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SLD MOL

Calculates neutron and X-ray reflectivity scattering length density (SLD) profiles from user supplied structures.

Accessibility

The SLD MOL module is accessible from the Calculate section of the main menu.

Basic Usage

The purpose of the module is to calculate theoretical neutron and X-ray reflectivity SLD profiles, SLD(z) vs z, from user supplied structures for comparison to experimentally-derived SLD profiles. Utilities for experimental planning and isotopic labeling as well as optimization of ensemble populations are supplied.

Notes

Screen Shots and Descriptions of Input Fields

These examples calculate SLD profiles from an ensemble of structures of the HIV1 gag protein on a surface, optimizing z0 and A0 of the average SLD by comparing to an experimentally-derived SLD profile. One such structure is shown below. The surface would be at the left side of the frame.

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NOTE: The ensemble used in these examples contains 225 structures. Typically, more than 10,000 structures are required to adequately sample the possible conformations that can occur at a surface. Some conformations may need to be excluded due to packing effects at the surface, experimentally determined Rg value, etc. A number of ensembles may need to be tested before a suitable result that matches the experimental data is obtained.

Case 1: Optimize z0 and A0 of Average SLD

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Example Output

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./run_0/sld_mol/average_sld.txt
./run_0/sld_mol/rg_lt70_results.txt

average_sld.txt contains the average SLD profile of the ensemble.

rg_lt70_results.txt contains the z0, A0 and chi-squared values for the average SLD profile.

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Plot of experimental SLD and optimized average SLD. Recall that there are only 225 structures in this test ensemble. A better match to the experimental SLD can likely be obtained with a larger starting ensemble.

Files Used and Created in Example

Case 2: Calculate Individual SLDs using Optimzed z0 and A0 values

An examination of the rg_lt70_results.txt file created in the above example shows the optimzed z0 and A0 values for the average SLD.

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This example now calculates the individual SLDs using the optimzed values: z0 = -10.0 and A0 = 0.27.

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Example Output

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./run_1/sld_mol/average_sld.txt
./run_1/sld_mol/rg_lt70_results.txt
./run_1/sld_mol/bestworstfile.txt
./run_1/sld_mol/sldfile_00001.txt
.
.
.
./run_1/sld_mol/sldfile_00225.txt

average_sld.txt contains the average SLD profile of the ensemble.

rg_lt70_results.txt contains the z0, A0 and chi-squared values for the average SLD profile.

bestworstfile.txt contains the names of the files with the best and worst chi-squared values.

sldfile_00001.txt to sldfile_00225.txt contain the individual SLD profiles.

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Plot of experimental SLD, average SLD, best-fit SLD and worst-fit SLD. Recall that there are only 225 structures in this test ensemble. A better match to the experimental SLD can likely be obtained with a larger starting ensemble.

Files Used and Created in Example

Case 3: Applying an Experimental SLD Offset Correction

There are times when it may be desirable to offset the z-position of the experimental SLD before performing any optimizations.

This example shows how to compare the average SLD to the experimental SLD using an experimental SLD offset correction of 10.0 angstroms. The experimental z-offset is taken into account when calculating chi-squared.

z0 and A0 are not optimized in this example. But, this can be easily accomplished by following Case 1 with the adjustments for the non-zero z-offset that are shown in this example.

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Example Output

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./run_2/sld_mol/average_sld.txt
./run_2/sld_mol/rg_lt70_results.txt

average_sld.txt contains the average SLD profile of the ensemble.

rg_lt70_results.txt contains the z0, A0 and chi-squared values for the average SLD profile.

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Plot of experimental SLD and the average SLD. Compare this to the plot in Case 1.

IMPORTANT NOTE While the z-axis of the experimental SLD has been shifted in this plot to take the z-offset into account, the experimental SLD file is NOT rewritten with the offset z values.

Files Used and Created in Example

Reference(s) and Citations

Electrostatic interactions and binding orientation of HIV-1 matrix, studied by neutron reflectivity H. Nanda, S. A. K. Datta, F. Heinrich, A. Rein, S. Krueger, J. E. Curtis, Biophys. J. 99, 2516-2524 (2010). BIBTex EndNote Plain Text

SLDMOL: A tool for the structural characterization of thermally disordered membrane proteins
J. E. Curtis, H. Zhang, H. Nanda, Comp. Phys. Comm. 185, 3010-3015 (2014). BIBTex EndNote Plain Text

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