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Introduction for Task 1:
In a real experimental , experimental situation, we have never complete set of distances between each pair of protons. The NOE crosspeaks are detectable for distances up to around 5 Angstrom. From these, many signal would share the
same frequency in the spectrum, and thus, assignment between signal and atom (atom pair) can be done only within some group, or not at all. Furthermore, the experimentally-derived distances contain various sources of error.
Partly, it is due to random noise, but partly due to incompletely resolved relayed transfer and partly due to different (local) dynamics influencing the cross-relaxation rate.
Let's start anyway with the unrealistic situation, where we know all the distances within 5.5 A, accurately.
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- In 000_cyana subfolder, look into at the configuration file, CALC.cya..
- ( execute in terminal/console: cd 030_proteinGetExactDistancesProtein/000_cyana )
- cat CALC.cya
- Start the calculation by
cyana 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 (cat demo.ovw)
See the target functions, its variation.
See the RMSD - root mean square displacement. - To view the structure, use
vmd demo.pdb #the same name will be produced in all trials of this tutorial
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 using a ready protein-ligand structure (final.pdb), in the 030 folder,
run ./proteinLigandCalcNOESY.py final.pdb (can take 20 min on some architectures, this same command can be used in all examples with protein and/or ligand) obviously doing different tasks.
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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 Angstrom for the strongest and 5.5 to the weakest. Here we try to get the actual distances.
031 - structure of protein from approximate distances
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- Check some of the simulated buildups, the buildupsLinearized in the supplied folders.
- cd ~/exercises/031_getApproximateDistancesProtein/buildupsLinarized
- open buidupsLin.pdf
- Without further effort, what are the chances to get accurate distances from these?
- Check how many distance restraints we have:
- cd ../000_cyana
- wc -l PxPapp.upl
- Start the structure calculation (cyana CALC.cya), or see the ready demo.pdb and demo.ovw file.
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- Check how many distances are left.
- cd ~/exercises/032_getApproximateDistancesProteinOnlyShortX1p5/000_cyana
- wc -l PxPapp1p5.upl
- Visualize the structure in VMD (vmd demo.pdb), instead of using only one Drawing Method, press Create Rep in Graphical representation. Keep one as Lines and other as NewCartoon.
- (Doublecklick on one of the copy would hide its visibility.)
- What can be problem when using only this short distances?
- Is the result satisfactory?
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- Check how many are left, what is the statistics of the structure calculation. And
- cd ~/exercises/034_getApproximateDistancesProteinX1p75Every10th/000_tryCyanaForProtein
- wc -l PxPapp.upl
- And visualize the structure in vmd.
- Switch again to NewCartoon drawing method. What happens?
- What do you think, were these attempts good enough?
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