Re: [Ifeffit] Ifeffit Digest, Vol 169, Issue 9

[Bruce Ravel]

On 03/14/2017 06:15 AM, Abhinav Prabhakar wrote:

Attached is the CIF file in question. The crystal is Tobermorite 14A,
taken from COD website.



Abhinav,

I don't understand the contents of the CIF file in the context of the 
copy of the International Tables that I have in front of me.  The list 
of equivalent positions given in the CIF file just doesn't seem to be 
right for space group 9.


The CIF file is clearly using the C axis as the unique axis since the z 
coordinate is the negated coordinate.  But the list of positions does 
not correspond to any of the three cell choices.


While this could be a problem in Artemis, I am inclined to think that 
the authors of the paper cited in the CIF file made some kind of 
non-standard choice for the setting of their crystal.


As I said before, Artemis does what the International Tables tell it to 
do.  If the author of a crystallography paper makes some non-standard 
choice, Artemis won't know how to deal with it.


B



--
 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Building 743, Room 114
 Upton NY, 11973

 Homepage:http://bruceravel.github.io/home/
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
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Re: [Ifeffit] Ifeffit Digest, Vol 169, Issue 9

[Abhinav Prabhakar]

Hello,

Thank you for your reply.

Attached is the CIF file in question. The crystal is Tobermorite 14A, taken
from COD website.

However, the structure has partial occupancy and it is modified to include
full occupancy. The modified CIF file shows a space group of B11b (and
cannot be recognized by Artemis). I tried a C1c1 space group (it works) but
it shows the same structural values as a P11b.

Regards,
AP


On Tue, Mar 14, 2017 at 1:00 AM, 
wrote:

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> Today's Topics:
>
>1. Re: Space group type in Artemis (Bruce Ravel)
>2. Data export and coordination number (Abhinav Prabhakar)
>3. Re: Data export and coordination number (Bruce Ravel)
>
>
> --
>
> Message: 1
> Date: Mon, 13 Mar 2017 09:20:14 -0400
> From: Bruce Ravel 
> To: XAFS Analysis using Ifeffit 
> Subject: Re: [Ifeffit] Space group type in Artemis
> Message-ID: <3853f1f7-61fd-6886-306f-040c540ec...@bnl.gov>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> On 03/11/2017 05:56 AM, Abhinav Prabhakar wrote:
> > Hello,
> >
> > I have a question about the working of Artemis as a new user.
> >
> > Artemis does not recognize the space group B11b. When importing a cif
> > file of a crystal with this symmetry, it sends a prompt message that the
> > space group symbol cannot be recognized. As a result, I changed it to
> > P11b and it works. But would this change any crystal information (for
> > eg. Degen, Reff values) significantly?
>
> I am not a crystallography expert in any sense.  When I wrote Artemis, I
> meticulously followed what I found in the fourth edition of the
> International Tables for Crystallography, Volume A.  Every symbol
> defined in there is recognized by Artemis.  (Well, I guess I should say
> that every symbol is /supposed to be/ recognized by Artemis.  If one is
> missing,  that's a bug and should be reported.)
>
> "B11b" is not a symbol that I found in my copy of ITC volume A.  As
> Robert suggested, there may be a way to rotate group 9 so that "B11b" is
> an interpretable symbol in the abstract.  But Artemis does not know how
> to do that.  (Nor do I.)
>
> "P11b" is a setting for space group #7.  If, as Robert suggests, your
> CIF file is for space group #9, then the answer to your last question is
> yes.  It is plainly obvious that using a different space group will
> change the degeneracies and distances.
>
>
> Of course, you did not bother to include a copy of the CIF file in
> question to your original email, so it is not actually possible for
> Robert or I or anyone else to actually help you effectively.
>
> At the risk of sounding like an annoyingly broken record, everyone
> should take the time to ask a good question or write an actionable bug
> report:
>
>http://bruceravel.github.io/demeter/documents/SinglePage/help.html
>http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html
>
> B
>
>
> --
>   Bruce Ravel   bra...@bnl.gov
>
>   National Institute of Standards and Technology
>   Synchrotron Science Group at NSLS-II
>   Building 743, Room 114
>   Upton NY, 11973
>
>   Homepage:http://bruceravel.github.io/home/
>   Software:https://github.com/bruceravel
>   Demeter: http://bruceravel.github.io/demeter/
>
>
> --
>
> Message: 2
> Date: Mon, 13 Mar 2017 21:48:31 +0800
> From: Abhinav Prabhakar 
> To: ifeffit@millenia.cars.aps.anl.gov
> Subject: [Ifeffit] Data export and coordination number
> Message-ID:
>  com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello,
>
> As a new user, I have some questions related to the use of Athena and
> Artemis:
>
> i) Is it possible to extract the normalized/background corrected data from
> Athena (in E-,k- and R- space) and export it as numbers (to Excel perhaps)?
>
> ii) Using Artemis, how can coordination numbers (N) be expressed as 'guess'
> parameters (Artemis allows only numerical values for N)?
>
> Thank you.
>
> Regards,
>
> Abhinav Prabhakar (Mr.)
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