[phenixbb] Problems running phenix.rosetta_refine
Rebuffet Etienne
etienne.rebuffet at inserm.fr
Thu Jun 4 01:01:42 PDT 2015
Nigel,
Thank you for your help. I forgot to say I am running the soft on linux
(LMDE). I am sure you will respect strict confidentiality but I can't
send any file about this project. Based on your comment, I am going to
try running phenix.rosetta_refine with dataset from other proteins in
order to see if it is an input file issue. If not I will update my phenix.
Thank you again for your help.
Etienne
Le 03/06/2015 18:46, Nigel Moriarty a écrit :
> Etienne
>
> On OSX with a more recent version of phenix (dev-2057 should be fine)
> and exactly the same Rosetta version, I have not trouble running on the
> command line or in the GUI. Perhaps you could send me your files to be
> sure it's not an input error.
>
> NB. Any files sent to me will be held in strictest confidence.
>
>
> 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 <http://CCI.LBL.gov>
>
> On Wed, Jun 3, 2015 at 12:08 AM, Rebuffet Etienne
> <etienne.rebuffet at inserm.fr <mailto:etienne.rebuffet at inserm.fr>> wrote:
>
> Dear all,
>
> I get the same error message as Thomas and I would appreciate any
> help about this issue. I am currently running :
> Phenix: 1.6-1692
> Rosetta: 2015.19.57819
>
> Thanks,
>
> Etienne
>
>
>
> Le 28/05/2015 20:59, Klose, Thomas a écrit :
>
> Dear all,
>
> I was trying to set up phenix.rosetta_refine to test it for the
> refinement of a 4.5Å structure. I installed the latest phenix
> release and compiled the latest rosetta version (2015.19) using
> rosetta.build_phenix_interface. However, when I try to run
> phenix.rosetta_refine I get the following error message:
>
> ….
> Generating 5 models on 4 processors...
>
> DEBUG dumping error message
> ERROR: Rosetta exited with status 1
> stderr output:
> Sorry:
>
> Wrong map type requested: %%map_type%%
> Allowed format is: [p][m]Fo+[q][D]Fc[kick][filled]
> where [p] and [q] are any numbers (optional),
> [m] and [D] indicate if the requested map is sigmaa
> (optional),
> Fo and Fc are Fobs and Fcalc,
> [kick] is for Average Kick Map (optional),
> [filled] is for missing Fobs filled map.
> Examples: 2mFo-DFc, 3.2Fo-2.3Fc, mFobs-DFcalc_kick,
> 2mFobs-DFcalc_filled, Fc,
> 2mFobs-DFcalc_kick_fill, anom, anom_diff,
> anomalous_difference, Fo
>
>
> ERROR: PhenixInterface::calculateDensityMap() : error writing map
> ERROR:: Exit from: src/core/scoring/cryst/PhenixInterface.cc
> line: 1122
>
> This happens with our actual data as well as test data that I
> downloaded (PDB: 1yip).
>
> Any help in solving this problem would be greatly appreciated.
>
> Thanks,
> Thomas
>
>
>
>
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