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- In 000_... subfolder, look into the configuration file, CALC.cya, using a text editor/browser.
The set of structures will be written in demo.pdb - Start the calculation by
cyana CALC.cya - After the calculation is ready, look at the .owv file.
See the target functions, its variation.
See the RMSD - root mean square displacement. - To view the structure, use
vmd demo.pdb
In VMD, the default view shows the interatomic bonds as lines. - Go to Graphics->Representations
and change the Drawing Method to CPK.
To see the common representation for proteins,
choose NewCartoon as the Drawing method.
See how alpha-helices, beta-sheets and loops are identified.
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