[phenixbb] Problems running phenix.rosetta_refine

[Rebuffet Etienne]

Nigel,

I updated my phenix to dev-2057 and it works. Thank you for your input.
I hope it help other person who had issues running phenix.rosetta_refine

Cheers

Etienne

_______________________________________
Etienne Rebuffet, PhD
Tel: +334 86 97 73 34

Laboratory of 'integrative Structural & Chemical Biology (iSCB)'
Cancer Research Center of Marseille (CRCM)
CNRS UMR 7258; INSERM U 1068; Université Aix-Marseille
Institut Paoli Calmettes
27 Boulevard Leï Roure BP30059
13273 Marseille Cedex 9
France

Le 04/06/2015 10:01, Rebuffet Etienne a écrit :
> 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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>
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