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Lecture slides can be downloaded here: presentation.pdf
At wolf.ncbr.muni.cz, paste these commands (from "module add vmd" to "cd exercises") to the terminal/console and press enter (for other machine, follow the instructions at the end of the page).
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Get a copy of the python scripts and of the exercises:
- download exercises.tgz, for example, to your home (~/), and unpack them (in console/terminal, execute: tar xzvf exercises.tgz).
- download the pythonScripts.tgz, if you wish to do the calculations yourself (many are somewhat time consuming).
- place the python directory, e.g., to the bin folder. In steps: create by mkdir bin, then, if the scripts were in the Downloads folder, use mv Downloads/python.tgz bin; cd bin; tar xzvf python.tgz, and ensure that the bin/python is in the $PYTHONPATH:
- in terminal, execute: export PYTHONPATH=$PYTHONPATH:$HOME/bin/python
- be sure to have also these python libraries installed:
- scipy, numpy, networkx, sympy, matplotlib, ipython
- (at the moment, one library of the pythonScripts.tgz is only as a binary, so unfortunately, the exercises may fully work only with python3.11 and 3.12, please contact me if you encounter problems and if you would like to have the scripts working in your environment)
Installing an additional software:
- for visualization of molecules, install vmd https://www.ks.uiuc.edu/Research/vmd/
- for structure calculation using NOESY-derived restraints, install cyana http://www.cyana.org/wiki/Main_Page
Introduction for Task 1:
In a real, experimental
(If you open a new terminal/console, paste and execute again the first three commands)
Introduction for Task 1:
In a real, 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 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
- 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
045 -
Here the populations (concentrations) are take into account correctly, so also the intermolecular distances are calibrated correctly.
- 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:
(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
- 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
045 -
Here the populations (concentrations) are take into account correctly, so also the intermolecular distances are calibrated correctly.
- 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
- download exercises.tgz, for example, to Documents, and unpack them (in console/terminal, execute: cd Documents; tar xzvf exercises.tgz).
- 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. In steps: create by mkdir bin, then, if the scripts were in the Downloads folder, use mv Downloads/python.tgz bin; cd bin; tar xzvf python.tgz, and ensure that the bin/python is in the $PYTHONPATH:
- in terminal, execute: export PYTHONPATH=$PYTHONPATH:$HOME/bin/python
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Prepared 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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