Problem in giving DFIX to symmetry generated atoms

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tomarkapil
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Problem in giving DFIX to symmetry generated atoms

Post by tomarkapil » 09 Sep 2017, 17:50

Dear All,

I have a structure (space group P21/c) which has a 4,4'-bipyridine type molecule coordinated to the metal center. the problem is that half of the molecule is symmetry generated and the distance between the two carbon atoms is coming very less. My problem is how to give a DFIX command to the two symmetry generated atoms to make the distance reasonable?
problem.docx
I have attached the image of the part of the crystal structure depicting the molecule.
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HorstPuschmann
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Re: Problem in giving DFIX to symmetry generated atoms

Post by HorstPuschmann » 10 Sep 2017, 12:14

Grow it in Olex2. Select the two atoms you want to restrain (or the bond between them) and type your dfix command (e.g. 'dfix 0.01 1.52'). Refine.

tomarkapil
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Re: Problem in giving DFIX to symmetry generated atoms

Post by tomarkapil » 10 Sep 2017, 15:49

Thank you HorstPuschmann,
I have tried as you have told by growing the atom.... and its done....Othermwise, I was puzzled as to how give the DFIX to the same atom :D

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wlewis
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Re: Problem in giving DFIX to symmetry generated atoms

Post by wlewis » 10 Sep 2017, 22:53

OLEX2 is doing a shortcut for you here (and making life easier :-).

If you go into the .lst file from SHELXL, and find the "Connectivity List", this will give you the bond you are looking for, and critically, the symmetry equivalent that is forming this bond. You can then use EQIV in combination with DFIX to fix the bond length.

tomarkapil
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Re: Problem in giving DFIX to symmetry generated atoms

Post by tomarkapil » 11 Sep 2017, 07:34

Yes wlewis, I have noticed the EQIV command along with the DFIX when i have refined the structure in the OLEX program. :)

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