[phenixbb] problem with hhr files in phenix_mr.rosetta

[Dr G. Bunkoczi]

Hi Miguel,

thanks for reporting this! Indeed, the problem is with parsing the 
hhr-file, more specifically a missing midline between the target and the 
query blocks. I have changed the parser so that this line is now optional; 
this will be available in the next nightly build. Since the change is 
really small, you can just replace the affected module and you can get 
going straight away (please get in touch if you decide to go with this). 
Alternatively, you can put two spaces to each line between the query and 
target sequence block and it will work (I can see that this is not 
practical when you have many hits).

Let me know if there are any further problems!

Best wishes, Gabor

On Jun 2 2011, Miguel Ortiz Lombardia wrote:

>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!
>
>
>

-- 
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     Dr Gabor Bunkoczi

     Cambridge Institute for Medical Research
     Wellcome Trust/MRC Building
     Addenbrooke's Hospital
     Hills Road
     Cambridge CB2 0XY
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