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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Wed, Jun 3, 2015 at 12:08 AM, Rebuffet Etienne < [email protected]> 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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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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov http://CCI.LBL.gov

On Wed, Jun 3, 2015 at 12:08 AM, Rebuffet Etienne mailto:[email protected]> 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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