[phenixbb] problem with hhr files in phenix_mr.rosetta

[Dr G. Bunkoczi]

Hi Daniel,

sorry for the late reply, I am currently away.

Your problem is the presence of the character '|' in the query sequence 
name 'tr|Q5ZWR1|Q5ZW'. This has been fixed some time ago, but if you cannot 
update, just run awk on your hhr-file to replace 'tr|Q5ZWR1|Q5ZW' with 
'trQ5ZWR1Q5ZW' (or anything else non-blank) and it will work.

HTH, Gabor

On Jun 6 2011, Daniel Mattle wrote:

>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
>
>