From 6143475d2ea90ef71ce68ae077b1ad9ad159deeb Mon Sep 17 00:00:00 2001 From: Alexandre Bonvin Date: Mon, 18 Apr 2016 22:52:40 +0300 Subject: [PATCH] Corrected typos in README, added .gitignore --- .gitignore | 54 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ README.md | 30 +++++++++++++++--------------- 2 files changed, 69 insertions(+), 15 deletions(-) create mode 100644 .gitignore diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..a4d7d33 --- /dev/null +++ b/.gitignore @@ -0,0 +1,54 @@ +# Generic Files # +################### + +# Compiled source # +################### +*.com +*.class +*.dll +*.exe +*.o +*.so + +# Packages # +############ +# it's better to unpack these files and commit the raw source +# git has its own built in compression methods +*.7z +*.dmg +*.gz +*.iso +*.jar +*.rar +*.tar +*.tgz +*.zip + +# Logs and databases # +###################### +*.log +*.sql +*.sqlite + +# OS generated files # +###################### +.DS_Store +.DS_Store? +._* +.Spotlight-V100 +.Trashes +ehthumbs.db +Thumbs.db + +# Python Files # +################### +*.pyc + +# HADDOCK stuff # +###################### +cluster_struc +contact +T70-dimer +T70-dimer-full +T70-tetramer +T70-tetramer-full diff --git a/README.md b/README.md index 825fe70..1cb97e6 100644 --- a/README.md +++ b/README.md @@ -11,10 +11,10 @@ image: Our information-driven docking approach [HADDOCK](http://www.bonvinlab.org/software/haddock2.2) is a consistent top predictor and scorer since the start of its participation in the [CAPRI](http://www.ebi.ac.uk/msd-srv/capri) community-wide experiment. This sustained performance is due, in part, to its ability to integrate experimental data and/or bioinformatics information into the modelling process, and also to the overall robustness of the scoring function used to assess and rank the predictions. -This tutorial will demonstrate the use of HADDOCK for predicting target70 of the CASP-CAPRI experiment. This target was given to the CAPRI community as a tetramer, but there has been discussions weither the biological unit is a dimer or a tetramer. We will use this target to illustrate the ab-initio docking mode of HADDOCK, using a combination of [center-of-mass restraints](http://www.bonvinlab.org/software/haddock2.2/run/#disre) to bring the subunits together and [symmetry restraints](http://www.bonvinlab.org/software/haddock2.2/run/#sym) to define the symmetry of the assembly. +This tutorial will demonstrate the use of HADDOCK for predicting target70 of the CASP-CAPRI experiment. This target was given to the CAPRI community as a tetramer, but there has been discussions whether the biological unit is a dimer or a tetramer. We will use this target to illustrate the ab-initio docking mode of HADDOCK, using a combination of [center-of-mass restraints](http://www.bonvinlab.org/software/haddock2.2/run/#disre) to bring the subunits together and [symmetry restraints](http://www.bonvinlab.org/software/haddock2.2/run/#sym) to define the symmetry of the assembly. For this tutorial we will make use of the H[ADDOCK2.2 webserver](http://haddock.science.uu.nl/services/HADDOCK2.2). -A description of our web server van be found in the following publications: +A description of our web server can be found in the following publications: * G.C.P van Zundert, J.P.G.L.M. Rodrigues, M. Trellet, C. Schmitz, P.L. Kastritis, E. Karaca, A.S.J. Melquiond, M. van Dijk, S.J. de Vries and A.M.J.J. Bonvin. [The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes](http://dx.doi.org/doi:10.1016/j.jmb.2015.09.014). @@ -31,7 +31,7 @@ Further, multi-body docking and the use of symmetry restraints is described in t _Mol. Cell. Proteomics_, *9*, 1784-1794 (2010). Download the final author version here. -Throughout the tutorial, colored text will be used to refer to questions or +Throughout the tutorial, coloured text will be used to refer to questions or instructions, Linux and/or Pymol commands. This is a question prompt: try answering @@ -91,13 +91,13 @@ You will see three directories and one file: * **protein1.pdb**: this is the model we built for this target based on the sequence information that was provided to the CAPRI predictors. -* **runs**: this directory contains a script that allows you to download precalculated full docking runs. +* **runs**: this directory contains a script that allows you to download pre-calculated full docking runs.
