Merge branch 'master' into pets

Author: rvhonorato

_data/members.yml

@@ -91,6 +91,14 @@
 - name: Luca Gazolla
   position: Visiting Ph.D Candidate
   avatar: /images/people/Luca-Gazolla.png
+  
+- name: Cintia Leal
+  position: Visiting Ph.D Candidate
+  avatar: /images/people/Cintia-Leal.png
+
+- name: Andrea Villani
+  position: Visiting Ph.D Candidate
+  avatar: /images/people/Andrea-Villani.png
 
 - name: Jahaciel Villaverde Nogues
   position: M.Sc Student

education/HADDOCK24/RNA-Pol-III-2024/index.md

@@ -6,12 +6,13 @@ tags: [MS, Cross-links, cryo-EM, Interaction, HADDOCK, DISVIS, PowerFit, RNA Pol
 image:
   feature: pages/banner_education-thin.jpg
 ---
+
 This tutorial consists of the following sections:
 
 * table of contents
 {:toc}
 
-
+This tutorial was last updated on 02-03-2026. <br>
 
 <hr>
 ## Introduction
@@ -236,7 +237,7 @@ Let's now take a look at the models for the three monomers that we want to dock
 
 ### C82 AlphaFold model
 
-The C82 AlphaFold model can be accessed [here](https://alphafold.ebi.ac.uk/entry/A0A816BHH4){:target="\_blank"}.
+The C82 AlphaFold model can be accessed [here](https://alphafold.ebi.ac.uk/entry/P32349){:target="\_blank"}.
 
 <a class="prompt prompt-info">
 Inspect the 3D model and in particular the color-coding which indicates the model confidence.
@@ -252,7 +253,7 @@ Also consider the Predicted aligned error displayed as a matrix.
 
 <details style="background-color:#DAE4E7">
   <summary style="font-weight: bold">
-    <i>See the AlhpaFold model and PAE plot</i>
+    <i>See the AlphaFold model and PAE plot</i>
   <br>
   </summary>
   <figure align="center">
@@ -288,7 +289,7 @@ Also consider the Predicted aligned error displayed as a matrix.
 
 <details style="background-color:#DAE4E7">
   <summary style="font-weight: bold">
-    <i>See the AlhpaFold model and PAE plot</i>
+    <i>See the AlphaFold model and PAE plot</i>
   <br>
   </summary>
   <figure align="center">
@@ -402,7 +403,7 @@ Consider the Predicted aligned error displayed as a matrix.
 
 <details style="background-color:#DAE4E7">
   <summary style="font-weight: bold">
-    <i>See the AlhpaFold-multimer PAE plot</i>
+    <i>See the AlphaFold-multimer PAE plot</i>
   <br>
   </summary>
   <figure align="center">
@@ -445,7 +446,7 @@ Also consider the Predicted aligned error displayed as a matrix.
 
 <details style="background-color:#DAE4E7">
   <summary style="font-weight: bold">
-    <i>See the AlhpaFold model and PAE plot</i>
+    <i>See the AlphaFold model and PAE plot</i>
   <br>
   </summary>
   <figure align="center">
@@ -745,7 +746,7 @@ in the map and calculate a cross-correlation score for each of them.
 PowerFit is open-source and available for download from our [Github repository][link-powerfit]{:target="_blank"}.
 To facilitate its use, we have developed a [web portal][link-powerfit-web]{:target="_blank"} for it.
 
-The server makes use of either local resources on our cluster, using the multi-core version of the software, or GPGPU-accelerated grid resources of the
+The server makes use of either local resources on our cluster, using the multi-core version of the software, or GPU-accelerated grid resources of the
 [EGI](https://www.egi.eu){:target="_blank"} to speed up the calculations. It only requires a web browser to work and benefits from the latest
 developments in the software, based on a stable and tested workflow. Next to providing an automated workflow around
 PowerFit, the web server also summarizes and higlights the results in a single page including some additional postprocessing
@@ -758,7 +759,7 @@ For more details about PowerFit and its usage we refer to a related [online tuto
 
 To run PowerFit, go to
 
-<a class="prompt prompt-info" href="https://alcazar.science.uu.nl/services/POWERFIT" target="_blank">https://alcazar.science.uu.nl/services/POWERFIT</a>
+<a class="prompt prompt-info" href="https://wenmr.science.uu.nl/powerfit" target="_blank">https://wenmr.science.uu.nl/powerfit</a>
 
 On this page, you will find the most relevant information about the server as well as the links to the local and grid versions of the portal's submission page.
 
@@ -988,8 +989,8 @@ Download the best model and following the previously provided instructions to fi
 
 __Note__: The ChimeraX Fit in Map function does not move the model to the density if they are far apart. If this is the case you can first perform a more exhaustive search. Note that this might take a while since it is a large system 
 
-<a class="prompt promt-pymol">
-fitmap #model inMap #density search 100
+<a class="prompt prompt-pymol">
+fitmap #model inMap #density search 5
 </a>
 
 You can now optimize the fit by using the previously described instructions
@@ -1050,7 +1051,7 @@ Another explanation could be conformational changes in the structures that are n
 <hr>
 ### Setting up the full docking run using the cryo-EM fitted and refined core and C82 domains
 
-We will setup a docking run to model the full complex including some information about the C31 cross-links and the missing two first wHTH domains of C34. For this we will use the PowerFit/Chimera, HADDOCK-refined structure (Core+C82+C34wHTH3) which we have generated as starting point. We will fix those domains in their original positions for the initial rigid-body docking stage and dock the two missing C34 wHTH domains including fragments of C31 for which we have cross-links.
+We will setup a docking run to model the full complex including some information about the C31 cross-links and the missing two first wHTH domains of C34. For this we will use the PowerFit/ChimeraX, HADDOCK-refined structure (Core+C82+C34wHTH3) which we have generated as starting point. We will fix those domains in their original positions for the initial rigid-body docking stage and dock the two missing C34 wHTH domains including fragments of C31 for which we have cross-links.
 
