problem with ift

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alienhunter_D

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Mar 17, 2021, 4:31:36 AM3/17/21
to BioXTAS RAW
Hello I wanted to try out the program and as I am not only doing proteins I also wanted to try to get the IFT of SDS micelles but the IFT is always forced to be postive it seems.
In the picture you can clearly see that the part of the PDDF that should be negative due to the negative core contrast is at 0. I also had to change the dmax search value to 150 otherwise it would try to go to 400.
SDS_ift_fail.PNG

Maybe I made a simple mistake and do not see the option to allow negative pddf values.

I like the program so it would be nice to use it also for such systems.
Greetings Martin

Jesse Hopkins

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Mar 17, 2021, 4:25:13 PM3/17/21
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Hi,

As part of the current BIFT algorithm, positivity is strictly enforced, there's no way to turn off that constraint. I haven't tried it myself, but the BIFT functionality is also available through the BayesApp web interface, and that interface seems to allow for negative P(r) functions, so I would recommend you try that:

All the best.

- Jesse

----
Jesse Hopkins, PhD
Beamline Scientist
BioCAT, Sector 18
Advanced Photon Source


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alienhunter_D

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Mar 19, 2021, 6:20:55 AM3/19/21
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Hello Jesse thank you for the info. I did check the documentation for that and I am pretty sure it does not say anything about a positivity constraint for BIFT  except in the faq that negative pr(r) values are not be afraid of :) so I thought it would be possible.
When using GNOM it works also fine. 
Greetings Martin

Jesse Hopkins

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Mar 19, 2021, 8:54:27 AM3/19/21
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Hi,

Yes, let me clarify. The implementation of BIFT in RAW has positivity strictly enforced, because of how its programmed. That’s not a general constraint of the method, just our current implementation, so the version I linked I believe supports negative values. And you are correct in that negative values in the P(r) function are fine in some cases.

I’ve added the ability to turn off the BIFT positivity constraint to my list of requested features for RAW, but I can’t promise how soon I’ll be able to get to it.

All the best.

- Jesse


----
Jesse Hopkins, PhD
Beamline Scientist
BioCAT, Sector 18
Advanced Photon Source
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