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| ### Defining the position restraints locally |
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ambiguous interaction restraints (and not positions restraints)
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Note that we could also simplify this section by explaining the use of the haddock-restraints server - https://wenmr.science.uu.nl/haddock-restraints - using the advanced option the passive residues can automatically defined.
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I could add a sentence about the possibility of using the server ? But still keep the command lines about the position restraints, as it is a tutorial about the local usage of HADDOCK3 ?
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Yes - but the haddock-restraints tool might replace the haddock3-restraints one at some point. So good to have both
education/HADDOCK3/HADDOCK3-protein-protein-basic/plots/GOGO_scenario2/dockq_clt.html
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| preprocessing of those files will also be explained in this tutorial). The files have been processed | ||
| to facilitate their use in HADDOCK and for allowing comparison with the known reference | ||
| structure of the complex. For this _download and unzip the following_ | ||
| [zip archive](){:target="_blank"} |
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Add missing link to the zip archive
| alignto sele<br> | ||
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| <a class="prompt prompt-question"> |
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For these questions, I would add a note that in principle the analysis done above and the caprieval results should allow you to already answer those questions.
May-be this section should be changed, to have people select the clusters they want to visualise based on the capri analysis above. Then visualise them and compare them to the reference structure.
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| As explained in the introduction, the structure of the native complex has been determined by NMR (PDB ID [1GGR](https://www.ebi.ac.uk/pdbe/entry/pdb/1ggr){:target="_blank"}) using a combination of intermolecular NOEs and dipolar coupling restraints. We will now compare the docking models with this structure. | ||
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| If you still have all cluster representative open in PyMOL you can proceed with the sub-sequent analysis, otherwise load again each cluster representative as described above. Then, fetch the reference complex by typing in PyMOL: |
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This was never described previously. So some instructions on which structures to visualise should be given here.
(work in progress)
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This is the tutorial for basic protein-protein docking.