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 http://CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464 https://orcid.org/0000-0001-8857-9464

On Mon, Oct 14, 2024 at 1:24 PM Martin Malý 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_______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

hello On Mon, Oct 14, 2024, 9:46 PM Pavel Afonine wrote:

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#purpo...

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 ORCID : orcid.org/0000-0001-8857-9464

On Mon, Oct 14, 2024 at 1:24 PM Martin Malý 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_______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

_______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

_______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s