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‎education/HADDOCK3/HADDOCK3-protein-protein-basic/index.md‎

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@@ -674,6 +674,8 @@ In this execution mode the HADDOCK3 job should be submitted to the batch system
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### Scenario 1: 1000 rigidbody docking models, selection of top 200 and flexible refinement + EM
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Now that we have all data ready, and know about execution modes of HADDOCK3 it is time to setup the docking for the first scenario. The restraint file to use for this is `e2a-hpr_air.tbl`. We proceed to produce 1000 rigidbody docking models, from which 200 will be selected and refined through flexible refinement and energy minimization.
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This corresponds to the default docking scenario of the HADDOCK2.X version.
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For the analysis following the docking results, we are using the solved complex [1GGR](https://www.rcsb.org/structure/1GGR), named e2a-hpr_1GGR.pdb.
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The configuration file for this scenario is:
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@@ -756,6 +758,8 @@ submitting it to the batch system requesting in this local run mode a full node
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### Scenario 2: 1000 rigidbody docking models, FCC clustering and selection of max 20 models per cluster followed by flexible refinement and EM
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In scenario 2, we proceed to produce 1000 rigidbody docking models, from which we proceed to do a first clustering analysis. From the top clusters a flexible refinement then energy minization is done.
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This scenario illustrates the new flexibility of HADDOCK3, adding a clustering step after rigid-body docking, which is not possible in the HADDOCK2.X version.
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For the analysis following the docking results, we are using the solved complex [1GGR](https://www.rcsb.org/structure/1GGR), named e2a-hpr_1GGR.pdb.
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The configuration file for this scenario is:
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@@ -968,7 +972,7 @@ We are providing in the `scripts` directory a simple script that extract some cl
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To use is simply call the script with as argument the run directory you want to analyze, e.g.:
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<a class="prompt prompt-cmd">
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./scripts/extract-capri-stats-clt.sh ./scenario1
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./scripts/extract-capri-stats-clt.sh ./run1-full
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</a>
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<details style="background-color:#DAE4E7">
@@ -977,7 +981,7 @@ To use is simply call the script with as argument the run directory you want to
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</summary>
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<pre>
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==============================================
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== scenario1-full/02_caprieval/capri_clt.tsv
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== run1-full/02_caprieval/capri_clt.tsv
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==============================================
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Total number of acceptable or better clusters: 0 out of 1
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Total number of medium or better clusters: 0 out of 1
@@ -987,7 +991,7 @@ First acceptable cluster - rank: i-RMSD: Fnat: DockQ:
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First medium cluster - rank: i-RMSD: Fnat: DockQ:
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Best cluster - rank: - i-RMSD: 6.407 Fnat: 0.202 DockQ: 0.264
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==============================================
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== scenario1-full/04_caprieval/capri_clt.tsv
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== run1-full/04_caprieval/capri_clt.tsv
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==============================================
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Total number of acceptable or better clusters: 0 out of 1
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Total number of medium or better clusters: 0 out of 1
@@ -997,7 +1001,7 @@ First acceptable cluster - rank: i-RMSD: Fnat: DockQ:
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First medium cluster - rank: i-RMSD: Fnat: DockQ:
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Best cluster - rank: - i-RMSD: 6.407 Fnat: 0.202 DockQ: 0.264
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==============================================
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== scenario1-full/06_caprieval/capri_clt.tsv
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== run1-full/06_caprieval/capri_clt.tsv
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==============================================
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Total number of acceptable or better clusters: 1 out of 1
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Total number of medium or better clusters: 0 out of 1
@@ -1007,7 +1011,7 @@ First acceptable cluster - rank: - i-RMSD: 2.976 Fnat: 0.611 DockQ: 0.601
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First medium cluster - rank: i-RMSD: Fnat: DockQ:
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Best cluster - rank: - i-RMSD: 2.976 Fnat: 0.611 DockQ: 0.601
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==============================================
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== scenario1-full/08_caprieval/capri_clt.tsv
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== run1-full/08_caprieval/capri_clt.tsv
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==============================================
