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  • download exercices.tgz to and untar (tar xzvf exercises.tgz) them in some accessible folder.
  • download  the pythonScripts.tgz, if you wish to do the calculations yourself (many are time consuming). 
    • place the python directory, e.g., to the bin folder, and ensure that the bin/python is in the $PYTHONPATH:
    • export PYTHONPATH=$PYTHONPATH:$HOME/bin/python
  • lecture slides presentation.pdf


Part 1

Introduction for task 1:

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Remark: CYANA is a proprietary software. For any installation problem, contact Peter Güntert, the author of CYANA.

Task 1

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(030)

  • In 000_... subfolder, look Look into the configuration file, CALC.cya, using a text editor/browser.
    The set of structure structures will be writen 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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Next, we can think that the number of (inaccurate) constraints is simply too large. Commonly we would expect up to
aroound around 10 constraints per amimoacid aminoacid residue.  In the previous example, it was still around 12800/97 > 100 restraints
per residue. Here we try to use, only every 10th restraints.

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