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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 population 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 exerticesexercices
- 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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Assembled by Dr. Jiří Mareš,shaped by discussion with Prof. Julien Orts, Florian Wolf M.Sc. and other members of the research group (https://bionmr.univie.ac.at/people/)
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