[phenixbb] phenix rosetta refine
nwmoriarty at lbl.gov
Mon Jul 6 14:11:38 PDT 2015
I believe that is all true and correct.
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:
> 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.
> 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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> > phenixbb at phenix-online.org
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