SASMOL

SASMOL is a software integrated among the models of GENFIT. It calculates the SAXS or SANS form factor of a Protein Data Bank (PDB) structure on the basis of the positions of each atom. The scattering contributions of the hydration layers are taken into account by finding the position of the water molecules in contact with the pdb structure and by assigning to them a relative mass density different from the one of bulk water molecules.

SASMOL can be executed under Windows or Linux/Mac machines. It needs to be compiled by gfortran.

M. G. Ortore, F. Spinozzi, P. Mariani, A. Paciaroni, L. R. S. Barbosa, H. Amenitsch, M. Steinhart, J. Ollivier and D. Russo, J. R. Soc. Interface. (2009) 6, S619-S634.

Installation

Windows

1) Download and install gfortran for your Windows machine. To be sure that the installation has been successful, open a prompt window and type gfortran: the system must recognize that the gfortran command exists. If not you have to include the folder where gfortran has been installed in the PATH variable

2) Download and uncompress the file sasmol_1.6_windows.rar (see below)

3) Open a prompt window, go into the folder sasmol_1.6_windows (it is a subfolder of the folder where the file sasmol_1.6_windows.rar has ben uncompressed) and run the command: compile.bat

4) To ensure the goodness of the installation, run the command: example_run.bat

5) The general command to excute sasmol is: sasmol16 <pdb>, where ,<pdb> is the four digit code of a pdb file. This file should be in the folder sasmol_1.6_windows

6) To execute sasmol from an other folder, copy the file sasmol16.ini in that folder. Open a prompt window, go into that folder and run the command: <folder_sasmol>\sasmol16 <pdb>, where, <folder_sasmol> is the complete path of the sasmol_1.6_windows folder

Linux/Mac

1) Download and install gfortran for your Mac or Linux machine.

2) Download and uncompress the file sasmol_1.6_linux.rar (see below).

3) Open a terminal window, go into the folder sasmol_1.6_linux (it is a subfolder of the folder where the file sasmol_1.6_linux.rar has ben uncompressed) and run the command: ./compile

4) To ensure the goodness of the installation, run the command: ./example_run

5) The general command to excute sasmol is: ./sasmol16 <pdb>, where ,<pdb> is the four digit code of a pdb file. This file should be in the folder sasmol_1.6_linux

6) To execute sasmol from an other folder, copy the file sasmol16.ini in that folder. Open a command window, go into that folder and run the command: <folder_sasmol>/sasmol16 <pdb>, where, <folder_sasmol> is the complete path of the sasmol_1.6_linux folder.

Use

1) To manage the parameters that control the calculation (e.g. SAXS, SANS with different ratio [D2O]/([H2O]+[D2O], relative mass density of hydration water) open with a text editor (e.g. notepad, emacs, vi) the file sasmol16.ini and enter the proper modifications.

2) The SAXS/SANS curve calculated by sasmol is in the file sasmol<pdb>.pq, with q=4πsinθ/λ in the first column (in Å^-1) and dσ/dΩ in the second column (in barn).

3) The output parameters of the calculation (e.g. molecular weight, displaced volume, hydration volume) are store in the file sasmol<pdb>.out.