs are created equal but the create
supercell does attempt to apply all symmetry operations, create as many
repeats as specified and then perform simple bonding on the result.

It looks like this is a bug - I am not sure how well anything is tested on
Windows 7 that we released. I do not have access to Windows 7 at the moment.

Thanks,

Marcus

Marcus D. Hanwell, Ph.D.
R&D Engineer, Kitware Inc.
(518) 881-4937

6

Hi Geoffrey,

I have attached two cif files.
The build supercell option works properly for 0001231.cif, but it does
not work for 8308100.cif. Both the cif files have the same file
structure, so as Marcus suggested, the problem is with the symmetry
application and subsequent bond formation for certain space groups. I
remember having this problem on Windows XP as well.

Regards,
Ramdas.

Quoting Geoffrey Hutchison geoff.hutchison@gmail.com:

Also, for some space groups (as in the one in this file), the
build-supercell builder-generate cell option does not seem to apply
the symmetry operators to the asymmetric unit.

If you have other examples of this behavior, please send them as
well. While CIF is supposed to be a standard, I can confirm from
discussions with other software authors, that there are many
non-standard CIFs which need careful testing.

So to anyone who finds problems with CIF support, please send us the
files for debugging.

Thanks and best regards,
-Geoff

Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev

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Ramdas Pophale
Department of Bioengineering
Rice University, Houston, TX
cell: 713-254-0924

7

Hi Geoffrey,

I’ve been having problems with displaying *.cif files as well (the two
attached). It seems like the symmetry operations are not being applied. I am
using Avogadro 1.0.0 on Linux.

Other than these small problems Avogadro works great. Thanks again for
developing such a great and helpful piece of software.

Sincerely,
Yung-Jin

On Tue, Sep 28, 2010 at 1:32 PM, Ramdas Sunil Pophale ramdas@rice.eduwrote:

Hi Geoffrey,

I have attached two cif files.
The build supercell option works properly for 0001231.cif, but it does not
work for 8308100.cif. Both the cif files have the same file structure, so as
Marcus suggested, the problem is with the symmetry application and
subsequent bond formation for certain space groups. I remember having this
problem on Windows XP as well.

Regards,
Ramdas.

Quoting Geoffrey Hutchison geoff.hutchison@gmail.com:

Also, for some space groups (as in the one in this file), the

build-supercell builder-generate cell option does not seem to apply the
symmetry operators to the asymmetric unit.

If you have other examples of this behavior, please send them as well.
While CIF is supposed to be a standard, I can confirm from discussions with
other software authors, that there are many non-standard CIFs which need
careful testing.

So to anyone who finds problems with CIF support, please send us the files
for debugging.

Thanks and best regards,
-Geoff

Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev

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Ramdas Pophale
Department of Bioengineering
Rice University, Houston, TX
cell: 713-254-0924

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and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev

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

8

I’ve been having problems with displaying *.cif files as well (the two attached). It seems like the symmetry operations are not being applied. I am using Avogadro 1.0.0 on Linux.

Thanks, I’d be happy to continue to get any buggy CIF files. It seems like the CIF “standard” is much more flexible than I knew. I am seeing space groups which don’t exactly line up with their “official” versions.

These should be fixed with the next version of Open Babel and Avogadro.

-Geoff