 Connect to the [HADDOCK2.4 interface](https://wenmr.science.uu.nl/haddock2.4/submit/1){:target="_blank"} of the HADDOCK web server.
 
@@ -1303,7 +1304,7 @@ ranking cluster, `clusterX_1.pdb`.
 In the ChimeraX command window type:
 
 <a class="prompt prompt-pymol">
-color by chain<br>
+color bychain<br>
 hide atoms<br>
 show cartoon<br>
 distance /B:50@CB /F:91@CB<br>
@@ -1494,7 +1495,7 @@ color bychain
 In order to perform the fit, we will use the Command Line more:
 
 <a class="prompt prompt-pymol">
-fitmap #model inMap #density search 100<br>
+fitmap #model inMap #density search 5<br>
 </a>
 
 When the fit completes, a window will appear showing the fit results in terms of correlation coefficients.
@@ -1564,7 +1565,6 @@ our [HADDOCK forum](https://ask.bioexcel.eu/c/haddock){:target="_blank"} hosted
 [link-haddock-register]: https://wenmr.science.uu.nl/auth/register/"HADDOCK web server registration"
 [link-molprobity]: http://molprobity.biochem.duke.edu "MolProbity"
 [link-powerfit]: https://github.com/haddocking/powerfit "PowerFit"
-[link-powerfit-web]: https://alcazar.science.uu.nl/services/POWERFIT/ "PowerFit web server"
-[link-powerfit-register]: https://wenmr.science.uu.nl/auth/register  "PowerFit registration"
-[link-powerfit-submit]: https://alcazar.science.uu.nl/cgi/services/POWERFIT/powerfit/submit "PowerFit submission"
-[link-powerfit-help]: https://alcazar.science.uu.nl/cgi/services/POWERFIT/powerfit/help "PowerFit submission"
+[link-powerfit-web]: https://wenmr.science.uu.nl/powerfit "PowerFit web server"
+[link-powerfit-submit]: https://wenmr.science.uu.nl/powerfit "PowerFit submission"
+

education/NMRMolmod/index.md

@@ -154,7 +154,7 @@ Inspect the surface.
 As final step save the molecule as a new PDB file which we will call: *e2a_1F3G.pdb*<br>
 For this in the PyMOL menu on top select:
 
-<a class="prompt prompt-info">File -> Save molecule...</a>
+<a class="prompt prompt-info">File -> Export structure -> Export molecule...</a>
 <a class="prompt prompt-info">Select 1F3G and click on the save button</a>
 <a class="prompt prompt-info">Name your file *e2a_1F3G.pdb*, make sure to select *PDB* as format and note the location of the saved file</a>
 
@@ -424,7 +424,7 @@ The E2A-HPR complex is involved in phosphate-transfer, in which a phosphate grou
 
 <a class="prompt prompt-pymol">
 select histidines, resn HIS+NEP<br>
-show spheres, histidines<br>
+show sticks, histidines<br>
 util.cnc<br>
 </a>
 
@@ -510,7 +510,7 @@ In CAPRI, the l-RMSD value defines the quality of a model:
 * high quality model: l-RMSD<1Å
 
 <a class="prompt prompt-question">
-Q19: What is based on this CAPRI criterion the quality of the best model?
+Q19: Based on this CAPRI criterion, what is the quality of the best model?
 </a>
 
 **Note:** On some machines the pymol rms_cur command can fail due to a bug in the PyMOL software. In this case you can use the following command instead:
@@ -622,7 +622,7 @@ Q20: Explain the concept of NMR chemical shift perturbation data? How are these
 <a class="prompt prompt-question">
 Q21: Referring to the article describing the NMR structure of this complex (Wang et al. 2000), next to chemical shift perturbation data, what are the other types of NMR restraints that have been used to calculate the structure of the complex?
 </a>
-[Wang *et al*, EMBO J (2000)](http://onlinelibrary.wiley.com/doi/10.1093/emboj/19.21.5635/abstract)
+[Wang *et al*, EMBO J (2000)](https://pmc.ncbi.nlm.nih.gov/articles/PMC305802/)
 
 <a class="prompt prompt-question">
 Q22: Which optimization techniques discussed in the MolMod lectures are used by HADDOCK?
@@ -635,8 +635,8 @@ Q23: Referring to the desciption of the last stage of HADDOCK (final refinement
 
 ## Submitting your report
 
-Your report should be submitted in the form of a PDF file at the latest on Friday April 8rd before midnight. 
-Submission should be done via Blackboard (assignment in Docking Practical under Course Content).
+Your report should be submitted in the form of a PDF file at the latest on Friday April 3rd before midnight. 
+Submission should be done via Brightspace (assignment in Docking Practical under Course Content).
 
 
 [link-pymol]: http://www.pymol.org/ "PyMOL"

education/Others/index.md

@@ -14,7 +14,7 @@ In this page you can find links and tutorials to two HADDOCK-complementary softw
 
 * [**PowerFit web server tutorial**](/education/Others/powerfit-webserver/): A small introduction into
   PowerFit to automatically place a high-resolution atomic structure in a
-  lower-resolution cryo-electron microscopy density map making use of our [web portal](https://alcazar.science.uu.nl/cgi/services/POWERFIT/powerfit)
+  lower-resolution cryo-electron microscopy density map making use of our [web portal](https://wenmr.science.uu.nl/powerfit)
   (does not require Linux).
 
 * [**DisVis web server tutorial**](/education/Others/disvis-webserver/): A small introduction into