[phenixbb] ERRASER Updates

Caleb Geniesse calebgeniesse at gmail.com
Thu Nov 5 00:47:47 PST 2015

Hi Pavel,

Thanks for bringing this up.

I believe the issue was resolved last spring (though, not publicized
very well). So yes, Phenix-Erraser should work inside current Phenix if a
relatively recent release of Rosetta is installed on the same machine.

(source: I'm that student!)


On Thursday, November 5, 2015, Pavel Afonine <pafonine at lbl.gov> wrote:

> Caleb,
> thanks for updates!
> Could you please confirm that Phenix-Erraser works in current Phenix:
> https://www.phenix-online.org/download/nightly_builds.cgi
> ?
> My recollection is that Phenix-Erraser stopped working starting at some
> point a while back, quoting Fang-Chieh Chou (1/21/15):
> """
> (...)
> Erraser is currently imcompatible with the latest phenix release, due to
> changes in Phenix API. Tom and I have some discussions on how to fix it,
> but I was too busy to fix Erraser as I am working on other projects toward
> graduation.
> For now you may use erraser with an earlier phenix version. We have a new
> student and he will be in charge of fixing and maintaining erraser in the
> future. He is still wrapping up another project so we may start fixing it
> in one or two months later.
> (...)
> """
> Thanks,
> Pavel
> On 11/4/15 09:10, Caleb Geniesse wrote:
> Hi all,
> My name is Caleb and I am a research programmer in the Das lab who has
> taken over the maintenance of ERRASER.
> ERRASER (Enumerative Real-space Refinment ASsisted by Electron-density
> under Rosetta) is an application for improving RNA crystal structures based
> on Rosetta and Phenix.
> While benchmarking the current state of ERRASER, I uncovered some
> discrepancies in the clash scores and outliers of the resulting models
> (compared to the original benchmark in Chou FC et al., 2012). Accordingly,
> I've made some updates to the ERRASER code within Rosetta addressing these
> issues.
> *To avoid possible inaccuracies introduced by these bugs,* *all
> PHENIX-ERRASER users should download/install a weekly build of Rosetta
> 2015.35 (released Sept. 24, 2015) or later.*
> For more extensive PHENIX-ERRASER documentation and installation notes,
> please see:
> https://www.phenix-online.org/documentation/reference/erraser.html.
> Please let me know if you have any questions!
> All the best,
> Caleb Geniesse
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Caleb W. Geniesse

E-mail: calebgeniesse at gmail.com
Phone: +1 (630) 335 0285
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