[phenixbb] ERRASER Updates

Pavel Afonine pafonine at lbl.gov
Thu Nov 5 04:51:32 PST 2015


Hi Caleb,

thanks for update and good news!

Pavel

On 11/5/15 00:47, Caleb Geniesse wrote:
> 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!)
>
> Cheers,
> Caleb
>
> On Thursday, November 5, 2015, Pavel Afonine <pafonine at lbl.gov 
> <mailto: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 <mailto:calebgeniesse at gmail.com>
> Phone: +1 (630) 335 0285
>

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