Merge pull request #752 from haddocking/surfdrive

amjjbonvin · web-flow · commit 96e55fb19fcf · 2025-11-04T13:17:38.000+01:00
Updated surfdrive download files
diff --git a/education/HADDOCK/HADDOCK-CASP-CAPRI-T70/index.md b/education/HADDOCK/HADDOCK-CASP-CAPRI-T70/index.md
@@ -234,10 +234,10 @@ Let's have a more detailed look at the quality and ranking of the generated mode
 
 In order to perform the more quantitative analysis, download the full run from the results page (provide in a link in the first line of the result page) and unpack it. Alternatively, download the pre-calculated data from the following links:
 
-* T70 tetramer docking - reduced settings: [link](https://surfdrive.surf.nl/files/index.php/s/rGOGKnVwF8wjjU1/download)
-* T70 tetramer docking - full sampling: [link](https://surfdrive.surf.nl/files/index.php/s/T9HOh5lAWgtO3nD/download)
-* T70 dimer docking - reduced settings: [link](https://surfdrive.surf.nl/files/index.php/s/1RSEiHK80uIL30l/download)
-* T70 dimer docking - full sampling: [link](https://surfdrive.surf.nl/files/index.php/s/b7qEcpzOPQfvXif/download)
+* T70 tetramer docking - reduced settings: [link](https://surfdrive.surf.nl/public.php/dav/files/rGOGKnVwF8wjjU1)
+* T70 tetramer docking - full sampling: [link](https://surfdrive.surf.nl/public.php/dav/files/T9HOh5lAWgtO3nD)
+* T70 dimer docking - reduced settings: [link](https://surfdrive.surf.nl/public.php/dav/files/1RSEiHK80uIL30l)
+* T70 dimer docking - full sampling: [link](https://surfdrive.surf.nl/public.php/dav/files/b7qEcpzOPQfvXif)
 
 Then start the quantitative analysis in the directory where you saved and unpacked the run with the following command:
 
diff --git a/education/HADDOCK/XL-MS-oligomer/index.md b/education/HADDOCK/XL-MS-oligomer/index.md
@@ -445,10 +445,10 @@ Remember that we have increased the weight of the distance restraints for our ru
 
 <details style="background-color:#DAE4E7"><summary><b>Don't want to wait for your results?</b>
 </summary>
-<li> <a href="https://surfdrive.surf.nl/files/index.php/s/tQuToprVwHZORnb" target="_blank">Download dimer HADDOCK run</a></li>
-<li> <a href="https://surfdrive.surf.nl/files/index.php/s/za9ILYprxF9gDVw" target="_blank">Download trimer HADDOCK run</a></li>
-<li> <a href="https://surfdrive.surf.nl/files/index.php/s/VkiC8cZBosVALBR" target="_blank">Download tetramer HADDOCK run</a></li>
-<li> <a href="https://surfdrive.surf.nl/files/index.php/s/sAh09Cf2bJNykbk" target="_blank">Download pentamer HADDOCK run</a></li>
+<li> <a href="https://surfdrive.surf.nl/public.php/dav/files/tQuToprVwHZORnb" target="_blank">Download dimer HADDOCK run</a></li>
+<li> <a href="https://surfdrive.surf.nl/public.php/dav/files/za9ILYprxF9gDVw" target="_blank">Download trimer HADDOCK run</a></li>
+<li> <a href="https://surfdrive.surf.nl/public.php/dav/files/VkiC8cZBosVALBR" target="_blank">Download tetramer HADDOCK run</a></li>
+<li> <a href="https://surfdrive.surf.nl/public.php/dav/files/sAh09Cf2bJNykbk" target="_blank">Download pentamer HADDOCK run</a></li>
 
 </details>
 <br>
diff --git a/education/HADDOCK24/HADDOCK24-CASP-CAPRI-T70/index.md b/education/HADDOCK24/HADDOCK24-CASP-CAPRI-T70/index.md
@@ -251,10 +251,10 @@ Let's have a more detailed look at the quality and ranking of the generated mode
 
 In order to perform the more quantitative analysis, download the full run from the results page (provide in a link in the first line of the result page) and unpack it. Alternatively, download the pre-calculated data from the following links:
 