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Total number of acceptable or better clusters: 1 out of 1
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Total number of medium or better clusters: 1 out of 1
@@ -1017,7 +1021,7 @@ First acceptable cluster - rank: - i-RMSD: 1.673 Fnat: 0.736 DockQ: 0.727
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First medium cluster - rank: - i-RMSD: 1.673 Fnat: 0.736 DockQ: 0.727
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Best cluster - rank: - i-RMSD: 1.673 Fnat: 0.736 DockQ: 0.727
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==============================================
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== scenario1-full/11_caprieval/capri_clt.tsv
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== run1-full/11_caprieval/capri_clt.tsv
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==============================================
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Total number of acceptable or better clusters: 3 out of 4
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Total number of medium or better clusters: 1 out of 4
@@ -1035,7 +1039,7 @@ Similarly some simple statistics can be extracted from the single model `capriev
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<a class="prompt prompt-cmd">
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./scripts/extract-capri-stats.sh ./runs/scenario1-surface
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./scripts/extract-capri-stats.sh ./runs/run1-full
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</a>
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<details style="background-color:#DAE4E7">
@@ -1044,7 +1048,7 @@ Similarly some simple statistics can be extracted from the single model `capriev
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</summary>
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<pre>
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==============================================
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== scenario1-full/02_caprieval/capri_ss.tsv
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== run1-full/02_caprieval/capri_ss.tsv
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==============================================
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Total number of acceptable or better models: 365 out of 1000
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Total number of medium or better models: 199 out of 1000
@@ -1054,7 +1058,7 @@ First acceptable model - rank: 3 i-RMSD: 1.153 Fnat: 0.556 DockQ: 0.711
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First medium model - rank: 3 i-RMSD: 1.153 Fnat: 0.556 DockQ: 0.711
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Best model - rank: 46 i-RMSD: 1.145 Fnat: 0.556 DockQ: 0.713
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==============================================
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== scenario1-full/04_caprieval/capri_ss.tsv
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== run1-full/04_caprieval/capri_ss.tsv
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==============================================
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Total number of acceptable or better models: 144 out of 200
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Total number of medium or better models: 137 out of 200
@@ -1064,7 +1068,7 @@ First acceptable model - rank: 3 i-RMSD: 1.153 Fnat: 0.556 DockQ: 0.711
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First medium model - rank: 3 i-RMSD: 1.153 Fnat: 0.556 DockQ: 0.711
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Best model - rank: 46 i-RMSD: 1.145 Fnat: 0.556 DockQ: 0.713
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==============================================
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== scenario1-full/06_caprieval/capri_ss.tsv
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== run1-full/06_caprieval/capri_ss.tsv
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==============================================
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Total number of acceptable or better models: 147 out of 200
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Total number of medium or better models: 118 out of 200
@@ -1074,7 +1078,7 @@ First acceptable model - rank: 2 i-RMSD: 1.221 Fnat: 0.694 DockQ: 0.727
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First medium model - rank: 2 i-RMSD: 1.221 Fnat: 0.694 DockQ: 0.727
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Best model - rank: 30 i-RMSD: 0.883 Fnat: 0.750 DockQ: 0.823
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==============================================
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== scenario1-full/08_caprieval/capri_ss.tsv
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== run1-full/08_caprieval/capri_ss.tsv
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==============================================
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Total number of acceptable or better models: 147 out of 200
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Total number of medium or better models: 118 out of 200
@@ -1084,7 +1088,7 @@ First acceptable model - rank: 1 i-RMSD: 1.219 Fnat: 0.833 DockQ: 0.787
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First medium model - rank: 1 i-RMSD: 1.219 Fnat: 0.833 DockQ: 0.787
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Best model - rank: 39 i-RMSD: 0.807 Fnat: 0.833 DockQ: 0.862
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==============================================
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== scenario1-full/11_caprieval/capri_ss.tsv
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== run1-full/11_caprieval/capri_ss.tsv
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==============================================
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Total number of acceptable or better models: 141 out of 185
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Total number of medium or better models: 116 out of 185
@@ -1232,7 +1236,7 @@ cluster_rank cluster_id n under_eval score score_std
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Use the `extract-capri-stats-clt.sh` script to extract some simple cluster statistics for this run.
