Haddock3 protein protein basic tutorial #730
Conversation
education/HADDOCK3/HADDOCK3-protein-protein-basic/HADDOCK2-stages.png
Outdated
Show resolved
Hide resolved
education/HADDOCK3/HADDOCK3-protein-protein-basic/HADDOCK3-workflow-scheme.png
Outdated
Show resolved
Hide resolved
|
|
||
| <hr> | ||
|
|
||
| ### Defining the position restraints locally |
There was a problem hiding this comment.
ambiguous interaction restraints (and not positions restraints)
There was a problem hiding this comment.
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.
There was a problem hiding this comment.
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 ?
There was a problem hiding this comment.
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
Outdated
Show resolved
Hide resolved
There was a problem hiding this comment.
I would list the protein-protein basic tutorial as first one as it is the most basic one
| 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"} |
There was a problem hiding this comment.
Add missing link to the zip archive
| delete 1F3G | ||
| </a> | ||
|
|
||
| In a terminal, change the chain of e2a from a to B. |
There was a problem hiding this comment.
E2A is the first molecule and should have chain A. And HPR should have chain B.
There was a problem hiding this comment.
And as command I would recommend in this case:
pdb_chain -A e2a_1F3G.pdb |pdb_chainxseg >e2a_1F3G_A.pdb
and similarly for HPR further down.
To be consistent with the HADDOCK2.4 tutorial. The reference structure also has to A/B chainID for E2A/HPR
| <a class="prompt prompt-info">Select as ouptut format PDB (*.pdb *.pdb.gz)</a> | ||
| <a class="prompt prompt-info">Name your file *hpr-ensemble.pdb* and note its location</a> | ||
|
|
||
|
|
There was a problem hiding this comment.
Add here the pdb-tools command to assign it chain B
| # compute mode | ||
| mode = "local" | ||
| # 1 nodes x 96 ncores | ||
| ncores = 96 |
There was a problem hiding this comment.
I would change the value to e.g. 50
|
|
||
|
|
||
| <a class="prompt prompt-cmd"> | ||
| ./scripts/extract-capri-stats.sh ./runs/scenario1-surface |
There was a problem hiding this comment.
Make consistent with previous command - same run directory and name
| 9 12 11 - -100.932 9.238 10.829 0.016 0.132 0.01218.562 0.153 0.108 0.004 17.755 0.101 32.367 14.729 1645.305 104.797 -18.030 2.335 -232.574 32.271 -239.830 42.371 -39.624 7.4289 | ||
| ... | ||
| </pre> | ||
| </details> |
| Use the `extract-capri-stats-clt.sh` script to extract some simple cluster statistics for this run. | ||
|
|
||
| <a class="prompt prompt-cmd"> | ||
| ./scripts/extract-capri-stats-clt.sh runs/scenario2/ |
There was a problem hiding this comment.
Make similar commands consistent, e.g. ./runs/scenario2 - and use for all similar commands the pre-calculated runs
| alignto sele<br> | ||
| </a> | ||
|
|
||
| <a class="prompt prompt-question"> |
There was a problem hiding this comment.
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.
|
|
||
| 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. | ||
|
|
||
| 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: |
There was a problem hiding this comment.
This was never described previously. So some instructions on which structures to visualise should be given here.
This is the tutorial for basic protein-protein docking.