Hi Pavel,<div><br></div><div>Thanks for bringing this up.</div><div><br></div><div>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.</div><div><br></div><div>(source: I'm that student!)</div><div><br></div><div>Cheers,</div><div>Caleb<br><br>On Thursday, November 5, 2015, Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Caleb,<br>
<br>
thanks for updates!<br>
<br>
Could you please confirm that Phenix-Erraser works in current
Phenix:<br>
<br>
<a href="https://www.phenix-online.org/download/nightly_builds.cgi" target="_blank">https://www.phenix-online.org/download/nightly_builds.cgi</a><br>
<br>
?<br>
<br>
My recollection is that Phenix-Erraser stopped working starting at
some point a while back, quoting Fang-Chieh Chou (1/21/15):<br>
<br>
"""<br>
(...)<br>
<div>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.</div>
<div><br>
</div>
<div>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.</div>
(...)<br>
""" <br>
<br>
Thanks,<br>
Pavel<br>
<br>
<div>On 11/4/15 09:10, Caleb Geniesse wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>Hi all,<br>
<br>
My name is Caleb and I am a research programmer in the Das lab
who has taken over the maintenance of ERRASER. <br>
<br>
ERRASER (Enumerative Real-space Refinment ASsisted by
Electron-density under
Rosetta) is an application for improving RNA crystal
structures based on
Rosetta and Phenix.<br>
<br>
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.<br>
<br>
<b>To avoid possible inaccuracies introduced by these bugs,</b>
<b><i>all PHENIX-ERRASER users should download/install a
weekly build of Rosetta 2015.35 (released Sept. 24, 2015)
or later</i>.</b><br>
<br>
For more extensive PHENIX-ERRASER documentation and
installation notes, please see: <a href="https://www.phenix-online.org/documentation/reference/erraser.html" target="_blank">https://www.phenix-online.org/documentation/reference/erraser.html</a>.<br>
</div>
<div><br>
Please let me know if you have any questions!<br>
<br>
</div>
All the best, <br>
<div>Caleb Geniesse<br>
</div>
</div>
<br>
<fieldset></fieldset>
<br>
<pre>_______________________________________________
phenixbb mailing list
<a href="javascript:_e(%7B%7D,'cvml','phenixbb@phenix-online.org');" target="_blank">phenixbb@phenix-online.org</a>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a>
Unsubscribe: <a href="javascript:_e(%7B%7D,'cvml','phenixbb-leave@phenix-online.org');" target="_blank">phenixbb-leave@phenix-online.org</a></pre>
</blockquote>
<br>
</div>
</blockquote></div><br><br>-- <br><div dir="ltr"><span style="color:rgb(68,68,68)"><span style="background-color:rgb(255,255,255)">Caleb W. Geniesse<br><br>E-mail: <a href="mailto:calebgeniesse@gmail.com" target="_blank">calebgeniesse@gmail.com</a><br></span></span><span style="color:rgb(68,68,68)"><span style="background-color:rgb(255,255,255)">Phone: +1 (630) 335 0285</span></span></div><br>