-* T70 tetramer docking - reduced settings: [link](https://surfdrive.surf.nl/files/index.php/s/jUjk3gbLRkylPo4/download)
-* T70 tetramer docking - full sampling: [link](https://surfdrive.surf.nl/files/index.php/s/NQe3VPuPF05iFVY/download)
-* T70 dimer docking - reduced settings: [link](https://surfdrive.surf.nl/files/index.php/s/tnT2sZKcpDNmZeP/download)
-* T70 dimer docking - full sampling: [link](https://surfdrive.surf.nl/files/index.php/s/t7wIYpuddJqhlFn/download)
+* T70 tetramer docking - reduced settings: [link](https://surfdrive.surf.nl/public.php/dav/files/jUjk3gbLRkylPo4)
+* T70 tetramer docking - full sampling: [link](https://surfdrive.surf.nl/public.php/dav/files/NQe3VPuPF05iFVY)
+* T70 dimer docking - reduced settings: [link](https://surfdrive.surf.nl/public.php/dav/files/tnT2sZKcpDNmZeP)
+* T70 dimer docking - full sampling: [link](https://surfdrive.surf.nl/public.php/dav/files/t7wIYpuddJqhlFn)
 
 Then start the quantitative analysis in the directory where you saved and unpacked the run with the following command:
 
diff --git a/education/HADDOCK24/HADDOCK24-local-tutorial/index.md b/education/HADDOCK24/HADDOCK24-local-tutorial/index.md
@@ -1093,7 +1093,7 @@ There are various steps that can be performed:
 * Performing cluster analysis
 * Rerunning the analysis for a single cluster
 
-In order to work with real data, we have performed full runs on this system. Download and unpack the following [gzipped tar archive](https://surfdrive.surf.nl/files/index.php/s/sf2FUVau1Iasocd){:target="_blank"}.
+In order to work with real data, we have performed full runs on this system. Download and unpack the following [gzipped tar archive](https://surfdrive.surf.nl/public.php/dav/files/sf2FUVau1Iasocd){:target="_blank"}.
 
 <a class="prompt prompt-cmd">
   tar xfz antibody-antigen.tgz
diff --git a/education/HADDOCK24/HADDOCK24-protein-DNA-advanced/index.md b/education/HADDOCK24/HADDOCK24-protein-DNA-advanced/index.md
@@ -82,7 +82,7 @@ We will be using the HADDOCK 2.4 webserver [https://wenmr.science.uu.nl/haddock2
 
 #### Tutorial data set
 
-In this tutorial you will perform a protein-DNA docking using the bacteriophage 434 Cro repressor protein and the OR1 operator as an example case. All the tutorial data are made available as a *gzipped* tar archive (.tgz) in the following address [https://surfdrive.surf.nl/files/index.php/s/CuyiqNVryeN2wNz](https://surfdrive.surf.nl/files/index.php/s/CuyiqNVryeN2wNz). 
+In this tutorial you will perform a protein-DNA docking using the bacteriophage 434 Cro repressor protein and the OR1 operator as an example case. All the tutorial data are made available as a *gzipped* tar archive (.tgz) in the following address [https://surfdrive.surf.nl/public.php/dav/files/CuyiqNVryeN2wNz](https://surfdrive.surf.nl/public.php/dav/files/CuyiqNVryeN2wNz). 
 
 #### Virtual Machine
 
@@ -154,7 +154,7 @@ Cro distorts the normal B-form DNA conformation: the OR1 DNA is bent (curved) by
 
 ### Tutorial setup
 
-The tutorial data is present as a zipped file in the following address [https://surfdrive.surf.nl/files/index.php/s/CuyiqNVryeN2wNz](https://surfdrive.surf.nl/files/index.php/s/CuyiqNVryeN2wNz).
+The tutorial data is present as a zipped file in the following address [https://surfdrive.surf.nl/public.php/dav/files/CuyiqNVryeN2wNz](https://surfdrive.surf.nl/public.php/dav/files/CuyiqNVryeN2wNz).
 
