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dkotzamp merged 7 commits into from
Mar 9, 2026
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powerfit webserver update #764

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powerfit webserver update
AnnaEngel98 Feb 17, 2026
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CLI update
AnnaEngel98 Feb 18, 2026
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update to integrative tutorial
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AnnaEngel98 Feb 18, 2026
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Merge branch 'master' into powerfit_updates
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12 changes: 6 additions & 6 deletions education/HADDOCK24/RNA-Pol-III-2024/index.md
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Expand Up @@ -745,7 +745,7 @@ 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 +1050,7 @@ 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 +1303,7 @@ 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 +1564,7 @@ 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"
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[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"
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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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