<html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"></head><body >Thanks, Nigel!<br><br><div>-------- Original message --------</div><div>From: Nigel Moriarty <nwmoriarty@lbl.gov> </div><div>Date:2015/07/06 14:11 (GMT-08:00) </div><div>To: Jens Kaiser <kaiser@caltech.edu> </div><div>Cc: phenixbb@phenix-online.org </div><div>Subject: Re: [phenixbb] phenix rosetta refine </div><div><br></div><div dir="ltr">Jens<div><br></div><div>I believe that is all true and correct.</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 64R0246B, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div>
<br><div class="gmail_quote">On Mon, Jul 6, 2015 at 1:55 PM, Jens Kaiser <span dir="ltr"><<a href="mailto:kaiser@caltech.edu" target="_blank">kaiser@caltech.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Nigel,<br>
Sorry for the late reply, I was away from the office last week.<br>
Yes, I did follow these instructions. At the moment I'm using<br>
rosetta_bin_linux_2015.22.57859_bundle and phenix-1.10pre-2084. I<br>
requested 20 models (which I get) but there are rosetta_##.sh files<br>
created that are empty and subdirectories _ros_temp?????? that contain<br>
files with _adp_refine in their names. I'm just wondering if it is<br>
really running as intended.<br>
<br>
Cheers,<br>
<br>
Jens<br>
<div class="HOEnZb"><div class="h5"><br>
On Mon, 2015-06-29 at 10:25 -0700, Nigel Moriarty wrote:<br>
> Jens<br>
><br>
><br>
> Have you followed the instructions?<br>
><br>
><br>
> <a href="http://www.phenix-online.org/documentation/reference/rosetta_refine.html" rel="noreferrer" target="_blank">http://www.phenix-online.org/documentation/reference/rosetta_refine.html</a><br>
><br>
><br>
> Cheers<br>
><br>
><br>
> Nigel<br>
><br>
><br>
> ---<br>
> Nigel W. Moriarty<br>
> Building 64R0246B, Physical Biosciences Division<br>
> Lawrence Berkeley National Laboratory<br>
> Berkeley, CA 94720-8235<br>
> Phone : <a href="tel:510-486-5709" value="+15104865709">510-486-5709</a> Email : NWMoriarty@LBL.gov<br>
> Fax : <a href="tel:510-486-5909" value="+15104865909">510-486-5909</a> Web : <a href="http://CCI.LBL.gov" rel="noreferrer" target="_blank">CCI.LBL.gov</a><br>
><br>
> On Sat, Jun 27, 2015 at 2:38 AM, Jens Kaiser <<a href="mailto:kaiser@caltech.edu">kaiser@caltech.edu</a>><br>
> wrote:<br>
> Hey there,<br>
> who would be the person to talk about setting up<br>
> phenix.rosetta_refine? I tried our SBgrid installation with<br>
> overrides to<br>
> "nightly" for phenix and rosetta; I tried a clean install of<br>
> rosetta and<br>
> phenix - production version and nightly's in all combinations<br>
> - and all<br>
> combinations of compiling (rosetta first, then<br>
> rosetta.build_phenix_interface, phenix first, then<br>
> rosetta.build_phenix_interface). The problem is that<br>
> "phenix.rosetta_refine" seems to run, and produce a log file<br>
> that looks<br>
> reasonable, but geometry params are worse than with an<br>
> ordinary refine.<br>
> I think I tracked it down to the fact that the "rosetta_XX.sh"<br>
> files are<br>
> empty, and rosetta actually does not run.<br>
><br>
> Any help is welcome - and any support will be extended.<br>
><br>
> Cheers,<br>
><br>
> Jens<br>
><br>
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><br>
><br>
<br>
<br>
</div></div></blockquote></div><br></div>
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