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- See the time-evolution of the cross-peak (first and last atom) as plotted in "relayedThroughHHorQ.pdf". What does it mean?
- open relayedThroughHHorQ.pdf
- In the script, change the "specIndex" from 10 to 50; now the NOESY will be simulated for tauMixing=2.5s
- rerun the script. Notice the changes in the output.
- see also the new "relayedThroughHHorQ.pdf" file.
What would be needed to recover the full relaxation matrix - mainly the exact cross-relaxation rates exactly? Would be such an effort useful?
040 - structure of the protein-ligand complex
In this exercise, we gather together interatomic distances obtained before, separately from protein (030), for ligand (035), and add the protein-ligand distances. In this first attempt, we have exact distances (assume we are able to obtain them), with the exception of the protein-ligand distances, since here we do not account for the concentration of the P, L and PL as discussed in (038), and hence the intermolecular calibration is incorrect, when using the known distance of protein atom pair. We will see the possible effect in this exercices
- In 000_cyana subdirectory, combine the ".upl" files obtained before like
cat PxP* PxL* LxL* > all.upl
- do the structure calculation (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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