Re: [phenixbb] phenix rosetta refine

Thanks, Nigel! <div>-------- Original message --------</div><div>From: Nigel Moriarty </div><div>Date:2015/07/06 14:11 (GMT-08:00) </div><div>To: Jens Kaiser </div><div>Cc: [email protected] </div><div>Subject: Re: [phenixbb] phenix rosetta refine </div><div> </div>Jens I believe that is all true and correct. Cheers Nigel --- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Mon, Jul 6, 2015 at 1:55 PM, Jens Kaiser wrote: Nigel, Sorry for the late reply, I was away from the office last week. Yes, I did follow these instructions. At the moment I'm using rosetta_bin_linux_2015.22.57859_bundle and phenix-1.10pre-2084. I requested 20 models (which I get) but there are rosetta_##.sh files created that are empty and subdirectories _ros_temp?????? that contain files with _adp_refine in their names. I'm just wondering if it is really running as intended. Cheers, Jens On Mon, 2015-06-29 at 10:25 -0700, Nigel Moriarty wrote:

Jens

Have you followed the instructions?

http://www.phenix-online.org/documentation/reference/rosetta_refine.html

Cheers

Nigel

--- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Sat, Jun 27, 2015 at 2:38 AM, Jens Kaiser wrote: Hey there, who would be the person to talk about setting up phenix.rosetta_refine? I tried our SBgrid installation with overrides to "nightly" for phenix and rosetta; I tried a clean install of rosetta and phenix - production version and nightly's in all combinations - and all combinations of compiling (rosetta first, then rosetta.build_phenix_interface, phenix first, then rosetta.build_phenix_interface). The problem is that "phenix.rosetta_refine" seems to run, and produce a log file that looks reasonable, but geometry params are worse than with an ordinary refine. I think I tracked it down to the fact that the "rosetta_XX.sh" files are empty, and rosetta actually does not run.

Any help is welcome - and any support will be extended.

Cheers,

Jens

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