 #### Extract the archive
 You need to decompress the tutorial data archive. Move the archive to your working directory of choice and extract it.
diff --git a/education/HADDOCK24/HADDOCK24-protein-DNA-basic/index.md b/education/HADDOCK24/HADDOCK24-protein-DNA-basic/index.md
@@ -59,7 +59,7 @@ Throughout the tutorial, coloured text will be used to refer to questions or ins
 ### Tutorial data set
 
 In this tutorial you will perform a protein-DNA docking using the bacteriophage 434 Cro repressor protein and the OR1 operator as an example case.
-All the tutorial data are made available as a zip archive and can be downloaded at the [following link](https://surfdrive.surf.nl/files/index.php/s/BWhfEEAEHtmqa5a/download).
+All the tutorial data are made available as a zip archive and can be downloaded at the [following link](https://surfdrive.surf.nl/public.php/dav/files/BWhfEEAEHtmqa5a).
 
 ### Extract the archive
 
diff --git a/education/HADDOCK24/RNA-Pol-III-2022/index.md b/education/HADDOCK24/RNA-Pol-III-2022/index.md
@@ -52,7 +52,7 @@ In order to follow this tutorial you will need a **web browser**, a **text edito
 We used our [**pdb-tools**](https://github.com/haddocking/pdb-tools){:target="_blank"} to pre-process PDB files for HADDOCK, 
 renumbering the core domains to avoid overlap in their residue numbering.
 Ready to dock models are provided as part of the material for this tutorial. 
-The required data to run this tutorial should be downloaded from [**here**](https://surfdrive.surf.nl/files/index.php/s/hM9IewpGD6dzSad/download){:target="_blank"}.
+The required data to run this tutorial should be downloaded from [**here**](https://surfdrive.surf.nl/public.php/dav/files/hM9IewpGD6dzSad){:target="_blank"}.
 Once downloaded, make sure to unpack/unzip the archive (for Windows system you can install the [7-zip](https://www.7-zip.org){:target="_blank"} software if needed to unpack tar archives).
 
 Also, if not provided with special workshop credentials to use the HADDOCK portal, make sure to register in order to be able to submit jobs. Use for this the following registration page: [https://wenmr.science.uu.nl/auth/register/haddock](https://wenmr.science.uu.nl/auth/register/haddock){:target="_blank"}.
diff --git a/education/HADDOCK24/RNA-Pol-III-2024/index.md b/education/HADDOCK24/RNA-Pol-III-2024/index.md
@@ -52,7 +52,7 @@ In order to follow this tutorial you will need a **web browser**, a **text edito
 We used our [**pdb-tools**](https://github.com/haddocking/pdb-tools){:target="_blank"} to pre-process PDB files for HADDOCK, 
 renumbering the core domains to avoid overlap in their residue numbering.
 Ready to dock models are provided as part of the material for this tutorial. 
-The required data to run this tutorial should be downloaded from [**here**](https://surfdrive.surf.nl/files/index.php/s/Nio76AwEgDYwjvG/download){:target="_blank"}.
+The required data to run this tutorial should be downloaded from [**here**](https://surfdrive.surf.nl/public.php/dav/files/Nio76AwEgDYwjvG){:target="_blank"}.
 Once downloaded, make sure to unpack/unzip the archive (for Windows system you can install the [7-zip](https://www.7-zip.org){:target="_blank"} software if needed to unpack tar archives).
 
 Also, if not provided with special workshop credentials to use the HADDOCK portal, make sure to register in order to be able to submit jobs. Use for this the following registration page: [https://wenmr.science.uu.nl/auth/register/haddock](https://wenmr.science.uu.nl/auth/register/haddock){:target="_blank"}.
diff --git a/education/HADDOCK3/HADDOCK3-antibody-antigen/index.md b/education/HADDOCK3/HADDOCK3-antibody-antigen/index.md
@@ -180,15 +180,15 @@ to facilitate their use in HADDOCK and to allow comparison with the known refere
 structure of the complex. 
 
 If you are running this tutorial on your own resources _download and unzip the following_
-[zip archive](https://surfdrive.surf.nl/files/index.php/s/R7VHGQM9nx8QuQn){:target="_blank"}
+[zip archive](https://surfdrive.surf.nl/public.php/dav/files/R7VHGQM9nx8QuQn){:target="_blank"}
 _and note the location of the extracted PDB files in your system_. 
 
