[phenixbb] phenix rosetta refine

[kaiser]

Thanks, Nigel!

<div>-------- Original message --------</div><div>From: Nigel Moriarty <nwmoriarty at lbl.gov> </div><div>Date:2015/07/06  14:11  (GMT-08:00) </div><div>To: Jens Kaiser <kaiser at caltech.edu> </div><div>Cc: phenixbb at phenix-online.org </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 : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Mon, Jul 6, 2015 at 1:55 PM, Jens Kaiser <kaiser at caltech.edu> 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 : NWMoriarty at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov
>
> On Sat, Jun 27, 2015 at 2:38 AM, Jens Kaiser <kaiser at caltech.edu>
> 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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