Just to be clear: it is Rosetta+Phenix integration that has been depreciated, not Rosetta itself!

If you manage to get it to work with an older version (as Nigel suggested)  -- that may be worth doing, as it does a very good job on tough cases (as shown in that paper : https://www.nature.com/articles/nmeth.2648

Full-models (proteins only) QM based refinement is also available

https://phenix-online.org/version_docs/dev-5480/reference/AQuaRef.html#purpose

as described here:

https://www.biorxiv.org/content/10.1101/2024.07.21.604493v1

Pavel

On 10/14/24 13:38, Martin Malý wrote:
Dear Nigel,
Thank you for a quick response. I thought it's a new tool (wrongly). If Rosetta has been depreciated, I suppose I should rather try something newer and fresh to solve my issues with low resolution data? Maybe the quantum mechanical restraints?
Cheers,
Martin

On 14/10/2024 21:32, Nigel Moriarty wrote:
Martin

The support for Rosetta has been depreciated. You should be able to install Rosetta into an earlier version of Phenix. I suggest 1.19.2.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : [email protected]
Web  : CCI.LBL.gov


On Mon, Oct 14, 2024 at 1:24 PM Martin Malý <[email protected]> wrote:
Dear colleagues,

I am dealing with a low resolution data set (~4 A, protein crystal
structure) so I would like to explore phenix.rosetta_refine. I followed
the instructions at
https://phenix-online.org/documentation/reference/rosetta_install.html .
I applied the patch in
${PHENIX_ROSETTA_PATH}/main/source/tools/build/site.settings . After
several minutes of compilation (command rosetta.build_phenix_interface),
I got an error. I re-run the command to get a log file which I'm
attaching. Please don't you have any idea what's wrong? I use Ubuntu 22.04.

Thank you. Best regards,
Martin_______________________________________________
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