[phenixbb] Problems running phenix.rosetta_refine
Rebuffet Etienne
etienne.rebuffet at inserm.fr
Thu Jun 4 05:48:09 PDT 2015
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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