Cif file

Hi everyone,

It seems Avogadro always generate cif files with " atom_site_Cartn" form.
Is there any option to save/convert it to “atom_site_fract” form?

Many thanks.

James

It seems Avogadro always generate cif files with “ atom_site_Cartn“ form. Is there any option to save/convert it to “atom_site_fract“ form?

Does your system in Avogadro have a unit cell defined? If there’s no unit cell information, I don’t think Avogadro (or more accurately Open Babel can convert to fractional space).

-Geoff

Yes cif file has all the information. It is quite straight forward to convert the format, but I did not find the option in Open Babel.

James

From: Geoffrey Hutchison [mailto:geoff.hutchison@gmail.com]
Sent: Wednesday, July 22, 2015 9:07 PM
To: avogadro-discuss@lists.sourceforge.net
Subject: Re: [Avogadro-Discuss] Cif file

It seems Avogadro always generate cif files with “ atom_site_Cartn“ form. Is there any option to save/convert it to “atom_site_fract“ form?

Does your system in Avogadro have a unit cell defined? If there’s no unit cell information, I don’t think Avogadro (or more accurately Open Babel can convert to fractional space).

-Geoff

Can you send me the file? What version of Avogadro are you using?

Thanks very much,
-Geoff

On Jul 23, 2015, at 2:58 AM, James Mao xjamesmao@gmail.com wrote:

Yes cif file has all the information. It is quite straight forward to convert the format, but I did not find the option in Open Babel.

James
<>
From: Geoffrey Hutchison [mailto:geoff.hutchison@gmail.com]
Sent: Wednesday, July 22, 2015 9:07 PM
To: avogadro-discuss@lists.sourceforge.net
Subject: Re: [Avogadro-Discuss] Cif file

It seems Avogadro always generate cif files with “ atom_site_Cartn“ form. Is there any option to save/convert it to “atom_site_fract“ form?

Does your system in Avogadro have a unit cell defined? If there’s no unit cell information, I don’t think Avogadro (or more accurately Open Babel can convert to fractional space).

-Geoff



Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net mailto:Avogadro-Discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-discuss https://lists.sourceforge.net/lists/listinfo/avogadro-discuss

Dear Geoff,

Basically, Avogadro can open CIF files correctly, regardless the data in CIF file are in fractional coordinates or Cartesian coordinates.

While it is saved as a CIF file, it seems always save in Cartesian coordinates. The problem is that many other popular programs,

such as VESTA or Murcury, cannot deal with CIF files in Cartesian format. I am not sure if there is an option in Open Babel to save
CIF files in fractional coordinates. If there is, that would be great.

I attached here 2 CIF files as example. The original one in fractional coordinates, another one was original one opened and saved by
Avogadro which changed to Cartesian coordinates.

My Avogadro is windows version 1.1.1, Open Babel 2.3.2.

Thank you very much!

James

From: Geoffrey Hutchison [mailto:geoff.hutchison@gmail.com]
Sent: Thursday, July 23, 2015 2:01 PM
To: avogadro-discuss@lists.sourceforge.net
Subject: Re: [Avogadro-Discuss] Cif file

Can you send me the file? What version of Avogadro are you using?

Thanks very much,

-Geoff

On Jul 23, 2015, at 2:58 AM, James Mao <xjamesmao@gmail.com mailto:xjamesmao@gmail.com > wrote:

Yes cif file has all the information. It is quite straight forward to convert the format, but I did not find the option in Open Babel.

James

From: Geoffrey Hutchison [mailto:geoff.hutchison@gmail.com]
Sent: Wednesday, July 22, 2015 9:07 PM
To: avogadro-discuss@lists.sourceforge.net mailto:avogadro-discuss@lists.sourceforge.net
Subject: Re: [Avogadro-Discuss] Cif file

It seems Avogadro always generate cif files with “ atom_site_Cartn“ form. Is there any option to save/convert it to “atom_site_fract“ form?

Does your system in Avogadro have a unit cell defined? If there’s no unit cell information, I don’t think Avogadro (or more accurately Open Babel can convert to fractional space).

-Geoff



Avogadro-Discuss mailing list
mailto:Avogadro-Discuss@lists.sourceforge.net Avogadro-Discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-discuss https://lists.sourceforge.net/lists/listinfo/avogadro-discuss

Yes, I just double checked with the latest version of Open Babel and it’s not a problem anymore. Which basically means we should work hard to get Avogadro v1.2 out with the latest OB version.

Cheers,
-Geoff


Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/

On Jul 29, 2015, at 4:44 PM, James Mao xjamesmao@gmail.com wrote:

Dear Geoff,

Basically, Avogadro can open CIF files correctly, regardless the data in CIF file are in fractional coordinates or Cartesian coordinates.
While it is saved as a CIF file, it seems always save in Cartesian coordinates. The problem is that many other popular programs,
such as VESTA or Murcury, cannot deal with CIF files in Cartesian format. I am not sure if there is an option in Open Babel to save
CIF files in fractional coordinates. If there is, that would be great.

I attached here 2 CIF files as example. The original one in fractional coordinates, another one was original one opened and saved by
Avogadro which changed to Cartesian coordinates.
<>
My Avogadro is windows version 1.1.1, Open Babel 2.3.2.

Thank you very much!
James

From: Geoffrey Hutchison [mailto:geoff.hutchison@gmail.com]
Sent: Thursday, July 23, 2015 2:01 PM
To: avogadro-discuss@lists.sourceforge.net
Subject: Re: [Avogadro-Discuss] Cif file

Can you send me the file? What version of Avogadro are you using?

Thanks very much,
-Geoff

On Jul 23, 2015, at 2:58 AM, James Mao <xjamesmao@gmail.com mailto:xjamesmao@gmail.com> wrote:

Yes cif file has all the information. It is quite straight forward to convert the format, but I did not find the option in Open Babel.

James

From: Geoffrey Hutchison [mailto:geoff.hutchison@gmail.com mailto:geoff.hutchison@gmail.com]
Sent: Wednesday, July 22, 2015 9:07 PM
To: avogadro-discuss@lists.sourceforge.net mailto:avogadro-discuss@lists.sourceforge.net
Subject: Re: [Avogadro-Discuss] Cif file

It seems Avogadro always generate cif files with “ atom_site_Cartn“ form. Is there any option to save/convert it to “atom_site_fract“ form?

Does your system in Avogadro have a unit cell defined? If there’s no unit cell information, I don’t think Avogadro (or more accurately Open Babel can convert to fractional space).

-Geoff



Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net mailto:Avogadro-Discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-discuss https://lists.sourceforge.net/lists/listinfo/avogadro-discuss

<avogadro.cif><urea-1980-293k.cif>------------------------------------------------------------------------------


Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net mailto:Avogadro-Discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-discuss https://lists.sourceforge.net/lists/listinfo/avogadro-discuss