Re: [Avogadro-Discuss] Cif file

[Geoffrey Hutchison]

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

avogadro.cif
Description: Binary data

--- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu/ On Jul 29, 2015, at 4:44 PM, James Mao <xjames...@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.hutchi...@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 <xjames...@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.hutchi...@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 https://lists.sourceforge.net/lists/listinfo/avogadro-discuss   <avogadro.cif><urea-1980-293k.cif>------------------------------------------------------------------------------ _______________________________________________ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss

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