Here we use the file example_4way_junction.cndo
, to demonstrate the use of this atomic model generator. The following steps are run in MATLAB.
Step 1. Add the two directories in the downloaded ZIP package to the MATLAB paths.
>> addpath cndo2atomic_v3.4
>> addpath topology2pdb_ver3_bulge
Step 2. Assign colors for the DNA strands. In this example, if a strand contains less than 100 nucleotides, then a color with the RGB value (190, 190, 190) is assigned to this strand. Otherwise a color with the RGB value (204, 121, 167) is assigned.
>> param.StrandColor = [190 190 190; 86 180, 233];
>> param.L_thres = 100;
Step 3. Assign the rendering resolution (typically between 3 and 6) and figure size (typically 640-by-480).
>> param.molmapResolution = 3;
>> param.WindowSize = [640 480];
Step 4. Assign the path to UCSF Chimera.
>> param.chimeraEXE = ‘”C:\Program Files\Chimera 1.8\bin\chimera.exe”‘;
>> param.chimeraOPTION = ‘––silent ––script’;
Step 5. Generate the atomic model
>> CAD_path = ‘example_4way_junction.cndo’;
>> work_DIR = ‘example_4way_junction’;
>> main_cndo2pdb(CAD_path, work_DIR, param);
Finally, a directory ‘example_4way_junction’ is created in the current working directory. The files in the directory ‘example_4way_junction’ should be the same as those in example_4way_junction.zip. The generated atomic structure is shown below.