[phenixbb] ERRASER Updates

Pavel Afonine pafonine at lbl.gov
Thu Nov 5 00:19:47 PST 2015


thanks for updates!

Could you please confirm that Phenix-Erraser works in current Phenix:



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.


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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