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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. - To simulate the NOESY spectrum, in the 030 folder,
run ./proteinLigandCalcNOESY.py final.pdb (can take 20 min on some architectures)
Introduction to Task 2
It used to be common to only simply classify the experimental NOE intensities to strong, medium and weak, and assign corresponding distance ranges of around 2 Angsrom for the strongest and 5.5 to the weakest.
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- We check the effect of the exchange rate on the resulting cross-relaxation rates.
See e.g. like: tail -n 15 outputKex5e* - What would be the consequence of "not so fast" exchange?
- run ./proteinLigandCalcNOESY.py triPepMod.pdb
- experiment with settings in parameters*.json files.
What is even more important is the population weighting of the intermolecular cross-rates (hence also NOEs)
The "Re weighted" matrix contains includes the correction, whereas the "weight averaged over P, L, PL" does not.
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