[phenixbb] ERRASER Updates
pafonine at lbl.gov
Thu Nov 5 04:51:32 PST 2015
thanks for update and good news!
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!)
> On Thursday, November 5, 2015, Pavel Afonine <pafonine at lbl.gov
> <mailto:pafonine at lbl.gov>> wrote:
> 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:
>> Please let me know if you have any questions!
>> All the best,
>> Caleb Geniesse
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> Unsubscribe:phenixbb-leave at phenix-online.org
> Caleb W. Geniesse
> E-mail: calebgeniesse at gmail.com <mailto:calebgeniesse at gmail.com>
> Phone: +1 (630) 335 0285
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