[phenixbb] problem with hhr files in phenix_mr.rosetta

[Daniel Mattle]

Hey Gabor,

I seem to have a similar problem, so how can I fix this the most easiest way? I don't really understand your solution by adding two spaces to each line.
 I am running it on a cluster, so I do not have any admin rights.

Best,

Daniel


On 02.06.2011, at 15:24, Dr G. Bunkoczi wrote:

> 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!
>> 
>> 
>> 
> 
> -- 
> ##################################################
> 
>    Dr Gabor Bunkoczi
> 
>    Cambridge Institute for Medical Research
>    Wellcome Trust/MRC Building
>    Addenbrooke's Hospital
>    Hills Road
>    Cambridge CB2 0XY
> ##################################################
> 
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________________________________
Daniel Mattle, MSc ETH
PhD student
Centre for Structural Biology
Department of Molecular Biology
University of Aarhus
Gustav Wieds Vej 10c
DK - 8000 Århus C, Denmark

Phone: +45 8942 5261
Mail:  dmattle at mb.au.dk

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