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- ./pdbSimNoeFrontEnd.py triPep4H.pdb. (or cat pdbSimNoeFrontEnd.out)
- follow the three tasks (printed by the script) to compare. Answer namely,
- how, in the NOESY spectrum, is the crosspeak between the first and last atom affected by merging the middle ones?
- how is the extracted cross-relaxation rate (again between the first and last atom) affected by this merging?
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- In 000_cyana subdirectory, combine the ".upl" files obtained before like
cat PxP* PxL* LxL* > all.upl
- do the structure calculation (
- cd ~/exercises/040_getCommplexUseProteinLigandDistancesWithoutCorrection/000_cyana
- cyana CALC.cya
- or check already the demo.ovw (cat demo.ovw)
- When viewing the complex using VMD, in Graphical representation, you can select the atoms of proteins by typing "protein" and the ligand as "not protein"
- Showing the protein structure as NewCartoon, we may miss a large portion, due to extra atoms - linker needed by CYANA to keep the ligand as a part of the same molecular graph with the protein
- Remove the linker (and other possible pseudoatoms) by
grep -v Q demo.pdb > demoClean.pdb
vmd demoClean.pdb
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- What is the difference WRT 040 ?
- for that, see first the .upl files, only the distances between protein and ligand:
- cd ~/exercises/045_getProteinLigandDistancesExactAndFixedWeights
- head PxLrewight.upl ../040_getCommplexUseProteinLigandDistancesWithoutCorrection/PxL.upl
- see then the resulting protein-ligand structure
- cd 000_cyana
- remove the Q atoms in demo.pdb as before and see in VMD
Instructions for different machine:
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