 __If running as part of a BioExcel workshop or summerschool see the instructions in the next section.__
 
 _Note_ that you can also download and unzip this archive directly from the Linux command line:
 
 <a class="prompt prompt-cmd">
-wget https://surfdrive.surf.nl/files/index.php/s/R7VHGQM9nx8QuQn/download -O HADDOCK3-antibody-antigen.zip<br>
+wget https://surfdrive.surf.nl/public.php/dav/files/R7VHGQM9nx8QuQn -O HADDOCK3-antibody-antigen.zip<br>
 unzip HADDOCK3-antibody-antigen.zip
 </a>
 
diff --git a/education/HADDOCK3/HADDOCK3-antibody-antigen/index.md-BioExcel2024 b/education/HADDOCK3/HADDOCK3-antibody-antigen/index.md-BioExcel2024
@@ -177,14 +177,14 @@ to facilitate their use in HADDOCK and to allow comparison with the known refere
 structure of the complex. 
 
 If you are running this tutorial on your own resources _download and unzip the following_
-[zip archive](https://surfdrive.surf.nl/files/index.php/s/R7VHGQM9nx8QuQn){:target="_blank"}
+[zip archive](https://surfdrive.surf.nl/public.php/dav/files/R7VHGQM9nx8QuQn){:target="_blank"}
 _and note the location of the extracted PDB files in your system_. 
 If running as part of the EU-ASEAN HPC school see the instructions below.
 
 _Note_ that you can also download and unzip this archive directly from the Linux command line:
 
 <a class="prompt prompt-cmd">
-wget https://surfdrive.surf.nl/files/index.php/s/R7VHGQM9nx8QuQn/download -O HADDOCK3-antibody-antigen.zip<br>
+wget https://surfdrive.surf.nl/public.php/dav/files/R7VHGQM9nx8QuQn -O HADDOCK3-antibody-antigen.zip<br>
 unzip HADDOCK3-antibody-antigen.zip
 </a>
 
diff --git a/education/HADDOCK3/HADDOCK3-antibody-antigen/index.md-Bratislava b/education/HADDOCK3/HADDOCK3-antibody-antigen/index.md-Bratislava
@@ -112,7 +112,7 @@ In it you should find the following directories and files:
 
 <hr>
 
-If you are working from your own computer please download [this zip archive](https://surfdrive.surf.nl/files/index.php/s/2NbStaQ4ub5Vgv1). Remember that on your local machine you'll have to install CNS and HADDOCK3.
+If you are working from your own computer please download [this zip archive](https://surfdrive.surf.nl/public.php/dav/files/2NbStaQ4ub5Vgv1). Remember that on your local machine you'll have to install CNS and HADDOCK3.
 
 ## HADDOCK general concepts
 
diff --git a/education/HADDOCK3/HADDOCK3-nanobody-antigen/index.md b/education/HADDOCK3/HADDOCK3-nanobody-antigen/index.md
@@ -72,7 +72,7 @@ Further we are providing pre-processed PDB files for docking and analysis (but t
 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](https://surfdrive.surf.nl/files/index.php/s/5w4wi4yLgSngUul){:target="_blank"}
+[zip archive](https://surfdrive.surf.nl/public.php/dav/files/5w4wi4yLgSngUul){:target="_blank"}
 _and note the location of the extracted files in your system_. In it you should find the following directories:
 
 * `haddock3`: Contains HADDOCK3 configuration and job files for the various scenarios in this tutorial
diff --git a/education/HADDOCK3/HADDOCK3-protein-DNA-basic/index.md b/education/HADDOCK3/HADDOCK3-protein-DNA-basic/index.md
@@ -22,7 +22,7 @@ This tutorial demonstrates how to setup a Haddock3 workflow dedicated to predict
 
 Please note that we do not cover the processing of literature data into docking restraints; for more information, please refer to the [advanced tutorial](https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-protein-DNA-advanced/){:target="_blank"}. 
 
