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EM to SANS

Calculates a small-angle neutron scattering profile from a user-supplied electron density map.


Accessibility

The EM to SANS module is accessible from the Calculate section of the main menu.


Basic Usage

The purpose of the module is to calculate the SANS intensity, I(q), and the distance distribution function, P(r), from an EM density map.


Notes


Screen Shots and Description of Input Fields


These examples show the calculation of P(r) and I(q) from MRC and Gaussian cube files.


Case 1: GroEl/GroES Complex (MRC file)

An EM density map, emd_1180.map, of a GroEL/GroES complex was obtained from the EM database.

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The inputs for EM to SANS are shown below.

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Example Output

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The output includes plots of the calculated P(r) and I(q) profiles.

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Results are written to a new directory within the given "run name" as noted above.

./run_0/em_to_sans/emd_1180.pdb
./run_0/em_to_sans/emd_1180.pdb.xyz
./run_0/em_to_sans/emd_1180.pr
./run_0/em_to_sans/emd_1180.iq
./run_0/em_to_sans/dum.inp (input file for SCAT)

Files Used and Created in Example


A Note on Threshold Values

When a threshold value of 0.6 was used, the resultant P(r) curve contained a large plateau at 1.0 (the largest value was scaled to 1.0 for easy comparison to other curves) and the I(q) curve did not contain the subsidiary maxima that would be expected for a symmetric molecule such as GroEl/GroES. As shown in the plots below, a threshold value of 1.2 or greater was needed in order to obtain more reasonalbe P(r) and I(q) curves. As the threshold was increased from 1.2 to 1.4, the maximum distance, Dmax, in the molecule decreased, along with the calculated Rg value.

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Although a threshold value of 1.2 or 1.4 will provide a reasonable idea of the shapes of the SANS P(r) and I(q) curves, it is important to examine a range of threshold values when comparing the calculated curves to measured SANS data!


Case 2: Segment of HIV-1 Gag Protein (Gaussian cube file)

A Gaussian cube density plot file was created for a segment of the HIV-1 Gag protein using Density Plot.

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The inputs for EM to SANS are shown below.

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Example Output

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The output includes plots of the calculated P(r) and I(q) profiles.

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Results are written to a new directory within the given "run name" as noted above.

./run_0/em_to_sans/gag_complete.pdb
./run_0/em_to_sans/gag_complete.pdb.xyz
./run_0/em_to_sans/gag_complete.pr
./run_0/em_to_sans/gag_complete.iq
./run_0/em_to_sans/dum.inp (input file for SCAT)

Files Used and Created in Example


Limitations


Reference(s) and Citations

  1. SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints J. E. Curtis, S. Raghunandan, H. Nanda, S. Krueger Comp. Phys. Comm. 183, 382-389 (2012). BIBTeX, EndNote, Plain Text

  2. Calculation of small-angle scattering profiles using Monte Carlo simulation S. Hansen J. Appl. Cryst. 23, 344-346 (1990). BIBTex, Endnote, Plain Text

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