Fractional coords

Hi,

is there a way to parse a,b,c and alpha, beta, gamma, as well as (most importantly) fractional coordinates from cif file in OB and/or Avogadro? I need that to setup CRYSTAL input as I work with >50 atoms molecules and copying pasting fractionals from cif, editing them to omit parentheses is very laborious

So is there a way to setup, say, another input format in Avogadro for CRYSTAL, as long as OB parses that info?

Jonas

is there a way to parse a,b,c and alpha, beta, gamma, as well as (most importantly) fractional coordinates from cif file in OB and/or Avogadro? I need that to setup CRYSTAL input as I work with >50 atoms molecules and copying pasting fractionals from cif, editing them to omit parentheses is very laborious

In the development version, there’s support in the Cartesian editor for pasting in fractional coordinates.

But I think what you want (as far as a file format) is the “Free Form Fractional”:
http://openbabel.org/wiki/Free_Form_Fractional

Cheers,
-Geoff

Yes! Is that free form supported in Avogadro? I requested in Features CRYSTAL input generation, maybe free form can be easily used for that?

Jonas

— On Tue, 3/23/10, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

From: Geoffrey Hutchison geoff.hutchison@gmail.com
Subject: Re: [Avogadro-devel] fractional coords
To: “Jonas Baltrusaitis” jasius_1@yahoo.com
Cc: “Avogadro-devel Devel” avogadro-devel@lists.sourceforge.net
Date: Tuesday, March 23, 2010, 7:42 AM

is there a way to parse a,b,c
and alpha, beta, gamma, as well as (most importantly)
fractional coordinates from cif file in OB and/or Avogadro?
I need that to setup CRYSTAL input as I work with >50
atoms molecules and copying pasting fractionals from cif,
editing them to omit parentheses is very laborious

In the development version, there’s support in the
Cartesian editor for pasting in fractional coordinates.

But I think what you want (as far as a file format) is the
"Free Form Fractional":
http://openbabel.org/wiki/Free_Form_Fractional

Cheers,
-Geoff

On Mar 23, 2010, at 10:47 AM, Jonas Baltrusaitis wrote:

Yes! Is that free form supported in Avogadro?

Avogadro reads any file format supported by Open Babel.

Best regards,
-Geoff

I would like to elaborate on my older question: is there a way to build supercell and fill it with atoms (either from cif and/or by inserting atoms manually) and then save the output in fractional coordinates? While I admit that OB should be able to work with fractionals, I can’t see how to export fractional coordinates using Avogadro after I built supercell

Jonas

and then save the output in fractional coordinates? While I admit that OB should be able to work with fractionals, I can’t see how to export fractional coordinates using Avogadro after I built supercell

Save as “file.cif” or “file.fract”.

Cheers,
-Geoff