-Computation within this tutorial should take 1.5 hours on 8 CPUs. The tutorial data, as well as precomputed results available [here](https://surfdrive.surf.nl/files/index.php/s/UCULEeLRUkYmr0d){:target="_blank"}.  
+Computation within this tutorial should take 1.5 hours on 8 CPUs. The tutorial data, as well as precomputed results available [here](https://surfdrive.surf.nl/public.php/dav/files/UCULEeLRUkYmr0d){:target="_blank"}.  
 
 ### Tutorial test case
 
@@ -74,7 +74,7 @@ In this tutorial we will use the PyMOL molecular visualisation system. If not al
 Please, download and decompress the tutorial data archive. Move the archive to your working directory of choice and extract it. You can download and unzip this archive directly from the Linux command line:
 
 <a class="prompt prompt-cmd">
-wget https://surfdrive.surf.nl/files/index.php/s/UCULEeLRUkYmr0d/download -O haddock3-protein-dna-basic.zip<br> 
+wget https://surfdrive.surf.nl/public.php/dav/files/UCULEeLRUkYmr0d -O haddock3-protein-dna-basic.zip<br> 
 unzip haddock3-protein-dna-basic.zip
 </a>
 
diff --git a/education/HADDOCK3/HADDOCK3-protein-glycan/index.md b/education/HADDOCK3/HADDOCK3-protein-glycan/index.md
@@ -67,7 +67,7 @@ Further we are providing pre-processed PDB files for docking and analysis (but t
 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](https://surfdrive.surf.nl/files/index.php/s/fNdwCbjtUtBeuXi){:target="_blank"}
+For this _download and unzip the following_ [zip archive](https://surfdrive.surf.nl/public.php/dav/files/fNdwCbjtUtBeuXi){:target="_blank"}
 _and note the location of the extracted PDB files in your system_. 
 Once unzipped, you should find the following directories:
 
diff --git a/education/HADDOCK3/HADDOCK3-protein-peptide/index.md b/education/HADDOCK3/HADDOCK3-protein-peptide/index.md
@@ -62,10 +62,10 @@ We assume that you have a working installation of HADDOCK3 on your system. If HA
 pip install haddock3
 ```
 
-Further, we are providing pre-processed haddock-compatible PDB and configuration files, as well as pre-computed docking results. Please download and unzip the provided [zip archive](https://surfdrive.surf.nl/files/index.php/s/3GE8k07b8EtuVK8) and make sure to note the location of the extracted folder on your system. There is also a linux command for it:
+Further, we are providing pre-processed haddock-compatible PDB and configuration files, as well as pre-computed docking results. Please download and unzip the provided [zip archive](https://surfdrive.surf.nl/public.php/dav/files/3GE8k07b8EtuVK8) and make sure to note the location of the extracted folder on your system. There is also a linux command for it:
 
 <a class="prompt prompt-cmd">
-wget https://surfdrive.surf.nl/files/index.php/s/3GE8k07b8EtuVK8/download -O HADDOCK3-protein-peptide.zip<br>
+wget https://surfdrive.surf.nl/public.php/dav/files/3GE8k07b8EtuVK8 -O HADDOCK3-protein-peptide.zip<br>
 unzip HADDOCK3-protein-peptide.zip
 </a>
  
diff --git a/education/biomolecular-simulations-2019/Metadynamics_tutorial/index.md b/education/biomolecular-simulations-2019/Metadynamics_tutorial/index.md
@@ -61,7 +61,7 @@ The following software packages will be used during the tutorial:
 * [HADDOCK2.4](https://wenmr.science.uu.nl/haddock2.4/): The HADDOCK web portal which allows to perform information-driven flexible docking among macromolecules and between a chemical compound and a macromolecule.
 
 
-You can download from [here](https://surfdrive.surf.nl/files/index.php/s/uChxo21NAp2QxSl) an archive containing the `tutorial_files` directory used in this tutorial. 
+You can download from [here](https://surfdrive.surf.nl/public.php/dav/files/uChxo21NAp2QxSl) an archive containing the `tutorial_files` directory used in this tutorial. 
 This contains all the materials and scripts needed to run the tutorial.
 
 
