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Topic: How to create a structure from CIF file?  (Read 9365 times)

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Offline AP

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How to create a structure from CIF file?
« on: November 22, 2013, 08:37:13 AM »
Hi all,

I have a CIF (Crystallographic information file) and want to draw structure!
How can do it? which software I can use?

Best Regards...
A.P.

Offline Archer

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Re: How to create a structure from CIF file?
« Reply #1 on: November 22, 2013, 08:47:22 AM »
“ I love him. He's hops. He's barley. He's protein. He's a meal. ”

Denis Leary.

Offline AP

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Re: How to create a structure from CIF file?
« Reply #2 on: November 22, 2013, 09:01:26 AM »
Thanks for your reply!

I used this software but it did not draw real strusture!
I attached CIF file please try with it! (I changed its extension from .cif to .txt to attach!)

B.R.
A.P
« Last Edit: November 22, 2013, 09:12:00 AM by AP »

Offline Archer

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Re: How to create a structure from CIF file?
« Reply #3 on: November 22, 2013, 10:10:00 AM »
I don't have access to this software presently. Please find attached a CIF as txt file, this one I know works see how that looks at your end.
“ I love him. He's hops. He's barley. He's protein. He's a meal. ”

Denis Leary.

Offline AWK

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Re: How to create a structure from CIF file?
« Reply #4 on: November 22, 2013, 11:42:56 AM »
CIF file always contains independent part of  structure. In the case of inorganic structures you sgould use packing options
AWK

Offline AP

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Re: How to create a structure from CIF file?
« Reply #5 on: November 23, 2013, 01:05:46 AM »
@Archer:
I opened the file you attached and drawed in the Mercury! I attached its image Archer.jpg  :)

@AWK:
Thanks for your hint. I used this feature but the structure is not correct! I attached image AWK.jpg. (blue atoms are Cobalt, Green atoms are Oxygen and Orange atoms are Iron)

Offline Archer

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Re: How to create a structure from CIF file?
« Reply #6 on: November 23, 2013, 02:31:13 AM »
I am not sure I can really help much more, the software is working (stucture downloaded from P Hakey et al, Acta Cryst. Sect E, 2008, 64(Pt 5): o940)

I am not an inorganic chemist, I only look at small organic molecules.

If you look at the CIF as a text file you can see it provides coordinate and bonding data so in my opinion there may something wrong with your data.

Where did your data come from? Did you collect it yourself? Do you have the structure factors (hkl file)?

Do you know what the compound is?
“ I love him. He's hops. He's barley. He's protein. He's a meal. ”

Denis Leary.

Offline curiouscat

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Re: How to create a structure from CIF file?
« Reply #7 on: November 23, 2013, 03:57:50 AM »
used this feature but the structure is not correct!

How do you know? GIGO perhaps?

Offline AP

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Re: How to create a structure from CIF file?
« Reply #8 on: November 23, 2013, 06:51:48 AM »
@Archer
tnx again for your investigation.
I download it from http://www.crystallography.net/cif/5/91/00/5910063.cif
here is refernece: http://www.crystallography.net/5910063.html
it is "Cobalt Ferrite" CIF that is very common and has Inverse Spinel Structure. All things about this compound available (hkl , ...)   :)

if you can draw its structure; may you send me its file (or image or anything)?

@curiouscat
I mean that CoFe2O4 structure is not correct! I know its real structure! I am inorganic chemistry student!!!   ;)

Offline curiouscat

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Re: How to create a structure from CIF file?
« Reply #9 on: November 23, 2013, 07:23:56 AM »
@curiouscat
I mean that CoFe2O4 structure is not correct! I know its real structure! I am inorganic chemistry student!!!   ;)

Yes, but then there's the CIF file itself. Are we sure it is syntactically right?

Offline AP

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Re: How to create a structure from CIF file?
« Reply #10 on: November 23, 2013, 07:58:54 AM »
Yes, but then there's the CIF file itself. Are we sure it is syntactically right?

I think it should be syntactically right! It is from reference website! ???

Offline curiouscat

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Re: How to create a structure from CIF file?
« Reply #11 on: November 23, 2013, 09:55:51 AM »
Yes, but then there's the CIF file itself. Are we sure it is syntactically right?

I think it should be syntactically right! It is from reference website! ???

My bet is still on a syntax issue. Look at the Wyckoff positions. Your cif file seems to have a multiplicity of 192. Mercury is only reading 18 of those.

http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-wp-list?gnum=227

Offline curiouscat

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Re: How to create a structure from CIF file?
« Reply #12 on: November 23, 2013, 10:13:37 AM »
If you are still not convinced check the syntactic accuracy here:

http://checkcif.iucr.org/

Lots of critical errors are thrown up.

Offline AP

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Re: How to create a structure from CIF file?
« Reply #13 on: November 23, 2013, 11:08:12 AM »
Well!! friends! :o
I chencked this file! some of this tools says that this file has syntax error!!! :o
what is happening?? this file is from http://www.crystallography.net/ and is very very common used file!!!  ???
What can do with this? should I contact with this site admins or file creator('Wyckoff, R. W. G.') for this errors??  ;D
++++++++++++++++++++++++++++++++++++
Is there any CIF for CoFe2O4 compound?

Offline curiouscat

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Re: How to create a structure from CIF file?
« Reply #14 on: November 23, 2013, 12:00:44 PM »

should I contact with this site admins or file creator('Wyckoff, R. W. G.') for this errors??  ;D


If you did indeed manage to establish contact with Wyckoff that'd be very impressive!  :)

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