LORES: Low resolution shape program for the calculation of small angle scattering profiles for biological macromolecules in solution

A program for determining the low resolution shape of biological macromolecules, based on the optimization of a small angle neutron scattering profile to experimental data, is presented. This program, termed LORES, relies on a Monte Carlo optimization procedure and will allow for multiple scattering length densities of complex structures. It is therefore more versatile than utilizing a form factor approach to produce low resolution structural models. LORES is easy to compile and use, and allows for structural modeling of biological samples in real time. To illustrate the effectiveness and versatility of the program, we present four specific biological examples, Apoferritin (shell model), Ribonuclease S (ellipsoidal model), a 10-mer dsDNA (duplex helix) and a construct of a 10-mer DNA/PNA duplex helix (heterogeneous structure). These examples are taken from protein and nucleic acid SANS studies, of both large and small scale structures. We find, in general, that our program will accurately reproduce the geometric shape of a given macromolecule, when compared with the known crystallographic structures. We also present results to illustrate the lower limit of the experimental resolution which the LORES program is capable of modeling.

Program summary

Title of program:LORESCatalogue identifier: ADVCProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVCProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandComputer:SGI Origin200, SGI Octane, SGI Linux, Intel Pentium PCOperating systems:UNIX64 6.5 and LINUX 2.4.7Programming language used:CMemory required to execute with typical data:8 MBNo. of lines in distributed program, including test data, etc.:2270No. of bytes in distributed program, including test data, etc.:13 302Distribution format:tar.gzExternal subprograms used:The entire code must be linked with the MATH library