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

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)

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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-040c540ecae1@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 ------------------------------------ bravel@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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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: 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.)