Calculating scattering intensity using alm file

Calculation of SAXS and SANS profiles (CRYSOL, CRYSON), superposition of models (SUPCOMB, DAMAVER, DAMCLUST), database DARA
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littlelamb
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Calculating scattering intensity using alm file

#1 Post by littlelamb » 2016.02.18 18:28

Hi all,

I have a question about how does Cryson calculate scattering intensity( included in *.int file) using partial scattering amplitude outputs (included in *.alm file). According to equation 11 in crysol 1995 paper, the partial scattering amplitudes in alm file should be the Sum of the scattering amplitudes for atoms, excluded volume and border.

alm file looks like following,

Evaliuated from pdb file ............................... : sle1s3.33-capb0.39-nacl3.01-noprm.pdb
Max order of harmonics ................................. : 15
Number of points ....................................... : 256

L: 0 M: 0
0.000000000000000E+000 (1192.92431640625,0.000000000000000E+000)
3.490196075290442E-003 (1181.47119140625,0.000000000000000E+000)
6.980392150580883E-003 (1148.36633300781,0.000000000000000E+000)
1.047058869153261E-002 (1095.48767089844,0.000000000000000E+000)
1.396078430116177E-002 (1026.04614257812,0.000000000000000E+000)


I assume that column 1 is scattering vector and column 2 and 3 are real and imaginary parts of partial scattering amplitudes. So I also assume adding the scattering amplitudes for different L and M at each scattering vector would give me scattering intensity. However, these numbers don't add up to the intensity file cryson prints out. I am wondering if anyone could help with this? ( corresponding alm file and int file are attached )

Thank you very much in advance!
Attachments
01.alm
alm file , to get to the ASCII file , I used conv_alm.exe , for the size limit of file, I only uploaded the alm file.
(274.13 KiB) Downloaded 69 times
01.int
int file
(18.08 KiB) Downloaded 64 times

ckerr
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Location: EMBL Hamburg

Re: Calculating scattering intensity using alm file

#2 Post by ckerr » 2016.02.19 15:39

You have to count all the non-zero M values twice (the values for positive and negative M are the same, so only the value for positive M is recorded)

ckerr
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Location: EMBL Hamburg

Re: Calculating scattering intensity using alm file

#3 Post by ckerr » 2016.02.19 15:44

(or possibly the value for negative M is the complex conjugate of the value for positive M; in any case it's the same once you take the square modulus)

littlelamb
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Re: Calculating scattering intensity using alm file

#4 Post by littlelamb » 2016.02.24 19:29

Thanks for your replies! I now consider the M negative cases as you suggested. Now the intensity it calculated have the same number as the cryson output(int file) with multiplied by 20. Any particular reason it have to be multiplied by 20??? Thank you and looking forward to your replies!

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