CRYSOL with multiple unit cells of PDB structure?

Calculation of SAXS and SANS profiles (CRYSOL, CRYSON), superposition of models (SUPCOMB, DAMAVER, DAMCLUST), database DARA
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akowals3
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CRYSOL with multiple unit cells of PDB structure?

#1 Post by akowals3 » 2018.03.21 23:26

I'm new to CRYSOL and attempting to determine the theoretical SAXS scattering from increasingly large sets of unit cells of a protein (PDB code 2fgs) as a way to extrapolate the scattering from the crystal itself.
For example I will feed CRYSOL the .pdb file for the monomer, then in Pymol I will create a structure with 4 unit cells and feed that to CRYSOL, and so on.
I have done this for monomer and 4-unit-cells and attached the .int files for both. The monomer scattering intensity decays smoothly while the 4-unit-cell version is peaked. Does this make sense and indicate the beginnings of some Bragg peaks?
Additionally, does anyone know what the axes units are supposed to be on these graphs and what each of the colored lines refer to? Presumably sample and background? I can't find a legend.
Thanks in advance for your help!
Attachments
4unitcell2fgs00.int
.int file for 4 unit cells of 2fgs
(3.63 KiB) Downloaded 119 times
2fgs00.int
.int file for 2fgs monomer
(3.63 KiB) Downloaded 107 times

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AL
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Please read the CRYSOL manual

#2 Post by AL » 2018.03.26 11:42

akowals3 wrote:... The monomer scattering intensity decays smoothly while the 4-unit-cell version is peaked. Does this make sense and indicate the beginnings of some Bragg peaks?
You've computed the scattering up to 0.5 A-1 using just 51 points - that's why it looks bumpy. These default parameters are okay for a quick-and-dirty check what a scattering pattern from an average-sized protein would look like. For a larger particle consider using more data points ('-ns' option, e.g. '-ns 501'). For a more accurate computation consider increasing the maximum order of harmonics ('-lm' option, e.g. '-lm 50').
akowals3 wrote:Additionally, does anyone know what the axes units are supposed to be on these graphs...
CRYSOL *.int files are in inverse angstroms (horizontal axis). The intensity is in arbitrary units (vertical axis).
akowals3 wrote:...and what each of the colored lines refer to? Presumably sample and background? I can't find a legend.
The CRYSOL manual describes the *.int output file:
The first line is a title. Five columns contain:
(1) experimental scattering vector in inverse angstroms,
(2) theoretical intensity in solution,
(3) in vacuo,
(4) the solvent scattering and
(5) the border layer scattering.

You are interested in the first curve, i.e. column (2). In PRIMUS you may go to 'Settings > Configure primus' and tick 'If data files contain multiple datasets, open and display only the first dataset'.

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