[phenixbb] problem with hhr files in phenix_mr.rosetta

[Miguel Ortiz Lombardia]

Dear phenix developers,

Trying to run a test job with phenix_mr.rosetta on a Mac (10.6.7) using
a command line such as (phenix is the dev-764 version):

phenix.mr_rosetta seq_file=this.seq data=P41212.mtz hhr_files=ed593l.hhr
hhr_files=ed593g.hhr fragment_files=frag3.gz fragment_files=frag9.gz
rescore_mr.relax=False rosetta_models=20 ncs_copies=3 space_group=p41212
use_all_plausible_sg=False nproc=100 group_run_command=qsub

I get this kind of error:

******************* ERROR ENDING ***************
Uninterpretable: 'Q ss_pred
--------------------------------------------------------------------------------\nQ
ed593           390
--------------------------------------------------------------------------------
 389 (593)\nQ Consensus       390
--------------------------------------------------------------------------------
 389 (593)\n\nT Consensus       623
~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 702 (1010)\nT 2xgj_A          623
GKDNYGWGAVVDFAKRINKRNPSAVYTDHESYIVNVVVNTMYIDSPVNLLKPFNPTLPEGIRPAEEGEKSICAVIPITLD
 702 (1010)\nT ss_dssp
TTEEEEEEEEEEEEECCCSSCTTCCCCTTTTEEEEEEEEEEETTSCGGGCCTTCCCCCTTCCBCCTTCCEEEEEEEECGG\nT
ss_pred
CccccceeEEEeeccccccCCCCceeeccccceeeeeecccccCCcccccccccccCccccCcccccccceeEEEEeehh\n\n\nQ
ss_pred
--------------------------------------------------------------------------------\nQ
ed593           390
--------------------------------------------------------------------------------
 389 (593)\nQ Consensus       390
--------------------------------------------------------------------------------
 389 (593)\n\nT Consensus       703
~i~~i~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~
 782 (1010)\nT 2xgj_A          703
SIKSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFLKLMKKIDVLNTKLSSNPLTNSMR
 782 (1010)\nT ss_dssp
GEEEEEEEECCCCSSTTCSSSHHHHHHHHHHHHHHSSSCCCBCCTTTTSCCCCHHHHHHHHHHHHHHHHHTTSHHHHSSS\nT
ss_pred
hhhcccceEEecCccccChHHHHHHHHHHHHHHHhCccCCcccCchhhccCCcHHHHHHHHHHHHHHHHHhcCccccCcC'

******************* ERROR ENDING ***************

I thought that could be due to different line endings in Macs vs. UNIX,
so I transformed the hhr files with (unix2mac is unix2dos 5.3
(2011-04-26)from Fink)

unix2mac ed593l.hhr
unix2mac ed593g.hhr

But then the same input line results in:

(...)
Loading PDB and alignment files from
/a/people/miguel/Lab/Rosetta/MR_ROSETTA_6/WORK_1/ed593l_1/ed593l_ed.hhr
Log file for mr_model_preparation is:
/a/people/miguel/Lab/Rosetta/MR_ROSETTA_6/WORK_1/ed593l_1/mr_model_preparation.log


******************* ERROR ENDING ***************
Incorrect file format

******************* ERROR ENDING ***************

Any other ideas?
Thank you!


-- 
Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombardia at afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

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