RE: [Ifeffit] Amplitude in Artemis
Hi Paul, How close are the distances for the 6 ligands? It is usually not possible to fit a single peak in the EXAFS spectrum by 6 independent signals. It sound like the distribution of distances for these 6 ligands is incorrect. I suggest that you try to fit just the first peak with one and then with two different shells with unknown coordination numbers and distances. This will give you some more information about what the data indicate the structure is like. If you send me an artemis file, I'll take a peak at it. Shelly skelly@anl.gov ________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Monday, February 27, 2006 6:31 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Amplitude in Artemis Hi Shelly Unfortunately the coordination number is 1 for all atoms present. I have the crystal structure of the complex, so I am currently including 6 ligating atoms all at distances defined by the structure in the input file. It seems to be the first shell that is causing the problems, with a quickfit first shell artemis fit giving nominally 13 ligating species (which is of course absurd). So I believe something else must be the problem. Cheers Paul ----- Original Message ----- From: Kelly, Shelly D. mailto:SKelly@anl.gov To: XAFS Analysis using Ifeffit mailto:ifeffit@millenia.cars.aps.anl.gov Sent: Tuesday, February 28, 2006 12:55 AM Subject: RE: [Ifeffit] Amplitude in Artemis Hi Paul, It seems possible that one of the other amplitude terms is also incorrect. Scott already mentioned the step height but what about the coordination number? The amplitude of the model is given by coordination number * S02. You mentioned that the S02 value was somewhere between 2 and 4. What is the value for coordination number * S02? If the coordination number is 1, then it is possible that the parameters are switched. Maybe the coordination number should be between 2 and 4 and S02 should be around 1. HTH, Shelly ________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Sunday, February 26, 2006 6:52 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Amplitude in Artemis I have just started a PhD and have been given alot of EXAFS data to simulate but I don't know much about artemis. I have tried to fit the data for quite some time now, but can't get any kind of good fit unless the amplitude is above 1. Is there any way amp can be above 1 and rationally explained? Cheers, Paul ________________________________ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Shelly: I took a look at Paul's data and this is what he was referring to. If the first shell is fit with a single scatterer of oxygen, it gives about 13 near neighbors. Carlo On Tue, 28 Feb 2006, Kelly, Shelly D. wrote:
Hi Paul,
How close are the distances for the 6 ligands? It is usually not possible to fit a single peak in the EXAFS spectrum by 6 independent signals. It sound like the distribution of distances for these 6 ligands is incorrect. I suggest that you try to fit just the first peak with one and then with two different shells with unknown coordination numbers and distances. This will give you some more information about what the data indicate the structure is like.
If you send me an artemis file, I'll take a peak at it.
Shelly
skelly@anl.gov
________________________________
From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Monday, February 27, 2006 6:31 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Amplitude in Artemis
Hi Shelly
Unfortunately the coordination number is 1 for all atoms present. I have the crystal structure of the complex, so I am currently including 6 ligating atoms all at distances defined by the structure in the input file. It seems to be the first shell that is causing the problems, with a quickfit first shell artemis fit giving nominally 13 ligating species (which is of course absurd). So I believe something else must be the problem.
Cheers
Paul
----- Original Message -----
From: Kelly, Shelly D. mailto:SKelly@anl.gov
To: XAFS Analysis using Ifeffit mailto:ifeffit@millenia.cars.aps.anl.gov
Sent: Tuesday, February 28, 2006 12:55 AM
Subject: RE: [Ifeffit] Amplitude in Artemis
Hi Paul,
It seems possible that one of the other amplitude terms is also incorrect. Scott already mentioned the step height but what about the coordination number? The amplitude of the model is given by coordination number * S02. You mentioned that the S02 value was somewhere between 2 and 4. What is the value for coordination number * S02? If the coordination number is 1, then it is possible that the parameters are switched. Maybe the coordination number should be between 2 and 4 and S02 should be around 1.
HTH,
Shelly
________________________________
From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Sunday, February 26, 2006 6:52 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Amplitude in Artemis
I have just started a PhD and have been given alot of EXAFS data to simulate but I don't know much about artemis. I have tried to fit the data for quite some time now, but can't get any kind of good fit unless the amplitude is above 1. Is there any way amp can be above 1 and rationally explained?
Cheers,
Paul
________________________________
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
-- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre@iit.edu http://www.iit.edu/~segre
Hi Shelly I've attached the artemis project files. Hopefully you get further with them than I have been able to. Cheers Paul ----- Original Message ----- From: Kelly, Shelly D. To: XAFS Analysis using Ifeffit Sent: Wednesday, March 01, 2006 1:50 AM Subject: RE: [Ifeffit] Amplitude in Artemis Hi Paul, How close are the distances for the 6 ligands? It is usually not possible to fit a single peak in the EXAFS spectrum by 6 independent signals. It sound like the distribution of distances for these 6 ligands is incorrect. I suggest that you try to fit just the first peak with one and then with two different shells with unknown coordination numbers and distances. This will give you some more information about what the data indicate the structure is like. If you send me an artemis file, I'll take a peak at it. Shelly skelly@anl.gov ------------------------------------------------------------------------------ From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Monday, February 27, 2006 6:31 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Amplitude in Artemis Hi Shelly Unfortunately the coordination number is 1 for all atoms present. I have the crystal structure of the complex, so I am currently including 6 ligating atoms all at distances defined by the structure in the input file. It seems to be the first shell that is causing the problems, with a quickfit first shell artemis fit giving nominally 13 ligating species (which is of course absurd). So I believe something else must be the problem. Cheers Paul ----- Original Message ----- From: Kelly, Shelly D. To: XAFS Analysis using Ifeffit Sent: Tuesday, February 28, 2006 12:55 AM Subject: RE: [Ifeffit] Amplitude in Artemis Hi Paul, It seems possible that one of the other amplitude terms is also incorrect. Scott already mentioned the step height but what about the coordination number? The amplitude of the model is given by coordination number * S02. You mentioned that the S02 value was somewhere between 2 and 4. What is the value for coordination number * S02? If the coordination number is 1, then it is possible that the parameters are switched. Maybe the coordination number should be between 2 and 4 and S02 should be around 1. HTH, Shelly ---------------------------------------------------------------------------- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Sunday, February 26, 2006 6:52 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Amplitude in Artemis I have just started a PhD and have been given alot of EXAFS data to simulate but I don't know much about artemis. I have tried to fit the data for quite some time now, but can't get any kind of good fit unless the amplitude is above 1. Is there any way amp can be above 1 and rationally explained? Cheers, Paul ---------------------------------------------------------------------------- _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ------------------------------------------------------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
participants (3)
-
Carlo Segre -
Kelly, Shelly D. -
Paul