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<a class="prompt prompt-cmd">
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./scripts/extract-capri-stats-clt.sh runs/scenario2/
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./scripts/extract-capri-stats-clt.sh runs/run2-full/
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</summary>
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<pre>
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==============================================
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== scenario2-cltsel-full/02_caprieval/capri_clt.tsv
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== run2-full/02_caprieval/capri_clt.tsv
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==============================================
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Total number of acceptable or better clusters: 0 out of 1
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Total number of medium or better clusters: 0 out of 1
@@ -1252,7 +1256,7 @@ First acceptable cluster - rank: i-RMSD: Fnat: DockQ:
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First medium cluster - rank: i-RMSD: Fnat: DockQ:
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Best cluster - rank: - i-RMSD: 6.407 Fnat: 0.202 DockQ: 0.264
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==============================================
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== scenario2-cltsel-full/05_caprieval/capri_clt.tsv
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== run2-full/05_caprieval/capri_clt.tsv
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Total number of acceptable or better clusters: 6 out of 33
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Total number of medium or better clusters: 1 out of 33
@@ -1262,7 +1266,7 @@ First acceptable cluster - rank: 2 i-RMSD: 1.193 Fnat: 0.563 DockQ: 0.701
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First medium cluster - rank: 2 i-RMSD: 1.193 Fnat: 0.563 DockQ: 0.701
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Best cluster - rank: 2 i-RMSD: 1.193 Fnat: 0.563 DockQ: 0.701
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== scenario2-cltsel-full/07_caprieval/capri_clt.tsv
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== run2-full/07_caprieval/capri_clt.tsv
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Total number of acceptable or better clusters: 0 out of 1
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Total number of medium or better clusters: 0 out of 1
@@ -1272,7 +1276,7 @@ First acceptable cluster - rank: i-RMSD: Fnat: DockQ:
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First medium cluster - rank: i-RMSD: Fnat: DockQ:
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Best cluster - rank: - i-RMSD: 8.237 Fnat: 0.104 DockQ: 0.121
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== scenario2-cltsel-full/09_caprieval/capri_clt.tsv
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== run2-full/09_caprieval/capri_clt.tsv
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==============================================
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Total number of acceptable or better clusters: 0 out of 1
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Total number of medium or better clusters: 0 out of 1
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First medium cluster - rank: i-RMSD: Fnat: DockQ:
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Best cluster - rank: - i-RMSD: 4.840 Fnat: 0.361 DockQ: 0.400
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== scenario2-cltsel-full/12_caprieval/capri_clt.tsv
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== run2-full/12_caprieval/capri_clt.tsv
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==============================================
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Total number of acceptable or better clusters: 4 out of 25
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Total number of medium or better clusters: 2 out of 25
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Similarly some simple statistics can be extracted from the single model `caprieval` `capri_ss.tsv` files with the `extract-capri-stats.sh` script:
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<a class="prompt prompt-cmd">
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./scripts/extract-capri-stats.sh ./runs/scenario2
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./scripts/extract-capri-stats.sh ./runs/run2-full
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</a>
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<details style="background-color:#DAE4E7">
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</summary>
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<pre>
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== scenario2-cltsel-full/02_caprieval/capri_ss.tsv
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== run2-full/02_caprieval/capri_ss.tsv
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Total number of acceptable or better models: 365 out of 1000
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Total number of medium or better models: 199 out of 1000
@@ -1318,7 +1322,7 @@ First acceptable model - rank: 3 i-RMSD: 1.153 Fnat: 0.556 DockQ: 0.711
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First medium model - rank: 3 i-RMSD: 1.153 Fnat: 0.556 DockQ: 0.711
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Best model - rank: 46 i-RMSD: 1.145 Fnat: 0.556 DockQ: 0.713
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== scenario2-cltsel-full/05_caprieval/capri_ss.tsv
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== run2-full/05_caprieval/capri_ss.tsv
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Total number of acceptable or better models: 62 out of 375
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Total number of medium or better models: 22 out of 375
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First medium model - rank: 3 i-RMSD: 1.153 Fnat: 0.556 DockQ: 0.711
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Best model - rank: 46 i-RMSD: 1.145 Fnat: 0.556 DockQ: 0.713
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== scenario2-cltsel-full/07_caprieval/capri_ss.tsv
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== run2-full/07_caprieval/capri_ss.tsv
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Total number of acceptable or better models: 74 out of 375
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Total number of medium or better models: 27 out of 375
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First medium model - rank: 6 i-RMSD: 1.081 Fnat: 0.750 DockQ: 0.771
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Best model - rank: 36 i-RMSD: 0.930 Fnat: 0.778 DockQ: 0.822
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== scenario2-cltsel-full/09_caprieval/capri_ss.tsv
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== run2-full/09_caprieval/capri_ss.tsv
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Total number of acceptable or better models: 74 out of 375
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Total number of medium or better models: 27 out of 375
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First medium model - rank: 3 i-RMSD: 0.991 Fnat: 0.806 DockQ: 0.821
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Best model - rank: 60 i-RMSD: 0.896 Fnat: 0.778 DockQ: 0.828
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== scenario2-cltsel-full/12_caprieval/capri_ss.tsv
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== run2-full/12_caprieval/capri_ss.tsv
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Total number of acceptable or better models: 65 out of 317
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Total number of medium or better models: 27 out of 317

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