Calculates a small-angle neutron scattering profile from a user-supplied electron density map.
The EM to SANS module is accessible from the Calculate section of the main menu.
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.
The 3-D map file format must be Gaussian cube (.cube) or MRC (.mrc). CCP4 (.map) files are very similar to MRC files and can also be read using the MRC file type.
The user must input a value for the cutoff threshold. See A Note on Threshold Values below for more information.
Each voxel in the map with an occupation greater than the threshold value is represented as a scattering center. The coordinates of each scattering center are written in a PDB-formatted file (C-atom) and a xyz-formatted file. The latter file is used by the SCAT program to calculate a SANS intensity, I(q), and a distance distribution function, P(r).
These examples show the calculation of P(r) and I(q) from MRC and Gaussian cube files.
An EM density map, emd_1180.map, of a GroEL/GroES complex was obtained from the EM database.
The inputs for EM to SANS are shown below.
run name User defined name of folder that will contain the results.
select EM file type Input map type. mrc is selected.
input EM density file File containing EM density map.
output file name (pdb) PDB file of balls that fit inside the EM map.
cutoff threshold Value to set the three dimensional contour to define the EM map. A value of 1.4 is provided.
ooutput SANS profile file name SANS profile file name from the EM map.
number of q points in SANS profile The number of I(q) values in the output SANS profile file.
maximum q in SANS profile Maximum q value (1/angstrom) in the output SANS profile file.
The output includes plots of the calculated P(r) and I(q) profiles.
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)
input files
output files
The shapes of the calculated P(r) and I(q) curves can be dramatically affected by the chosen threshold value! This can affect the calculated Rg and Dmax values of the structure as well.
Maps in the EMD database should contain a recommended threshold or "contour" level. In this case, the recommended value is 0.608. However, this should be considered a starting value and may not produce the best representation of a SANS curve from this complex.
When comparing calculated I(q) and/or P(r) curves to SANS data, a range of threshold values may need to be tested.
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.
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!
A Gaussian cube density plot file was created for a segment of the HIV-1 Gag protein using Density Plot.
The inputs for EM to SANS are shown below.
The output includes plots of the calculated P(r) and I(q) profiles.
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)
input files
output files
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
Calculation of small-angle scattering profiles using Monte Carlo simulation S. Hansen J. Appl. Cryst. 23, 344-346 (1990). BIBTex, Endnote, Plain Text