Public subversion / Enzyme design public app

[Anonymous]

I’m a student who’s been playing Rosetta 3 for a few weeks now, for use in a research project, and I was wondering if there is a public read-only account for the svn repository used by the Rosetta developers, so that I (and others) could have access to the latest development version of the software. Failing that, does anyone know when Rosetta 3.1 will be released (which I presume will have the enzyme design app)?

The reason I ask is that there seem to be several intentional omissions from the release. For example, there is protocol code for enzyme design but no public app to run. Do the fix- and flexbb enzyme design protocols in Rosetta 3 simply not work? Or could one of the Rosetta developers post some public application code that would allow one to use those protocols?

Thank you very much.

– Will A.
Brown University

[Anonymous]

There is no SVN access for non-developers (nor any plans to implement it). Generally speaking, apps wait for release until there’s a publication demonstrating that they actually work (or one close to publication). No sense in releasing unproven code…

Fixed backbone enzyme design is on the table for 3.1. I don’t know the status of the flexible backbone design.

We’re currently tracking down a memory leak in one application; once it’s found and the benchmarks pass again 3.1 will come out. “Soon” is the best answer I can give you.

[Anonymous]

hey will, yes, fixbb enzyme design will be in 3.1. in 3.0, it was a pilot app, i don’t know if you have access to those.

the flexbb protocol will also be available, although that is very experimental at this point and not really benchmarked. there also won’t be documentation for the flexbb stuff yet.

best, Florian Richter PhD student, baker group

> I’m a student who’s been playing Rosetta 3 for a few weeks now, for use in a research project, and I was wondering if there is a public read-only account for the svn repository used by the Rosetta developers, so that I (and others) could have access to the latest development version of the software. Failing that, does anyone know when Rosetta 3.1 will be released (which I presume will have the enzyme design app)? > > The reason I ask is that there seem to be several intentional omissions from the release. For example, there is protocol code for enzyme design but no public app to run. Do the fix- and flexbb enzyme design protocols in Rosetta 3 simply not work? Or could one of the Rosetta developers post some public application code that would allow one to use those protocols? > > Thank you very much. > > – Will A. > Brown University

[pbradley]

regarding flex bb design. As I mentioned before I tried doing fixbb/relax cycles with rosetta3 and am now comparing this to the Rosetta++ mvbb flex backbone design protocol. I am finding that the lr bb-bb hbonds are much better with the Rosetta++ protocol than doing fixbb/relax cycles I was doing with Rosetta3.

So, in conclusion, a good flexible backbone design app in Rosetta 3 would be a great help.

EDIT:

In fact, on closer inspection I was wrong about the above – the energies seem to be worse! So, please ignore.

[Anonymous]

Florian,

Does that mean that the fixbb enzdes protocol code in 3.0 works–an app I write that uses it should work correctly?

Thank you for your help.
– Will

[Anonymous]

hey will,
yes, it should work. i could send you an app .cc file that uses it. however, i think the 3.1 release is just around the corner (less than a month ), and that has a few improvements/bugfixes to enzdes. do you think you can wait for a few more weeks?

[Anonymous]

Hi Florian,

It would be great if you could send me the app source file, if that’s not too much trouble. My email address is william UNDERSCORE allen AT brown DOT edu. Thank you!

[Author]

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