<html>
<head>
<meta content="text/html; charset=utf-8" http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi Caleb,<br>
<br>
thanks for update and good news!<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 11/5/15 00:47, Caleb Geniesse wrote:<br>
</div>
<blockquote
cite="mid:CAMWscxQZ_yKJ2RqaT8q=xjuq1tXGeNx+5gTfme5S5iWft72+NA@mail.gmail.com"
type="cite">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
moz-do-not-send="true" href="mailto:pafonine@lbl.gov"><a class="moz-txt-link-abbreviated" href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a></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 moz-do-not-send="true"
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
moz-do-not-send="true"
href="https://www.phenix-online.org/documentation/reference/erraser.html"
target="_blank"><a class="moz-txt-link-freetext" href="https://www.phenix-online.org/documentation/reference/erraser.html">https://www.phenix-online.org/documentation/reference/erraser.html</a></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 moz-do-not-send="true" href="javascript:_e(%7B%7D,'cvml','phenixbb@phenix-online.org');" target="_blank">phenixbb@phenix-online.org</a>
<a moz-do-not-send="true" href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a>
Unsubscribe: <a moz-do-not-send="true" 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 moz-do-not-send="true"
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>
</blockquote>
<br>
</body>
</html>