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powerfit webserver update #764

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b920f08
powerfit webserver update
AnnaEngel98 Feb 17, 2026
b7fcb89
CLI update
AnnaEngel98 Feb 18, 2026
0ac9f6b
update to integrative tutorial
AnnaEngel98 Feb 18, 2026
26e1bad
add date
AnnaEngel98 Feb 18, 2026
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13 changes: 7 additions & 6 deletions education/HADDOCK24/RNA-Pol-III-2024/index.md
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Expand Up @@ -6,6 +6,7 @@ tags: [MS, Cross-links, cryo-EM, Interaction, HADDOCK, DISVIS, PowerFit, RNA Pol
image:
feature: pages/banner_education-thin.jpg
---
This tutorial was last updated on 18-02-2026. <br>
This tutorial consists of the following sections:

* table of contents
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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.

Expand Down Expand Up @@ -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>
Expand Down Expand Up @@ -1564,7 +1565,7 @@ 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-web]: https://wenmr.science.uu.nl/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-submit]: https://wenmr.science.uu.nl/powerfit "PowerFit submission"
[link-powerfit-help]: https://www.bonvinlab.org/powerfit/manual.html "PowerFit help"
2 changes: 1 addition & 1 deletion education/Others/index.md
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Expand Up @@ -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
Expand Down
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