Compiling rosetta to include rosetta_scripts_jd3

[Anonymous]

Hi,

I’ve currently installed rosetta3 on aws cloud vm under ubuntu OS (Ubuntu 20.04.2 LTS).

I try to use a protocol from Khersonsky et al. 2018 (PMID: 30270109).

In order to do so, a  rosetta_scripts_jd3.default.linuxgccrelease   file is needed.

However, I did not find such file under $ROSETTA/main/source/bin/ 

My rosetta version is: rosetta_src_2021.16.61629_bundle

I’ve compiled it with: ./scons.py -j8 mode=release bin

How to compile/install rosetta in order for the rosetta_scripts_jd3.default.linuxgccrelease  to be available ?

Thanks in advance,

Oz

[Anonymous]

The application is not yet public, and probably shouldn’t have been used for that paper.  In the coming weeks, the app will be moved to public and released with the associated paper. 

[Anonymous]

Thanks you jadolfbr.

I will check again for newer installtion in a couple of weeks.

Still, or maybe I’m confusing, but in Khersonsky et al. Mol. Cell 2018 (PMID: 30270109) in the sup. pdf (also in this link: https://www.cell.com/cms/10.1016/j.molcel.2018.08.033/attachment/aa873311-1ddc-466a-accf-723dba2789b4/mmc4)

 

they wrote:

” rosetta_scripts_jd3.default.linuxgccrelease @mutate.flags -in:file:job_definition_file job.xml “

Thanks again,

Oz

[Anonymous]

They did.  They had access to the developer source and at the time, this was my pilot app and not released. However, they would have been able to do what they did with more manual scripts or pyrosetta.  Still, it probably shouldn’t have been used – especially as at that time ithe code had just got written. 

[Anonymous]

Thanks for the clarifications

[Anonymous]

This is now in Rosetta and should be available in the next weekly release. 

Documentation is here: https://new.rosettacommons.org/docs/latest/RosettaScripts-JD3

Reference is here: https://www.biorxiv.org/content/10.1101/2021.09.27.462000v2

[Anonymous]

Thanks, this is very helpful.

Will the next version include binaries ?

 

 

[Anonymous]

Yes, next weekly release will include the app.  

[Anonymous]

Hi jadolfbr,

Do you know when the new weekly realese with the j3 is about to be published ?

I checked this url (that is the most recent link I found on this section of the website) :

https://www.rosettacommons.org/downloads/academic/2021/wk38/

and I couldn’t find the jd3 script among the bin files.

Thanks,

Oz

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