## Ab-initio, multi-body docking with symmetry restraints -We will launch two docking runs, one for the dimeric and one for the tetrametic form of this target. +We will launch two docking runs, one for the dimeric and one for the tetrameric form of this target. For this we will make us of the [multi-body interface](http://haddock.science.uu.nl/services/HADDOCK2.2/haddockserver-multi.html) of the HADDOCK web server, which does require guru level access (provided with course credential if given to you, otherwise register to the server and request this access level): @@ -154,10 +154,10 @@ Number of structures for the explicit solvent refinement -> 400 -**Note:** If you use course credentials, these numbers wil be reduced to 500/50/50 to save computing time and get back results faster. You can also manually decrease those numbers and download instead a full pre-calculated run for analysis (see setup above). +**Note:** If you use course credentials, these numbers will be reduced to 500/50/50 to save computing time and get back results faster. You can also manually decrease those numbers and download instead a full pre-calculated run for analysis (see setup above). -* **Step 7:** Define noncrystallographic symmetry restraint to enforce the various chains will have exaclty the same conformation. For this unfold the **Noncrystalligraphic symmetry restraints menu**: +* **Step 7:** Define noncrystallographic symmetry restraint to enforce the various chains will have exactly the same conformation. For this unfold the **Noncrystalligraphic symmetry restraints menu**: Use this type of restraints -> Check the box @@ -184,13 +184,13 @@ Use the **C2 symmetry segment pair** menu to define those six pairs of symmetry
-## First visual analyzis of the results +## First visual analysis of the results Once your run has completed you will be presented with a result page showing the cluster statistics and some graphical representation of the data. Such an example output page can be found [here](http://haddock.science.uu.nl/services/HADDOCK2.2/Files/E2A-HPr-demo/index.html) -**Note:** You can also view a result page from a downloaded pre-calculated docking run by opening in your favorite browser the `index.html` file provided in the run directory. +**Note:** You can also view a result page from a downloaded pre-calculated docking run by opening in your favourite browser the `index.html` file provided in the run directory. -The run with reduced numnber of models (course setting) should be returning only one cluster. Load a representative model and compare it to the crystal structure: +The run with reduced number of models (course setting) should be returning only one cluster. Load a representative model and compare it to the crystal structure: pymol cluster1_1.pdb $WDIR/30_70.2.pdb @@ -208,7 +208,7 @@ util.cbc -Does the model (or any of the cluster representatives in case of a full run) ressemble the reference crystal structure? +Does the model (or any of the cluster representatives in case of a full run) resemble the reference crystal structure? In case you found a reasonable prediction, check what was its rank in the server? @@ -241,7 +241,7 @@ $WDIR/run_all.csh *my-run-directory* **Note**: If you use the pre-calculated runs, this analysis has already been performed and you can skip the above step. -Be patient since this might take some time depending on wether you are analysing a full or reduced run. The script will calculate CAPRI statistics for all generated models (rigid-body (it0) - semi-flexible refinement (it1) - water refinement (water)). Those can be found in the unpack run directory under `structures/it0`, `structures/it1` and `structures/it1/water` directories, respectively. +Be patient since this might take some time depending on whether you are analysing a full or reduced run. The script will calculate CAPRI statistics for all generated models (rigid-body (it0) - semi-flexible refinement (it1) - water refinement (water)). Those can be found in the unpack run directory under `structures/it0`, `structures/it1` and `structures/it1/water` directories, respectively. Once the analysis script has completed you can get a first glimpse of the number of acceptable models or better using the following command: @@ -277,7 +277,7 @@ Which fraction of the acceptable models at it0 is selected for further refinemen -Considering that we are generating 10000 models for a full run at it0, how succesful was our scoring function in selecting acceptable models for further flexible refinement? +Considering that we are generating 10000 models for a full run at it0, how successful was our scoring function in selecting acceptable models for further flexible refinement? You can also check the cluster-based statistics with the following command: @@ -332,7 +332,7 @@ Did HADDOCK rank any acceptable model at the top? If not, try to find out what i You can also inspect the fraction of native contacts of the models by looking at the `file.nam_fnat` file. -Let's inspect the best generated model in terms of i-RMSDs. This is the top model listed in `i-RMSD-sorted.dat`. Upload it in pymol (or your favorite graphical program) and compare it to the crystal structure: +Let's inspect the best generated model in terms of i-RMSDs. This is the top model listed in `i-RMSD-sorted.dat`. Upload it in pymol (or your favourite graphical program) and compare it to the crystal structure: pymol *my-best-model* $WDIR/30_70.2.pdb @@ -357,7 +357,7 @@ cealign *my-best-model*, 30_70.2
## Comparing dimer and tetramer docking -You can follow the same steps described above to perform instead of a tetramer docking a dimer docking. Simply follow the provided instructions, but inputing to the HADDOCK server only two molecules. +You can follow the same steps described above to perform instead of a tetramer docking a dimer docking. Simply follow the provided instructions, but inputting to the HADDOCK server only two molecules. Repeat the analysis of the results and compare the success with tetramer docking.